Synthetic nucleic acid molecule compositions and methods of preparation

This application is a continuation of U.S. patent. application Ser. No. 10/943,508, filed Sep. 17, 2004, now U.S. Pat. No. 7,728,118, which is incorporated by reference herein.

Transcription, the synthesis of an RNA molecule from a sequence of DNA is the first step in gene expression. Sequences which regulate DNA transcription include promoter sequences, polyadenylation signals, transcription factor binding sites and enhancer elements. A promoter is a DNA sequence capable of specific initiation of transcription and consists of three general regions. The core promoter is the sequence where the RNA polymerase and its cofactors bind to the DNA. Immediately upstream of the core promoter is the proximal promoter which contains several transcription factor binding sites that are responsible for the assembly of an activation complex that in turn recruits the polymerase complex. The distal promoter, located further upstream of the proximal promoter also contains transcription factor binding sites. Transcription termination and polyadenylation, like transcription initiation, are site specific and encoded by defined sequences. Enhancers are regulatory regions, containing multiple transcription factor binding sites, that can significantly increase the level of transcription from a responsive promoter regardless of the enhancer's orientation and distance with respect to the promoter as long as the enhancer and promoter are located within the same DNA molecule. The amount of transcript produced from a gene may also be regulated by a post-transcriptional mechanism, the most important being RNA splicing that removes intervening sequences (introns) from a primary transcript between splice donor and splice acceptor sequences.

Natural selection is the hypothesis that genotype-environment interactions occurring at the phenotypic level lead to differential reproductive success of individuals and therefore to modification of the gene pool of a population. Some properties of nucleic acid molecules that are acted upon by natural selection include codon usage frequency, RNA secondary structure, the efficiency of intron splicing, and interactions with transcription factors or other nucleic acid binding proteins. Because of the degenerate nature of the genetic code, these properties can be optimized by natural selection without altering the corresponding amino acid sequence.

Under some conditions, it is useful to synthetically alter the natural nucleotide sequence encoding a polypeptide to better adapt the polypeptide for alternative applications. A common example is to alter the codon usage frequency of a gene when it is expressed in a foreign host cell. Although redundancy in the genetic code allows amino acids to be encoded by multiple codons, different organisms favor some codons over others. It has been found that the efficiency of protein translation in a non-native host cell can be substantially increased by adjusting the codon usage frequency but maintaining the same gene product (U.S. Pat. Nos. 5,096,825, 5,670,356, and 5,874,304).

However, altering codon usage may, in turn, result in the unintentional introduction into a synthetic nucleic acid molecule of inappropriate transcription regulatory sequences. This may adversely effect transcription, resulting in anomalous expression of the synthetic DNA. Anomalous expression is defined as departure from normal or expected levels of expression. For example, transcription factor binding sites located downstream from a promoter have been demonstrated to effect promoter activity (Michael et al., 1990; Lamb et al., 1998; Johnson et al., 1998; Jones et al., 1997). Additionally, it is not uncommon for an enhancer element to exert activity and result in elevated levels of DNA transcription in the absence of a promoter sequence or for the presence of transcription regulatory sequences to increase the basal levels of gene expression in the absence of a promoter sequence.

Thus, what is needed is a method for making synthetic nucleic acid molecules with altered codon usage without also introducing inappropriate or unintended transcription regulatory sequences for expression in a particular host cell.

The invention provides an isolated nucleic acid molecule (a polynucleotide) comprising a synthetic nucleotide sequence having reduced, for instance, 90% or less, e.g., 80%, 78%, 75%, or 70% or less, nucleic acid sequence identity relative to a parent nucleic acid sequence, e.g., a wild-type nucleic acid sequence, and having fewer regulatory sequences such as transcription regulatory sequences. In one embodiment, the synthetic nucleotide sequence has fewer regulatory sequences than would result if the sequence differences between the synthetic nucleotide sequence and the parent nucleic acid sequence, e.g., optionally the result of differing codons, were randomly selected. In one embodiment, the synthetic nucleotide sequence encodes a polypeptide that has an amino acid sequence that is at least 85%, 90%, 95%, or 99%, or 100%, identical to the amino acid sequence of a naturally-occurring (native or wild-type) corresponding polypeptide (protein). Thus, it is recognized that some specific amino acid changes may also be desirable to alter a particular phenotypic characteristic of a polypeptide encoded by the synthetic nucleotide sequence. Preferably, the amino acid sequence identity is over at least 100 contiguous amino acid residues. In one embodiment of the invention, the codons in the synthetic nucleotide sequence that differ preferably encode the same amino acids as the corresponding codons in the parent nucleic acid sequence.

Hence, in one embodiment, the invention provides an isolated nucleic acid molecule comprising a synthetic nucleotide sequence having a coding region for a selectable or screenable polypeptide, wherein the synthetic nucleotide sequence has 90%, e.g., 80%, or less nucleic acid sequence identity to a parent nucleic acid sequence encoding a corresponding selectable or screenable polypeptide, and wherein the synthetic nucleotide sequence encodes a selectable or screenable polypeptide with at least 85% amino acid sequence identity to the corresponding selectable or screenable polypeptide encoded by the parent nucleic acid sequence. The decreased nucleotide sequence identity may be a result of different codons in the synthetic nucleotide sequence relative to the codons in the parent nucleic acid sequence. The synthetic nucleotide sequence of the invention has a reduced number of regulatory sequences relative to the parent nucleic acid sequence, for example, relative to the average number of regulatory sequences resulting from random selections of codons or nucleotides at the sequences which differ between the synthetic nucleotide sequence and the parent nucleic acid sequence. In one embodiment, a nucleic acid molecule may include a synthetic nucleotide sequence which together with other sequences encodes a selectable or screenable polypeptide. For instance, a synthetic nucleotide sequence which forms part of an open reading frame for a selectable or screenable polypeptide may include at least 100, 150, 200, 250, 300 or more nucleotides of the open reading, which nucleotides have reduced nucleic acid sequence identity relative to corresponding sequences in a parent nucleic acid sequence. In one embodiment, the parent nucleic acid sequence is SEQ ID NO:1, SEQ ID NO:6, SEQ ID NO:15 or SEQ ID NO:41, the complement thereof, or a sequence that has 90%, 95% or 99% nucleic acid sequence identity thereto.

In one embodiment, the nucleic acid molecule of the invention comprises sequences which have been optimized for expression in mammalian cells, and more preferably, in human cells (see, e.g., WO 02/16944 which discloses methods to optimize sequences for expression in a cell of interest). For instance, nucleic acid molecules may be optimized for expression in eukaryotic cells by introducing a Kozak sequence and/or one or more introns or decreasing the number of other regulatory sequences, and/or altering codon usage to codons employed more frequently in one or more eukaryotic organisms, e.g., codons employed more frequently in an eukaryotic host cell to be transformed with the nucleic acid molecule.

In one embodiment, the synthetic nucleotide sequence is present in a vector, e.g., a plasmid, and such a vector may include other optimized sequences. In one embodiment, the synthetic nucleotide sequence encodes a polypeptide comprising a selectable polypeptide, which synthetic nucleotide sequence has at least 90% or more nucleic acid sequence identity to an open reading frame in a sequence comprising, for example, SEQ ID NO:5, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:30, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:70, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, SEQ ID NO:74, SEQ ID NO:80, SEQ ID NO:81, SEQ ID NO:82, SEQ ID NO:83, SEQ ID NO:84, the complement thereof, or a fragment thereof that encodes a polypeptide with substantially the same activity as the corresponding full-length and optionally wild-type (functional) polypeptide, e.g., a polypeptide encoded by SEQ ID NO:1, SEQ ID NO:6, SEQ ID NO:15 or SEQ ID NO:41, or a portion thereof which together with other parent or wild-type sequences encodes a polypeptide with substantially the same activity as the corresponding full-length and optionally wild-type polypeptide. As used herein, “substantially the same activity” is at least about 70%, e.g., 80%, 90% or more, the activity of a corresponding full-length and optionally wild-type (functional) polypeptide. In one embodiment, an isolated nucleic acid molecule encodes a fusion polypeptide comprising a selectable polypeptide.

Also provided is an isolated nucleic acid molecule comprising a synthetic nucleotide sequence having a coding region for a firefly luciferase, wherein the nucleic acid sequence identity of the synthetic nucleic acid molecule is 90% or less, e.g., 80%, 78%, 75% or less, compared to a parent nucleic acid sequence encoding a firefly luciferase, e.g., a parent nucleic acid sequence having SEQ ID NO:14 or SEQ ID NO:43, which synthetic nucleotide sequence has fewer regulatory sequences including transcription regulatory sequences than would result if the sequence differences, e.g., differing codons, were randomly selected. Preferably, the synthetic nucleotide sequence encodes a polypeptide that has an amino acid sequence that is at least 85%, preferably 90%, and most preferably 95% or 99% identical to the amino acid sequence of a naturally-occurring or parent polypeptide. Thus, it is recognized that some specific amino acid changes may be desirable to alter a particular phenotypic characteristic of the luciferase encoded by the synthetic nucleotide sequence. Preferably, the amino acid sequence identity is over at least 100 contiguous amino acid residues. In one embodiment, the synthetic nucleotide sequence encodes a polypeptide comprising a firefly luciferase, which synthetic nucleotide sequence has at least 90% or more nucleic acid sequence identity to an open reading frame in a sequence comprising, for example, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, the complement thereof, or a fragment thereof that encodes a polypeptide with substantially the same activity as the corresponding full-length and optionally wild-type (functional) polypeptide, e.g., a polypeptide encoded by SEQ ID NO:14 or SEQ ID NO:43, or a portion thereof which together with other sequences encodes a firefly luciferase. For instance, a synthetic nucleotide sequence which forms part of an open reading frame for a firefly luciferase may include at least 100, 150, 200, 250, 300 or more nucleotides of the open reading, which nucleotides have reduced nucleic acid sequence identity relative to corresponding sequences in a parent nucleic acid sequence.

In another embodiment, the invention provides an isolated nucleic acid molecule comprising a synthetic nucleotide sequence which does not include an open reading frame encoding a peptide or polypeptide of interest, e.g., the synthetic nucleotide sequence may have an open reading frame but it does not include sequences that encode a functional or desirable peptide or polypeptide, but may include one or more stop codons in one or more reading frames, one or more poly(A) adenylation sites, and/or a contiguous sequence for two or more restriction endonucleases (restriction enzymes), i.e., a multiple cloning region (also referred to as a multiple cloning site, “MCS”), and which is generally at least 20, e.g., at least 30, nucleotides in length and up to 1000 or more nucleotides, e.g., up to 10,000 nucleotides, which synthetic nucleotide sequence has fewer regulatory sequences such as transcription regulatory sequences relative to a corresponding parent nucleic acid sequence. In one embodiment, the synthetic nucleotide sequence which does not encode a peptide or polypeptide has 90% or less, e.g., 80%, or less nucleic acid sequence identity to a parent nucleic acid sequence, wherein the decreased sequence identity is a result of a reduced number of regulatory sequences in the synthetic nucleotide sequence relative to the parent nucleic acid sequence.

The regulatory sequences which are reduced in the synthetic nucleotide sequence include, but are not limited to, any combination of transcription factor binding sequences, intron splice sites, poly(A) adenylation sites (poly(A) sequences or poly(A) sites hereinafter), enhancer sequences, promoter modules, and/or promoter sequences, e.g., prokaryotic promoter sequences. Generally, a synthetic nucleic acid molecule lacks at least 10%, 20%, 50% or more of the regulatory sequences, for instance lacks substantially all of the regulatory sequences, e.g., 80%, 90% or more, for instance, 95% or more, of the regulatory sequences, present in a corresponding parent or wild-type nucleotide sequence. Regulatory sequences, e.g., transcription regulatory sequences, are well known in the art. The synthetic nucleotide sequence may also have a reduced number of restriction enzyme recognition sites, and may be modified to include selected sequences, e.g., sequences at or near the 5′ and/or 3′ ends of the synthetic nucleotide sequence such as Kozak sequences and/or desirable restriction enzyme recognition sites, for instance, restriction enzyme recognition sites useful to introduce a synthetic nucleotide sequence to a specified location, e.g., in a multiple cloning region 5′ and/or 3′ to a nucleic acid sequence of interest.

In one embodiment, the synthetic nucleotide sequence of the invention has a codon composition that differs from that of the parent or wild-type nucleic acid sequence. Preferred codons for use in the invention are those which are employed more frequently than at least one other codon for the same amino acid in a particular organism and/or those that are not low-usage codons in that organism and/or those that are not low-usage codons in the organism used to clone or screen for the expression of the synthetic nucleotide sequence (for example, E. coli ). Moreover, codons for certain amino acids (i.e., those amino acids that have three or more codons), may include two or more codons that are employed more frequently than the other (non-preferred) codon(s). The presence of codons in a synthetic nucleotide sequence that are employed more frequently in one organism than in another organism results in a synthetic nucleotide sequence which, when introduced into the cells of the organism that employs those codons more frequently, has a reduced risk of aberrant expression and/or is expressed in those cells at a level that may be greater than the expression of the wild type (unmodified) nucleic acid sequence in those cells under some conditions. For example, a synthetic nucleic acid molecule of the invention which encodes a selectable or screenable polypeptide may be expressed at a level that is greater, e.g., at least about 2, 3, 4, 5, 10-fold or more relative to that of the parent or wild-type (unmodified) nucleic acid sequence in a cell or cell extract under identical conditions (such as cell culture conditions, vector backbone, and the like). In one embodiment, the synthetic nucleotide sequence of the invention has a codon composition that differs from that of the parent or wild-type nucleic acid sequence at more than 10%, 20% or more, e.g., 30%, 35%, 40% or more than 45%, e.g., 50%, 55%, 60% or more of the codons.

In one embodiment of the invention, the codons that are different are those employed more frequently in a mammal, while in another embodiment the codons that are different are those employed more frequently in a plant. A particular type of mammal, e.g., human, may have a different set of preferred codons than another type of mammal. Likewise, a particular type of plant may have a different set of preferred codons than another type of plant. In one embodiment of the invention, the majority of the codons which differ are ones that are preferred codons in a desired host cell and/or are not low usage codons in a particular host cell. Preferred codons for mammals (e.g., humans) and plants are known to the art (e.g., Wada et al., 1990). For example, preferred human codons include, but are not limited to, CGC (Arg), CTG (Leu), AGC (Ser), ACC (Thr), CCC (Pro), GCC (Ala), GGC (Gly), GTG (Val), ACT (Ile), AAG (Lys), AAC (Asn), CAG (Gln), CAC (His), GAG (Glu), GAC (Asp), TAC (Tyr), TGC (Cys) and TTC (Phe) (Wada et al., 1990). Thus, synthetic nucleotide sequences of the invention have a codon composition which differs from a wild type nucleic acid sequence by having an increased number of preferred human codons, e.g. CGC, CTG, TCT, AGC, ACC, CCC, GCC, GGC, GTG, ACT, AAG, AAC, CAG, CAC, GAG, GAC, TAC, TGC, TTC, or any combination thereof. For example, the synthetic nucleotide sequence of the invention may have an increased number of AGC serine-encoding codons, CCC proline-encoding codons, and/or ACC threonine-encoding codons, or any combination thereof, relative to the parent or wild-type nucleic acid sequence. Similarly, synthetic nucleotide sequences having an increased number of codons that are employed more frequently in plants, have a codon composition which differs from a wild-type nucleic acid sequence by having an increased number of the plant codons including, but not limited to, CGC (Arg), CTT (Leu), TCT (Ser), TCC (Ser), ACC (Thr), CCA (Pro), CCT (Pro), GCT (Ser), GGA (Gly), GTG (Val), ATC (Ile), ATT (Ile), AAG (Lys), AAC (Asn), CAA (Gln), CAC (His), GAG (Glu), GAC (Asp), TAC (Tyr), TGC (Cys), TTC (Phe), or any combination thereof (Murray et al., 1989). Preferred codons may differ for different types of plants (Wada et al., 1990).

The nucleotide substitutions in the synthetic nucleic acid sequence may be influenced by many factors such as, for example, the desire to have an increased number of nucleotide substitutions such as those resulting in a silent nucleotide substitution (encodes the same amino acid) and/or decreased number of regulatory sequences. Under some circumstances (e.g., to permit removal of a transcription factor binding site) it may be desirable to replace a non-preferred codon with a codon other than a preferred codon or a codon other than the preferred codon in order to decrease the number of regulatory sequences.

The invention also provides an expression cassette or vector. The expression cassette or vector of the invention comprises a synthetic nucleotide sequence of the invention operatively linked to a promoter that is functional in a cell or comprises a synthetic nucleotide sequence, respectively. Preferred promoters are those functional in mammalian cells and those functional in plant cells. Optionally, the expression cassette may include other sequences, e.g., one or more restriction enzyme recognition sequences 5′ and/or 3′ to an open reading frame for a selectable polypeptide or luciferase and/or a Kozak sequence, and be a part of a larger polynucleotide molecule such as a plasmid, cosmid, artificial chromosome or vector, e.g., a viral vector, which may include a multiple cloning region for other sequences, e.g., promoters, enhancers, other open reading frames and/or poly(A) sites. In one embodiment, a vector of the invention includes SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, the complement thereof, or a sequence which has at least 80% nucleic acid sequence identity thereto and encodes a selectable and/or screenable polypeptide.

In one embodiment, the synthetic nucleotide sequence encoding a selectable or screenable polypeptide is introduced into a vector backbone, e.g., one which optionally has a poly(A) site 3′ to the synthetic nucleotide sequence, a gene useful for selecting transformed prokaryotic cells which optionally is a synthetic sequence, a gene useful for selecting transformed eukaryotic cells which optionally is a synthetic sequence, a noncoding region for decreasing transcription and/or translation into adjacent linked desirable open reading frames, and/or a multiple cloning region 5′ and/or 3′ to the synthetic nucleotide sequence encoding a selectable or screenable polypeptide which optionally includes one or more protein destabilization sequences (see U.S. application Ser. No. 10/664,341, filed Sep. 16, 2003, the disclosure of which is incorporated by reference herein). In one embodiment, the vector having a synthetic nucleotide sequence encoding a selectable or screenable polypeptide may lack a promoter and/or enhancer which is operably linked to that synthetic sequence. In another embodiment, the invention provides a vector comprising a promoter, e.g., a prokaryotic or eukaryotic promoter, operably linked to a synthetic nucleotide sequence encoding a selectable or screenable polypeptide. Such vectors optionally include one or more multiple cloning regions, such as ones that are useful to introduce an additional open reading frame and/or a promoter for expression of the open reading frame which promoter optionally is different than the promoter for the selectable or screenable polypeptide, and/or a prokaryotic origin of replication. A “vector backbone” as used herein may include sequences (open reading frames) useful to identify cells with those sequences, e.g., in prokaryotic cells, their promoters, an origin of replication for vector maintenance, e.g., in prokaryotic cells, and optionally one or more other sequences including multiple cloning regions e.g., for insertion of a promoter and/or open reading frame of interest, and sequences which inhibit transcription and/or translation.

Also provided is a host cell comprising the synthetic nucleotide sequence of the invention, an isolated polypeptide (e.g., a fusion polypeptide encoded by the synthetic nucleotide sequence of the invention), and compositions and kits comprising the synthetic nucleotide sequence of the invention, a polypeptide encoded thereby, or an expression cassette or vector comprising the synthetic nucleotide sequence in suitable container means and, optionally, instruction means. The host cell may be an eukaryotic cell such as a plant or vertebrate cell, e.g., a mammalian cell, including but not limited to a human, non-human primate, canine, feline, bovine, equine, ovine or rodent (e.g., rabbit, rat, ferret, hamster, or mouse) cell or a prokaryotic cell.

The invention also provides a method to prepare a synthetic nucleotide sequence of the invention by genetically altering a parent, e.g., a wild-type or synthetic, nucleic acid sequence. The method comprises altering (e.g., decreasing or eliminating) a plurality of regulatory sequences in a parent nucleic acid sequence, e.g., one which encodes a selectable or screenable polypeptide or one which does not encode a peptide or polypeptide, to yield a synthetic nucleotide sequence which has a decreased number of regulatory sequences and, if the synthetic nucleotide sequence encodes a polypeptide, it preferably encodes the same amino acids as the parent nucleic acid molecule. The transcription regulatory sequences which are reduced include but are not limited to any of transcription factor binding sequences, intron splice sites, poly(A) sites, enhancer sequences, promoter modules, and/or promoter sequences. Preferably, the alteration of sequences in the synthetic nucleotide sequence does not result in an increase in regulatory sequences. In one embodiment, the synthetic nucleotide sequence encodes a polypeptide that has at least 85%, 90%, 95% or 99%, or 100%, contiguous amino acid sequence identity to the amino acid sequence of the polypeptide encoded by the parent nucleic acid sequence.

Thus, in one embodiment, a method to prepare a synthetic nucleic acid molecule comprising an open reading frame is provided. The method includes altering the codons and/or regulatory sequences in a parent nucleic acid sequence which encodes a reporter protein such, as a firefly luciferase or a selectable polypeptide such as one encoding resistance to ampicillin, puromycin, hygromycin or neomycin, to yield a synthetic nucleotide sequence which encodes a corresponding reporter polypeptide and which has for instance at least 10% or more, e.g., 20%, 30%, 40%, 50% or more, fewer regulatory sequences relative to the parent nucleic acid sequence. The synthetic nucleotide sequence has 90%, e.g., 85%, 80%, or 78%, or less nucleic acid sequence identity to the parent nucleic acid sequence and encodes a polypeptide with at least 85% amino acid sequence identity to the polypeptide encoded by the parent nucleic acid sequence. The regulatory sequences which are altered include transcription factor binding sequences, intron splice sites, poly(A) sites, promoter modules, and/or promoter sequences. In one embodiment, the synthetic nucleic acid sequence hybridizes under medium stringency hybridization but not stringent conditions to the parent nucleic acid sequence or the complement thereof. In one embodiment, the codons which differ encode the same amino acids as the corresponding codons in the parent nucleic acid sequence.

Also provided is a synthetic (including a further synthetic) nucleotide sequence prepared by the methods of the invention, e.g., a further synthetic nucleotide sequence in which introduced regulatory sequences or restriction endonuclease recognition sequences are optionally removed. Thus, the method of the invention may be employed to alter the codon usage frequency and/or decrease the number of regulatory sequences in any open reading frame or to decrease the number of regulatory sequences in any nucleic acid sequence, e.g., a noncoding sequence. Preferably, the codon usage frequency in a synthetic nucleotide sequence which encodes a selectable or screenable polypeptide is altered to reflect that of the host organism desired for expression of that nucleotide sequence while also decreasing the number of potential regulatory sequences relative to the parent nucleic acid molecule.

Also provided is a method to prepare a synthetic nucleic acid molecule which does not code for a peptide or polypeptide. The method includes altering the nucleotides in a parent nucleic acid sequence having at least 20 nucleotides which optionally does not code for a functional or desirable peptide or polypeptide and which optionally may include sequences which inhibit transcription and/or translation, to yield a synthetic nucleotide sequence which does not include an open reading frame encoding a peptide or polypeptide of interest, e.g., the synthetic nucleotide sequence may have an open reading frame but it does not include sequences that encode a functional or desirable peptide or polypeptide, but may include one or more stop codons in one or more reading frames, one or more poly(A) adenylation sites, and/or a contiguous sequence for two or more restriction endonucleases, i.e., a multiple cloning region. The synthetic nucleotide sequence is generally at least 20, e.g., at least 30, nucleotides in length and up to 1000 or more nucleotides, e.g., up to 10,000 nucleotides, and has fewer regulatory sequences such as transcription regulatory sequences relative to a corresponding parent nucleic acid sequence which does not code for a peptide or polypeptide, e.g., a parent nucleic acid sequence which optionally includes sequences which inhibit transcription and/or translation. The nucleotides are altered to reduce one or more regulatory sequences, e.g., transcription factor binding sequences, intron splice sites, poly(A) sites, enhancer sequences, promoter modules, and/or promoter sequences, in the parent nucleic acid sequence.

The invention also provides a method to prepare an expression vector. The method includes providing a linearized plasmid having a nucleic molecule including a synthetic nucleotide sequence of the invention which encodes a selectable or screenable polypeptide which is flanked at the 5′ and/or 3′ end by a multiple cloning region. The plasmid is linearized by contacting the plasmid with at least one restriction endonuclease which cleaves in the multiple cloning region. The linearized plasmid and an expression cassette having ends compatible with the ends in the linearized plasmid are annealed, yielding an expression vector. In one embodiment, the plasmid is linearized by cleavage by at least two restriction endonucleases, only one of which cleaves in the multiple cloning region.

Also provided is a method to clone a promoter or open reading frame. The method includes comprising providing a linearized plasmid having a multiple cloning region and a synthetic sequence of the invention which encodes a selectable or screenable polypeptide and/or a synthetic sequence of the invention which does not encode a peptide or polypeptide, which is plasmid is linearized by contacting the plasmid with at least two restriction endonucleases at least one of which cleaves in the multiple cloning region; and annealing the linearized plasmid with DNA having a promoter or an open reading frame with ends compatible with the ends of the linearized plasmid.

Exemplary methods to prepare synthetic sequences for firefly luciferase and a number of selectable polypeptide nucleic acid sequences, as well as non-coding regions present in a vector backbone, are described hereinbelow. For instance, the methods may produce synthetic selectable polypeptide nucleic acid molecules which exhibit similar or significantly enhanced levels of mammalian expression without negatively effecting other desirable physical or biochemical properties and which were also largely devoid of regulatory elements.

Clearly, the present invention has applications with many genes and across many fields of science including, but not limited to, life science research, agrigenetics, genetic therapy, developmental science and pharmaceutical development.

FIG. 1 . Codons and their corresponding amino acids.

FIG. 2 . Design scheme for the pGL4 vector.

The term “nucleic acid molecule” or “nucleic acid sequence” as used herein, refers to nucleic acid, DNA or RNA, that comprises noncoding or coding sequences. Coding sequences are necessary for the production of a polypeptide or protein precursor. The polypeptide can be encoded by a full-length coding sequence or by any portion of the coding sequence, as long as the desired protein activity is retained. Noncoding sequences refer to nucleic acids which do not code for a polypeptide or protein precursor, and may include regulatory elements such as transcription factor binding sites, poly(A) sites, restriction endonuclease sites, stop codons and/or promoter sequences.

A “synthetic” nucleic acid sequence is one which is not found in nature, i.e., it has been derived using molecular biological, chemical and/or informatic techniques.

A “nucleic acid”, as used herein, is a covalently linked sequence of nucleotides in which the 3′ position of the pentose of one nucleotide is joined by a phosphodiester group to the 5′ position of the pentose of the next, and in which the nucleotide residues (bases) are linked in specific sequence, i.e., a linear order of nucleotides. A “polynucleotide”, as used herein, is a nucleic acid containing a sequence that is greater than about 100 nucleotides in length. An “oligonucleotide” or “primer”, as used herein, is a short polynucleotide or a portion of a polynucleotide. An oligonucleotide typically contains a sequence of about two to about one hundred bases. The word “oligo” is sometimes used in place of the word “oligonucleotide”.

Nucleic acid molecules are said to have a “5′-terminus” (5′ end) and a “3′-terminus” (3′ end) because nucleic acid phosphodiester linkages occur to the 5′ carbon and 3′ carbon of the pentose ring of the substituent mononucleotides. The end of a polynucleotide at which a new linkage would be to a 5′ carbon is its 5′ terminal nucleotide. The end of a polynucleotide at which a new linkage would be to a 3′ carbon is its 3′ terminal nucleotide. A terminal nucleotide, as used herein, is the nucleotide at the end position of the 3′- or 5′-terminus.

DNA molecules are said to have “5′ ends” and “3′ ends” because mononucleotides are reacted to make oligonucleotides in a manner such that the 5′ phosphate of one mononucleotide pentose ring is attached to the 3′ oxygen of its neighbor in one direction via a phosphodiester linkage. Therefore, an end of an oligonucleotides referred to as the “5′ end” if its 5′ phosphate is not linked to the 3′ oxygen of a mononucleotide pentose ring and as the “3′ end” if its 3′ oxygen is not linked to a 5′ phosphate of a subsequent mononucleotide pentose ring.

As used herein, a nucleic acid sequence, even if internal to a larger oligonucleotide or polynucleotide, also may be said to have 5′ and 3′ ends. In either a linear or circular DNA molecule, discrete elements are referred to as being “upstream” or 5′ of the “downstream” or 3′ elements. This terminology reflects the fact that transcription proceeds in a 5′ to 3′ fashion along the DNA strand. Typically, promoter and enhancer elements that direct transcription of a linked gene (e.g., open reading frame or coding region) are generally located 5′ or upstream of the coding region. However, enhancer elements can exert their effect even when located 3′ of the promoter element and the coding region. Transcription termination and polyadenylation signals are located 3′ or downstream of the coding region.

The term “codon” as used herein, is a basic genetic coding unit, consisting of a sequence of three nucleotides that specify a particular amino acid to be incorporation into a polypeptide chain, or a start or stop signal. The term “coding region” when used in reference to structural genes refers to the nucleotide sequences that encode the amino acids found in the nascent polypeptide as a result of translation of a mRNA molecule. Typically, the coding region is bounded on the 5′ side by the nucleotide triplet “ATG” which encodes the initiator methionine and on the 3′ side by a stop codon (e.g., TAA, TAG, TGA). In some cases the coding region is also known to initiate by a nucleotide triplet “TTG”.

By “protein”, “polypeptide” or “peptide” is meant any chain of amino acids, regardless of length or post-translational modification (e.g., glycosylation or phosphorylation). The nucleic acid molecules of the invention may also encode a variant of a naturally-occurring protein or a fragment thereof. Preferably, such a variant protein has an amino acid sequence that is at least 85%, preferably 90%, and most preferably 95% or 99% identical to the amino acid sequence of the naturally-occurring (native or wild-type) protein from which it is derived.

Polypeptide molecules are said to have an “amino terminus” (N-terminus) and a “carboxy terminus” (C-terminus) because peptide linkages occur between the backbone amino group of a first amino acid residue and the backbone carboxyl group of a second amino acid residue. The terms “N-terminal” and “C-terminal” in reference to polypeptide sequences refer to regions of polypeptides including portions of the N-terminal and C-terminal regions of the polypeptide, respectively. A sequence that includes a portion of the N-terminal region of a polypeptide includes amino acids predominantly from the N-terminal half of the polypeptide chain, but is not limited to such sequences. For example, an N-terminal sequence may include an interior portion of the polypeptide sequence including bases from both the N-terminal and C-terminal halves of the polypeptide. The same applies to C-terminal regions. N-terminal and C-terminal regions may, but need not, include the amino acid defining the ultimate N-terminus and C-terminus of the polypeptide, respectively.

The term “wild-type” as used herein, refers to a gene or gene product that has the characteristics of that gene or gene product isolated from a naturally occurring source. A wild-type gene is that which is most frequently observed in a population and is thus arbitrarily designated the “wild-type” form of the gene. In contrast, the term “mutant” refers to a gene or gene product that displays modifications in sequence and/or functional properties (i.e., altered characteristics) when compared to the wild-type gene or gene product. It is noted that naturally-occurring mutants can be isolated; these are identified by the fact that they have altered characteristics when compared to the wild-type gene or gene product.

The term “recombinant protein” or “recombinant polypeptide” as used herein refers to a protein molecule expressed from a recombinant DNA molecule. In contrast, the term “native protein” is used herein to indicate a protein isolated from a naturally occurring (i.e., a nonrecombinant) source. Molecular biological techniques may be used to produce a recombinant form of a protein with identical properties as compared to the native form of the protein.

The term “fusion polypeptide” refers to a chimeric protein containing a protein of interest (e.g., luciferase) joined to a heterologous sequence (e.g., a non-luciferase amino acid or protein).

The terms “cell,” “cell line,” “host cell,” as used herein, are used interchangeably, and all such designations include progeny or potential progeny of these designations. By “transformed cell” is meant a cell into which (or into an ancestor of which) has been introduced a nucleic acid molecule of the invention, e.g., via transient transfection. Optionally, a nucleic acid molecule synthetic gene of the invention may be introduced into a suitable cell line so as to create a stably-transfected cell line capable of producing the protein or polypeptide encoded by the synthetic gene. Vectors, cells, and methods for constructing such cell lines are well known in the art. The words “transformants” or “transformed cells” include the primary transformed cells derived from the originally transformed cell without regard to the number of transfers. All progeny may not be precisely identical in DNA content, due to deliberate or inadvertent mutations. Nonetheless, mutant progeny that have the same functionality as screened for in the originally transformed cell are included in the definition of transformants.

Nucleic acids are known to contain different types of mutations. A “point” mutation refers to an alteration in the sequence of a nucleotide at a single base position from the wild type sequence. Mutations may also refer to insertion or deletion of one or more bases, so that the nucleic acid sequence differs from the wild-type sequence.

The term “homology” refers to a degree of complementarity between two or more sequences. There may be partial homology or complete homology (i.e., identity). Homology is often measured using sequence analysis software (e.g., EMBOSS, the European Molecular Biology Open Software Suite available at http://www.hgmp.mrc.ac.uk/Software/EMBOSS/overview/html). Such software matches similar sequences by assigning degrees of homology to various substitutions, deletions, insertions, and other modifications. Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine.

The term “isolated” when used in relation to a nucleic acid, as in “isolated oligonucleotide” or “isolated polynucleotide” refers to a nucleic acid sequence that is identified and separated from at least one contaminant with which it is ordinarily associated in its source. Thus, an isolated nucleic acid is present in a form or setting that is different from that in which it is found in nature. In contrast, non-isolated nucleic acids (e.g., DNA and RNA) are found in the state they exist in nature. For example, a given DNA sequence (e.g., a gene) is found on the host cell chromosome in proximity to neighboring genes; RNA sequences (e.g., a specific mRNA sequence encoding a specific protein), are found in the cell as a mixture with numerous other mRNAs that encode a multitude of proteins. However, isolated nucleic acid includes, by way of example, such nucleic acid in cells ordinarily expressing that nucleic acid where the nucleic acid is in a chromosomal location different from that of natural cells, or is otherwise flanked by a different nucleic acid sequence than that found in nature. The isolated nucleic acid or oligonucleotide may be present in single-stranded or double-stranded form. When an isolated nucleic acid or oligonucleotide is to be utilized to express a protein, the oligonucleotide contains at a minimum, the sense or coding strand (i.e., the oligonucleotide may be single-stranded), but may contain both the sense and anti-sense strands (i.e., the oligonucleotide may be double-stranded).

The term “isolated” when used in relation to a polypeptide, as in “isolated protein” or “isolated polypeptide” refers to a polypeptide that is identified and separated from at least one contaminant with which it is ordinarily associated in its source. Thus, an isolated polypeptide is present in a form or setting that is different from that in which it is found in nature. In contrast, non-isolated polypeptides (e.g., proteins and enzymes) are found in the state they exist in nature.

The term “purified” or “to purify” means the result of any process that removes some of a contaminant from the component of interest, such as a protein or nucleic acid. The percent of a purified component is thereby increased in the sample.

The term “operably linked” as used herein refer to the linkage of nucleic acid sequences in such a manner that a nucleic acid molecule capable of directing the transcription of a given gene and/or the synthesis of a desired protein molecule is produced. The term also refers to the linkage of sequences encoding amino acids in such a manner that a functional (e.g., enzymatically active, capable of binding to a binding partner, capable of inhibiting, etc.) protein or polypeptide is produced.

The term “recombinant DNA molecule” means a hybrid DNA sequence comprising at least two nucleotide sequences not normally found together in nature.

The term “vector” is used in reference to nucleic acid molecules into which fragments of DNA may be inserted or cloned and can be used to transfer DNA segment(s) into a cell and capable of replication in a cell. Vectors may be derived from plasmids, bacteriophages, viruses, cosmids, and the like.

The terms “recombinant vector” and “expression vector” as used herein refer to DNA or RNA sequences containing a desired coding sequence and appropriate DNA or RNA sequences necessary for the expression of the operably linked coding sequence in a particular host organism. Prokaryotic expression vectors include a promoter, a ribosome binding site, an origin of replication for autonomous replication in a host cell and possibly other sequences, e.g. an optional operator sequence, optional restriction enzyme sites. A promoter is defined as a DNA sequence that directs RNA polymerase to bind to DNA and to initiate RNA synthesis. Eukaryotic expression vectors include a promoter, optionally a polyadenylation signal and optionally an enhancer sequence.

A polynucleotide having a nucleotide sequence encoding a protein or polypeptide means a nucleic acid sequence comprising the coding region of a gene, or in other words the nucleic acid sequence encodes a gene product. The coding region may be present in either a cDNA, genomic DNA or RNA form. When present in a DNA form, the oligonucleotide may be single-stranded (i.e., the sense strand) or double-stranded. Suitable control elements such as enhancers/promoters, splice junctions, polyadenylation signals, etc. may be placed in close proximity to the coding region of the gene if needed to permit proper initiation of transcription and/or correct processing of the primary RNA transcript. Alternatively, the coding region utilized in the expression vectors of the present invention may contain endogenous enhancers/promoters, splice junctions, intervening sequences, polyadenylation signals, etc. In further embodiments, the coding region may contain a combination of both endogenous and exogenous control elements.

The term “regulatory element” or “regulatory sequence” refers to a genetic element or sequence that controls some aspect of the expression of nucleic acid sequence(s). For example, a promoter is a regulatory element that facilitates the initiation of transcription of an operably linked coding region. Other regulatory elements include, but are not limited to, transcription factor binding sites, splicing signals, polyadenylation signals, termination signals and enhancer elements.

Transcriptional control signals in eukaryotes comprise “promoter” and “enhancer” elements. Promoters and enhancers consist of short arrays of DNA sequences that interact specifically with cellular proteins involved in transcription. Promoter and enhancer elements have been isolated from a variety of eukaryotic sources including genes in yeast, insect and mammalian cells. Promoter and enhancer elements have also been isolated from viruses and analogous control elements, such as promoters, are also found in prokaryotes. The selection of a particular promoter and enhancer depends on the cell type used to express the protein of interest. Some eukaryotic promoters and enhancers have a broad host range while others are functional in a limited subset of cell types. For example, the SV40 early gene enhancer is very active in a wide variety of cell types from many mammalian species and has been widely used for the expression of proteins in mammalian cells. Two other examples of promoter/enhancer elements active in a broad range of mammalian cell types are those from the human elongation factor 1 gene (Uetsuki et al., 1989; Kim et al., 1990; and Mizushima and Nagata, 1990) and the long terminal repeats of the Rous sarcoma virus (Gorman et al., 1982); and the human cytomegalovirus (Boshart et al., 1985).

The term “promoter/enhancer” denotes a segment of DNA containing sequences capable of providing both promoter and enhancer functions (i.e., the functions provided by a promoter element and an enhancer element as described above). For example, the long terminal repeats of retroviruses contain both promoter and enhancer functions. The enhancer/promoter may be “endogenous” or “exogenous” or “heterologous.” An “endogenous” enhancer/promoter is one that is naturally linked with a given gene in the genome. An “exogenous” or “heterologous” enhancer/promoter is one that is placed in juxtaposition to a gene by means of genetic manipulation (i.e., molecular biological techniques) such that transcription of the gene is directed by the linked enhancer/promoter.

The presence of “splicing signals” on an expression vector often results in higher levels of expression of the recombinant transcript in eukaryotic host cells. Splicing signals mediate the removal of introns from the primary RNA transcript and consist of a splice donor and acceptor site (Sambrook et al., 1989). A commonly used splice donor and acceptor site is the splice junction from the 16S RNA of SV40.

Efficient expression of recombinant DNA sequences in eukaryotic cells requires expression of signals directing the efficient termination and polyadenylation of the resulting transcript. Transcription termination signals are generally found downstream of the polyadenylation signal and are a few hundred nucleotides in length. The term “poly(A) site” or “poly(A) sequence” as used herein denotes a DNA sequence which directs both the termination and polyadenylation of the nascent RNA transcript. Efficient polyadenylation of the recombinant transcript is desirable, as transcripts lacking a poly(A) tail are unstable and are rapidly degraded. The poly(A) signal utilized in an expression vector may be “heterologous” or “endogenous.” An endogenous poly(A) signal is one that is found naturally at the 3′ end of the coding region of a given gene in the genome. A heterologous poly(A) signal is one which has been isolated from one gene and positioned 3′ to another gene. A commonly used heterologous poly(A) signal is the SV40 poly(A) signal. The SV40 poly(A) signal is contained on a 237 bp BamH I/Bcl I restriction fragment and directs both termination and polyadenylation (Sambrook et al., 1989).

Eukaryotic expression vectors may also contain “viral replicons” or “viral origins of replication.” Viral replicons are viral DNA sequences which allow for the extrachromosomal replication of a vector in a host cell expressing the appropriate replication factors. Vectors containing either the SV40 or polyoma virus origin of replication replicate to high copy number (up to 10 4 copies/cell) in cells that express the appropriate viral T antigen. In contrast, vectors containing the replicons from bovine papillomavirus or Epstein-Barr virus replicate extrachromosomally at low copy number (about 100 copies/cell).

The term “in vitro” refers to an artificial environment and to processes or reactions that occur within an artificial environment. In vitro environments include, but are not limited to, test tubes and cell lysates. The term “in vivo” refers to the natural environment (e.g., an animal or a cell) and to processes or reactions that occur within a natural environment.

The term “expression system” refers to any assay or system for determining (e.g., detecting) the expression of a gene of interest. Those skilled in the field of molecular biology will understand that any of a wide variety of expression systems may be used. A wide range of suitable mammalian cells are available from a wide range of sources (e.g., the American Type Culture Collection, Rockland, Md.). The method of transformation or transfection and the choice of expression vehicle will depend on the host system selected. Transformation and transfection methods are described, e.g., in Ausubel et al., 1992. Expression systems include in vitro gene expression assays where a gene of interest (e.g., a reporter gene) is linked to a regulatory sequence and the expression of the gene is monitored following treatment with an agent that inhibits or induces expression of the gene. Detection of gene expression can be through any suitable means including, but not limited to, detection of expressed mRNA or protein (e.g., a detectable product of a reporter gene) or through a detectable change in the phenotype of a cell expressing the gene of interest. Expression systems may also comprise assays where a cleavage event or other nucleic acid or cellular change is detected.

All amino acid residues identified herein are in the natural L-configuration. In keeping with standard polypeptide nomenclature, abbreviations for amino acid residues are as shown in the following Table of Correspondence.

The terms “complementary” or “complementarity” are used in reference to a sequence of nucleotides related by the base-pairing rules. For example, for the sequence 5′ “A-G-T” 3′, is complementary to the sequence 3′ “T-C-A” 5′. Complementarity may be “partial,” in which only some of the nucleic acids' bases are matched according to the base pairing rules. Or, there may be “complete” or “total” complementarity between the nucleic acids. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands. This is of particular importance in amplification reactions, as well as detection methods which depend upon hybridization of nucleic acids.

When used in reference to a double-stranded nucleic acid sequence such as a cDNA or a genomic clone, the term “substantially homologous” refers to any probe which can hybridize to either or both strands of the double-stranded nucleic acid sequence under conditions of low stringency as described herein.

“Probe” refers to an oligonucleotide designed to be sufficiently complementary to a sequence in a denatured nucleic acid to be probed (in relation to its length) and is bound under selected stringency conditions.

“Hybridization” and “binding” in the context of probes and denatured nucleic acids are used interchangeably. Probes that are hybridized or bound to denatured nucleic acids are base paired to complementary sequences in the polynucleotide. Whether or not a particular probe remains base paired with the polynucleotide depends on the degree of complementarity, the length of the probe, and the stringency of the binding conditions. The higher the stringency, the higher must be the degree of complementarity and/or the longer the probe.

The term “hybridization” is used in reference to the pairing of complementary nucleic acid strands. Hybridization and the strength of hybridization (i.e., the strength of the association between nucleic acid strands) is impacted by many factors well known in the art including the degree of complementarity between the nucleic acids, stringency of the conditions involved such as the concentration of salts, the Tm (melting temperature) of the formed hybrid, the presence of other components (e.g., the presence or absence of polyethylene glycol), the molarity of the hybridizing strands and the G:C content of the nucleic acid strands.

The term “stringency” is used in reference to the conditions of temperature, ionic strength, and the presence of other compounds, under which nucleic acid hybridizations are conducted. With “high stringency” conditions, nucleic acid base pairing will occur only between nucleic acid fragments that have a high frequency of complementary base sequences. Thus, conditions of “medium” or “low” stringency are often required when it is desired that nucleic acids that are not completely complementary to one another be hybridized or annealed together. The art knows well that numerous equivalent conditions can be employed to comprise medium or low stringency conditions. The choice of hybridization conditions is generally evident to one skilled in the art and is usually guided by the purpose of the hybridization, the type of hybridization (DNA-DNA or DNA-RNA), and the level of desired relatedness between the sequences (e.g., Sambrook et al., 1989; Nucleic Acid Hybridization, A Practical Approach, IRL Press, Washington D.C., 1985, for a general discussion of the methods).

The stability of nucleic acid duplexes is known to decrease with increasing numbers of mismatched bases, and further to be decreased to a greater or lesser degree depending on the relative positions of mismatches in the hybrid duplexes. Thus, the stringency of hybridization can be used to maximize or minimize stability of such duplexes. Hybridization stringency can be altered by: adjusting the temperature of hybridization; adjusting the percentage of helix destabilizing agents, such as formamide, in the hybridization mix; and adjusting the temperature and/or salt concentration of the wash solutions. For filter hybridizations, the final stringency of hybridizations often is determined by the salt concentration and/or temperature used for the post-hybridization washes.

“High stringency conditions” when used in reference to nucleic acid hybridization comprise conditions equivalent to binding or hybridization at 42° C. in a solution consisting of 5×SSPE (43.8 g/l NaCl, 6.9 g/l NaH 2 PO 4 H 2 O and 1.85 g/l EDTA, pH adjusted to 7.4 with NaOH), 0.5% SDS, 5× Denhardt's reagent and 100 μg/ml denatured salmon sperm DNA followed by washing in a solution comprising 0.1×SSPE, 1.0% SDS at 42° C. when a probe of about 500 nucleotides in length is employed.

“Medium stringency conditions” when used in reference to nucleic acid hybridization comprise conditions equivalent to binding or hybridization at 42° C. in a solution consisting of 5×SSPE (43.8 g/l NaCl, 6.9 g/l NaH 2 PO 4 H 2 O and 1.85 g/l EDTA, pH adjusted to 7.4 with NaOH), 0.5% SDS, 5× Denhardt's reagent and 100 μg/ml denatured salmon sperm DNA followed by washing in a solution comprising 1.0×SSPE, 1.0% SDS at 42° C. when a probe of about 500 nucleotides in length is employed.

“Low stringency conditions” comprise conditions equivalent to binding or hybridization at 42° C. in a solution consisting of 5×SSPE (43.8 g/l NaCl, 6.9 g/l NaH 2 PO 4 H 2 O and 1.85 g/l EDTA, pH adjusted to 7.4 with NaOH), 0.1% SDS, 5× Denhardt's reagent [50× Denhardt's contains per 500 ml: 5 g Ficoll (Type 400, Pharmacia), 5 g BSA (Fraction V; Sigma)] and 100 g/ml denatured salmon sperm DNA followed by washing in a solution comprising 5×SSPE, 0.1% SDS at 42° C. when a probe of about 500 nucleotides in length is employed.

The term “T m ” is used in reference to the “melting temperature”. The melting temperature is the temperature at which 50% of a population of double-stranded nucleic acid molecules becomes dissociated into single strands. The equation for calculating the T m of nucleic acids is well-known in the art. The Tm of a hybrid nucleic acid is often estimated using a formula adopted from hybridization assays in 1 M salt, and commonly used for calculating Tm for PCR primers: [(number of A+T)×2° C.+(number of G+C)×4° C.]. (C. R. Newton et al., PCR, 2nd Ed., Springer-Verlag (New York, 1997), p. 24). This formula was found to be inaccurate for primers longer than 20 nucleotides. (Id.) Another simple estimate of the T m value may be calculated by the equation: T m =81.5+0.41 (% G+C), when a nucleic acid is in aqueous solution at 1 M NaCl. (e.g., Anderson and Young, Quantitative Filter Hybridization, in Nucleic Acid Hybridization, 1985). Other more sophisticated computations exist in the art which take structural as well as sequence characteristics into account for the calculation of T m . A calculated T m is merely an estimate; the optimum temperature is commonly determined empirically.

The term “promoter/enhancer” denotes a segment of DNA containing sequences capable of providing both promoter and enhancer functions (i.e., the functions provided by a promoter element and an enhancer element as described above). For example, the long terminal repeats of retroviruses contain both promoter and enhancer functions. The enhancer/promoter may be “endogenous” or “exogenous” or “heterologous.” An “endogenous” enhancer/promoter is one that is naturally linked with a given gene in the genome. An “exogenous” or “heterologous” enhancer/promoter is one that is placed in juxtaposition to a gene by means of genetic manipulation (i.e., molecular biological techniques) such that transcription of the gene is directed by the linked enhancer/promoter.

The term “sequence homology” means the proportion of base matches between two nucleic acid sequences or the proportion of amino acid matches between two amino acid sequences. When sequence homology is expressed as a percentage, e.g., 50%, the percentage denotes the proportion of matches over the length of sequence from one sequence that is compared to some other sequence. Gaps (in either of the two sequences) are permitted to maximize matching; gap lengths of 15 bases or less are usually used, 6 bases or less are preferred with 2 bases or less more preferred. When using oligonucleotides as probes or treatments, the sequence homology between the target nucleic acid and the oligonucleotide sequence is generally not less than 17 target base matches out of 20 possible oligonucleotide base pair matches (85%); preferably not less than 9 matches out of 10 possible base pair matches (90%), and more preferably not less than 19 matches out of 20 possible base pair matches (95%).

Two amino acid sequences are homologous if there is a partial or complete identity between their sequences. For example, 85% homology means that 85% of the amino acids are identical when the two sequences are aligned for maximum matching. Gaps (in either of the two sequences being matched) are allowed in maximizing matching; gap lengths of 5 or less are preferred with 2 or less being more preferred. Alternatively and preferably, two protein sequences (or polypeptide sequences derived from them of at least 100 amino acids in length) are homologous, as this term is used herein, if they have an alignment score of at more than 5 (in standard deviation units) using the program ALIGN with the mutation data matrix and a gap penalty of 6 or greater. See Dayhoff, M. O., in Atlas of Protein Sequence and Structure, 1972, volume 5, National Biomedical Research Foundation, pp. 101-110, and Supplement 2 to this volume, pp. 1-10. The two sequences or parts thereof are more preferably homologous if their amino acids are greater than or equal to 85% identical when optimally aligned using the ALIGN program.

The following terms are used to describe the sequence relationships between two or more polynucleotides: “reference sequence”, “comparison window”, “sequence identity”, “percentage of sequence identity”, and “substantial identity”. A “reference sequence” is a defined sequence used as a basis for a sequence comparison; a reference sequence may be a subset of a larger sequence, for example, as a segment of a full-length cDNA or gene sequence given in a sequence listing, or may comprise a complete cDNA or gene sequence. Generally, a reference sequence is at least 20 nucleotides in length, frequently at least 25 nucleotides in length, and often at least 50 or 100 nucleotides in length. Since two polynucleotides may each (1) comprise a sequence (i.e., a portion of the complete polynucleotide sequence) that is similar between the two polynucleotides, and (2) may further comprise a sequence that is divergent between the two polynucleotides, sequence comparisons between two (or more) polynucleotides are typically performed by comparing sequences of the two polynucleotides over a “comparison window” to identify and compare local regions of sequence similarity.

A “comparison window”, as used herein, refers to a conceptual segment of at least 20 contiguous nucleotides and wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) of 20 percent or less as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences.

Methods of alignment of sequences for comparison are well known in the art. Thus, the determination of percent identity between any two sequences can be accomplished using a mathematical algorithm. Preferred, non-limiting examples of such mathematical algorithms are the algorithm of Myers and Miller (1988); the local homology algorithm of Smith and Waterman (1981); the homology alignment algorithm of Needleman and Wunsch (1970); the search-for-similarity-method of Pearson and Lipman (1988); the algorithm of Karlin and Altschul (1990), modified as in Karlin and Altschul (1993).

Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Such implementations include, but are not limited to: ClustalW (available, e.g., at http://www.ebi.ac.uk/clustalw/); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Version 8. Alignments using these programs can be performed using the default parameters. The CLUSTAL program is well described by Higgins et al. (1988); Higgins et al. (1989); Corpet et al. (1988); Huang et al. (1992); and Pearson et al. (1994). The ALIGN program is based on the algorithm of Myers and Miller, supra. The BLAST programs of Altschul et al. (1990), are based on the algorithm of Karlin and Altschul supra. To obtain gapped alignments for comparison purposes, Gapped BLAST (in BLAST 2.0) can be utilized as described in Altschul et al. (1997). Alternatively, PSI-BLAST (in BLAST 2.0) can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al., supra. When utilizing BLAST, Gapped BLAST, PSI-BLAST, the default parameters of the respective programs (e.g. BLASTN for nucleotide sequences, BLASTX for proteins) can be used. See http://www.ncbi.nlm.nih.gov. Alignment may also be performed manually by inspection

The term “sequence identity” means that two polynucleotide sequences are identical (i.e., on a nucleotide-by-nucleotide basis) over the window of comparison. The term “percentage of sequence identity” means that two polynucleotide sequences are identical (i.e., on a nucleotide-by-nucleotide basis) for the stated proportion of nucleotides over the window of comparison. The term “percentage of sequence identity” is calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, U, or I) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity. The terms “substantial identity” as used herein denote a characteristic of a polynucleotide sequence, wherein the polynucleotide comprises a sequence that has at least 60%, preferably at least 65%, more preferably at least 70%, up to about 85%, and even more preferably at least 90 to 95%, more usually at least 99%, sequence identity as compared to a reference sequence over a comparison window of at least 20 nucleotide positions, frequently over a window of at least 20-50 nucleotides, and preferably at least 300 nucleotides, wherein the percentage of sequence identity is calculated by comparing the reference sequence to the polynucleotide sequence which may include deletions or additions which total 20 percent or less of the reference sequence over the window of comparison. The reference sequence may be a subset of a larger sequence.

As applied to polypeptides, the term “substantial identity” means that two peptide sequences, when optimally aligned, such as by the programs GAP or BESTFIT using default gap weights, share at least about 85% sequence identity, preferably at least about 90% sequence identity, more preferably at least about 95% sequence identity, and most preferably at least about 99% sequence identity.

Synthetic Nucleotide Sequences and Methods of the Invention

The invention provides compositions comprising synthetic nucleotide sequences, as well as methods for preparing those sequences which yield synthetic nucleotide sequences that are efficiently expressed as a polypeptide or protein with desirable characteristics including reduced inappropriate or unintended transcription characteristics, or do not result in inappropriate or unintended transcription characteristics, when present in a particular cell type.

Natural selection is the hypothesis that genotype-environment interactions occurring at the phenotypic level lead to differential reproductive success of individuals and hence to modification of the gene pool of a population. It is generally accepted that the amino acid sequence of a protein found in nature has undergone optimization by natural selection. However, amino acids exist within the sequence of a protein that do not contribute significantly to the activity of the protein and these amino acids can be changed to other amino acids with little or no consequence. Furthermore, a protein may be useful outside its natural environment or for purposes that differ from the conditions of its natural selection. In these circumstances, the amino acid sequence can be synthetically altered to better adapt the protein for its utility in various applications.

Likewise, the nucleic acid sequence that encodes a protein is also optimized by natural selection. The relationship between coding DNA and its transcribed RNA is such that any change to the DNA affects the resulting RNA. Thus, natural selection works on both molecules simultaneously. However, this relationship does not exist between nucleic acids and proteins. Because multiple codons encode the same amino acid, many different nucleotide sequences can encode an identical protein. A specific protein composed of 500 amino acids can theoretically be encoded by more than 10 150 different nucleic acid sequences.

Natural selection acts on nucleic acids to achieve proper encoding of the corresponding protein. Presumably, other properties of nucleic acid molecules are also acted upon by natural selection. These properties include codon usage frequency, RNA secondary structure, the efficiency of intron splicing, and interactions with transcription factors or other nucleic acid binding proteins. These other properties may alter the efficiency of protein translation and the resulting phenotype. Because of the redundant nature of the genetic code, these other attributes can be optimized by natural selection without altering the corresponding amino acid sequence.

Under some conditions, it is useful to synthetically alter the natural nucleotide sequence encoding a protein to better adapt the protein for alternative applications. A common example is to alter the codon usage frequency of a gene when it is expressed in a foreign host. Although redundancy in the genetic code allows amino acids to be encoded by multiple codons, different organisms favor some codons over others. The codon usage frequencies tend to differ most for organisms with widely separated evolutionary histories. It has been found that when transferring genes between evolutionarily distant organisms, the efficiency of protein translation can be substantially increased by adjusting the codon usage frequency (see U.S. Pat. Nos. 5,096,825, 5,670,356 and 5,874,304).

In one embodiment, the sequence of a reporter gene is modified as the codon usage of reporter genes often does not correspond to the optimal codon usage of the experimental cells. In another embodiment, the sequence of a reporter gene is modified to remove regulatory sequences such as those which may alter expression of the reporter gene or a linked gene. Examples include β-galactosidase (β-gal) and chloramphenicol acetyltransferase (cat) reporter genes that are derived from E. coli and are commonly used in mammalian cells; the β-glucuronidase (gus) reporter gene that is derived from E. coli and commonly used in plant cells; the firefly luciferase (luc) reporter gene that is derived from an insect and commonly used in plant and mammalian cells; and the Renilla luciferase, and green fluorescent protein (up) reporter genes which are derived from coelenterates and are commonly used in plant and mammalian cells. To achieve sensitive quantitation of reporter gene expression, the activity of the gene product must not be endogenous to the experimental host cells. Thus, reporter genes are usually selected from organisms having unique and distinctive phenotypes. Consequently, these organisms often have widely separated evolutionary histories from the experimental host cells.

Previously, to create genes having a more optimal codon usage frequency but still encoding the same gene product, a synthetic nucleic acid sequence was made by replacing existing codons with codons that were generally more favorable to the experimental host cell (see U.S. Pat. Nos. 5,096,825, 5,670,356 and 5,874,304.) The result was a net improvement in codon usage frequency of the synthetic gene. However, the optimization of other attributes was not considered and so these synthetic genes likely did not reflect genes optimized by natural selection.

In particular, improvements in codon usage frequency are intended only for optimization of a RNA sequence based on its role in translation into a protein. Thus, previously described methods did not address how the sequence of a synthetic gene affects the role of DNA in transcription into RNA. Most notably, consideration had not been given as to how transcription factors may interact with the synthetic DNA and consequently modulate or otherwise influence gene transcription. For genes found in nature, the DNA would be optimally transcribed by the native host cell and would yield an RNA that encodes a properly folded gene product. In contrast, synthetic genes have previously not been optimized for transcriptional characteristics. Rather, this property has been ignored or left to chance.

This concern is important for all genes, but particularly important for reporter genes, which are most commonly used to quantitate transcriptional behavior in the experimental host cells, and vector backbone sequences for genes. Hundreds of transcription factors have been identified in different cell types under different physiological conditions, and likely more exist but have not yet been identified. All of these transcription factors can influence the transcription of an introduced gene or sequences linked thereto. A useful synthetic reporter gene or vector backbone of the invention has a minimal risk of influencing or perturbing intrinsic transcriptional characteristics of the host cell because the structure of that gene or vector backbone has been altered. A particularly useful synthetic reporter gene or vector backbone will have desirable characteristics under a new set and/or a wide variety of experimental conditions. To best achieve these characteristics, the structure of the synthetic gene or synthetic vector backbone should have minimal potential for interacting with transcription factors within a broad range of host cells and physiological conditions. Minimizing potential interactions between a reporter gene or vector backbone and a host cell's endogenous transcription factors increases the value of a reporter gene or vector backbone by reducing the risk of inappropriate transcriptional characteristics of the gene or vector backbone within a particular experiment, increasing applicability of the gene or vector backbone in various environments, and increasing the acceptance of the resulting experimental data.

In contrast, a reporter gene comprising a native nucleotide sequence, based on a genomic or cDNA clone from the original host organism, or a vector backbone comprising native sequences found in one or a variety of different organisms, may interact with transcription factors when present in an exogenous host. This risk stems from two circumstances. First, the native nucleotide sequence contains sequences that were optimized through natural selection to influence gene transcription within the native host organism. However, these sequences might also influence transcription when the sequences are present in exogenous hosts, i.e., out of context, thus interfering with its performance as a reporter gene or vector backbone. Second, the nucleotide sequence may inadvertently interact with transcription factors that were not present in the native host organism, and thus did not participate in its natural selection. The probability of such inadvertent interactions increases with greater evolutionary separation between the experimental cells and the native organism of the reporter gene or vector backbone.

These potential interactions with transcription factors would likely be disrupted when using a synthetic reporter gene having alterations in codon usage frequency. However, a synthetic reporter gene sequence, designed by choosing codons based only on codon usage frequency, or randomly replacing sequences or randomly juxtaposing sequences in a vector backbone, is likely to contain other unintended transcription factor binding sites since the resulting sequence has not been subjected to the benefit of natural selection to correct inappropriate transcriptional activities. Inadvertent interactions with transcription factors could also occur whenever an encoded amino acid sequence is artificially altered, e.g., to introduce amino acid substitutions. Similarly, these changes have not been subjected to natural selection, and thus may exhibit undesired characteristics.

Thus, the invention provides a method for preparing synthetic nucleotide sequences that reduce the risk of undesirable interactions of the nucleotide sequence with transcription factors and other trans-acting factors when expressed in a particular host cell, thereby reducing inappropriate or unintended characteristics. Preferably, the method yields synthetic genes containing improved codon usage frequencies for a particular host cell and with a reduced occurrence of regulatory sequences such as transcription factor binding sites and/or vector backbone sequences with a reduced occurrence of regulatory sequences. The invention also provides a method of preparing synthetic genes containing improved codon usage frequencies with a reduced occurrence of transcription factor binding sites and additional beneficial structural attributes. Such additional attributes include the absence of inappropriate RNA splicing junctions, poly(A) addition signals, undesirable restriction enzyme recognition sites, ribosomal binding sites, and/or secondary structural motifs such as hairpin loops.

In one embodiment, a parent nucleic acid sequence encoding a polypeptide is optimized for expression in a particular cell. For example, the nucleic acid sequence is optimized by replacing codons in the wild-type sequence with codons which are preferentially employed in a particular (selected) cell, which codon replacement also reduces the number of regulatory sequences. Preferred codons have a relatively high codon usage frequency in a selected cell, and preferably their introduction results in the introduction of relatively few regulatory sequences such as transcription factor binding sites, and relatively few other undesirable structural attributes. Thus, the optimized nucleotide sequence may have an improved level of expression due to improved codon usage frequency, and a reduced risk of inappropriate transcriptional behavior due to a reduced number of undesirable transcription regulatory sequences. In another embodiment, a parent vector backbone sequence is altered to remove regulatory sequences and optionally restriction endonuclease sites, and optionally retain or add other desirable characteristics, e.g., the presence of one or more stop codons in one or more reading frames, one or more poly(A) sites, and/or restriction endonuclease sites.

The invention may be employed with any nucleic acid sequence, e.g., a native sequence such as a cDNA or one that has been manipulated in vitro. Exemplary genes include, but are not limited to, those encoding lactamase (β-gal), neomycin resistance (Neo), hygromycin resistance (Hyg), puromycin resistance (Puro), ampicillin resistance (Amp), CAT, GUS, galactopyranoside, GFP, xylosidase, thymidine kinase, arabinosidase, luciferase and the like. As used herein, a “reporter gene” is a gene that imparts a distinct phenotype to cells expressing the gene and thus permits cells having the gene to be distinguished from cells that do not have the gene. Such genes may encode either a selectable or screenable polypeptide, depending on whether the marker confers a trait which one can ‘select’ for by chemical means, i.e., through the use of a selective agent (e.g., a herbicide, antibiotic, or the like), or whether it is simply a “reporter” trait that one can identify through observation or testing, i.e., by ‘screening’. Included within the terms selectable or screenable marker genes are also genes which encode a “secretable marker” whose secretion can be detected as a means of identifying or selecting for transformed cells. Examples include markers that encode a secretable antigen that can be identified by antibody interaction, or even secretable enzymes which can be detected by their catalytic activity. Secretable proteins fall into a number of classes, including small, diffusible proteins detectable, e.g., by ELISA, and proteins that are inserted or trapped in the cell membrane.

Elements of the present disclosure are exemplified in detail through the use of particular genes and vector backbone sequences. Of course, many examples of suitable genes and vector backbones are known to the art and can be employed in the practice of the invention. Therefore, it will be understood that the following discussion is exemplary rather than exhaustive. In light of the techniques disclosed herein and the general recombinant techniques that are known in the art, the present invention renders possible the alteration of any gene or vector backbone sequence.

Exemplary genes include, but are not limited to, a neo gene, a puro gene, an amp gene, a β-gal gene, a gus gene, a cat gene, a gpt gene, a hyg gene, a hisD gene, a ble gene, a mprt gene, a bar gene, a nitrilase gene, a mutant acetolactate synthase gene (ALS) or acetoacid synthase gene (AAS), a methotrexate-resistant dhfr gene, a dalapon dehalogenase gene, a mutated anthranilate synthase gene that confers resistance to 5-methyl tryptophan (WO 97/26366), an R-locus gene, a β-lactamase gene, a xylE gene, an α-amylase gene, a tyrosinase gene, a luciferase (luc) gene (e.g., a Renilla reniformis luciferase gene, a firefly luciferase gene, or a click beetle luciferase ( Pyrophorus plagiophthalamus gene), an aequorin gene, or a fluorescent protein gene.

The method of the invention can be performed by, although it is not limited to, a recursive process. The process includes assigning preferred codons to each amino acid in a target molecule, e.g., a native nucleotide sequence, based on codon usage in a particular species, identifying potential transcription regulatory sequences such as transcription factor binding sites in the nucleic acid sequence having preferred codons, e.g., using a database of such binding sites, optionally identifying other undesirable sequences, and substituting an alternative codon (i.e., encoding the same amino acid) at positions where undesirable transcription factor binding sites or other sequences occur. For codon distinct versions, alternative preferred codons are substituted in each version. If necessary, the identification and elimination of potential transcription factor or other undesirable sequences can be repeated until a nucleotide sequence is achieved containing a maximum number of preferred codons and a minimum number of undesired sequences including transcription regulatory sequences or other undesirable sequences. Also, optionally, desired sequences, e.g., restriction enzyme recognition sites, can be introduced. After a synthetic nucleotide sequence is designed and constructed, its properties relative to the parent nucleic acid sequence can be determined by methods well known to the art. For example, the expression of the synthetic and target nucleic acids in a series of vectors in a particular cell can be compared.

Thus, generally, the method of the invention comprises identifying a target nucleic acid sequence, and a host cell of interest, for example, a plant (dicot or monocot), fungus, yeast or mammalian cell. Preferred host cells are mammalian host cells such as CHO, COS, 293, Hela, CV-1 and NIH3T3 cells. Based on preferred codon usage in the host cell(s) and, optionally, low codon usage in the host cell(s), e.g., high usage mammalian codons and low usage E. coli and mammalian codons, codons to be replaced are determined. Concurrent, subsequent or prior to selecting codons to be replaced, desired and undesired sequences, such as undesired transcriptional regulatory sequences, in the target sequence are identified. These sequences, including transcriptional regulatory sequences and restriction endonuclease sites, can be identified using databases and software such as TRANSFAC® (Transcription Factor Database, http://www.gene-regulation.com/), Match™ (http://www.gene-regulation.com/), MatInspector (Genomatix, http://www.genomatix.de), EPD (Eukaryotic Promoter Database, http://www.epd.isb-sib.ch/), REBASE® (Restriction Enzyme Database, NEB, http://rebase.neb.com), TESS (Transcription Element Search System, http://www.cbil.upenn.edu/tess/), MAR-Wiz (Futuresoft, http://www.futuresoft.org), Lasergene® (DNASTAR, http://www.dnastar.com), Vector NTI™ (Invitrogen, http://www.invitrogen.com), and Sequence Manipulation Suite (http://www.bioinformatics.org/SMS/index.html). Links to other databases and sequence analysis software are listed at http://www.expasy.org/alinks.html. After one or more sequences are identified, the modification(s) may be introduced. Once a desired synthetic nucleotide sequence is obtained, it can be prepared by methods well known to the art (such as nucleic acid amplification reactions with overlapping primers), and its structural and functional properties compared to the target nucleic acid sequence, including, but not limited to, percent homology, presence or absence of certain sequences, for example, restriction sites, percent of codons changed (such as an increased or decreased usage of certain codons) and/or expression rates.

As described below, the method was used to create synthetic reporter genes encoding firefly luciferases and selectable polypeptides, and synthetic sequences for vector backbones. Synthetic sequences may support greater levels of expression and/or reduced aberrant expression than the corresponding native or parent sequences for the protein. The native and parent sequences may demonstrate anomalous transcription characteristics when expressed in mammalian cells, which are likely not evident in the synthetic sequences.

Exemplary Uses of the Synthetic Nucleotide Sequences

The synthetic genes of the invention preferably encode the same proteins as their native counterpart (or nearly so), but have improved codon usage while being largely devoid of regulatory elements in the coding (it is recognized that a small number of amino acid changes may be desired to enhance a property of the native counterpart protein, e.g. to enhance luminescence of a luciferase) and noncoding regions. This increases the level of expression of the protein the synthetic gene encodes and reduces the risk of anomalous expression of the protein. For example, studies of many important events of gene regulation, which may be mediated by weak promoters, are limited by insufficient reporter signals from inadequate expression of the reporter proteins. Also, the use of some selectable markers may be limited by the expression of that marker in an exogenous cell. Thus, synthetic selectable marker genes which have improved codon usage for that cell, and have a decrease in other undesirable sequences, (e.g., transcription factor binding sites), can permit the use of those markers in cells that otherwise were undesirable as hosts for those markers.

Promoter crosstalk is another concern when a co-reporter gene is used to normalize transfection efficiencies. With the enhanced expression of synthetic genes, the amount of DNA containing strong promoters can be reduced, or DNA containing weaker promoters can be employed, to drive the expression of the co-reporter. In addition, there may be a reduction in the background expression from the synthetic reporter genes of the invention. This characteristic makes synthetic reporter genes more desirable by minimizing the sporadic expression from the genes and reducing the interference resulting from other regulatory pathways.

The use of reporter genes in imaging systems, which can be used for in vivo biological studies or drug screening, is another use for the synthetic genes of the invention. Due to their increased level of expression, the protein encoded by a synthetic gene is more readily detectable by an imaging system. In fact, using a synthetic Renilla luciferase gene, luminescence in transfected CHO cells was detected visually without the aid of instrumentation.

In addition, the synthetic genes may be used to express fusion proteins, for example fusions with secretion leader sequences or cellular localization sequences, to study transcription in difficult-to-transfect cells such as primary cells, and/or to improve the analysis of regulatory pathways and genetic elements. Other uses include, but are not limited to, the detection of rare events that require extreme sensitivity (e.g., studying RNA recoding), use with IRES, to improve the efficiency of in vitro translation or in vitro transcription-translation coupled systems such as TnT (Promega Corp., Madison, Wis.), study of reporters optimized to different host organisms (e.g., plants, fungus, and the like), use of multiple genes as co-reporters to monitor drug toxicity, as reporter molecules in multiwell assays, and as reporter molecules in drug screening with the advantage of minimizing possible interference of reporter signal by different signal transduction pathways and other regulatory mechanisms.

Additionally, uses for the synthetic nucleotide sequences of the invention include fluorescence activated cell sorting (FACS), fluorescent microscopy, to detect and/or measure the level of gene expression in vitro and in vivo, (e.g., to determine promoter strength), subcellular localization or targeting (fusion protein), as a marker, in calibration, in a kit (e.g., for dual assays), for in vivo imaging, to analyze regulatory pathways and genetic elements, and in multi-well formats.

Further, although reporter genes are widely used to measure transcription events, their utility can be limited by the fidelity and efficiency of reporter expression. For example, in U.S. Pat. No. 5,670,356, a firefly luciferase gene (referred to as luc+) was modified to improve the level of luciferase expression. While a higher level of expression was observed, it was not determined that higher expression had improved regulatory control.

The invention will be further described by the following nonlimiting examples. In particular, the synthetic nucleic acid molecules of the invention may be derived by other methods as well as by variations on the methods described herein.

aGAaGCtATGAAGCGCTAtGGgCTGAAtACaAACCAtCGgATCGTGGTGT

AaGGgCTGCAaAAGATCCTcAACGTGCAaAAGAAGCTaCCgATCATaCAa

AGtAGtGGCAGtACCGGatTgCCcAAGGGCGTaGCCCTaCCgCACCGCAC

AGATtCAatctGCCCTGCTGGTGCCCACaCTaTTtAGcTTCTTCGCtAAG

ATCGCCGTGTAATAATTCTAGA.

For vectors with a BglI site in the multiple cloning region, the BglI site present in the firefly sequence can be removed. The luciferase gene from hluc+ver2AF8, which lacks a BglI site, displays an average of a 7.2-fold increase in expression when assayed in four mammalian cell lines, i.e., NIH3T3, CHO, HeLa and HEK293 cells.

hluc+ver2A8 has the following sequence:

(SEQ ID NO: 23)

aGAaGCtATGAAGCGCTAtGGgCTGAAtACaAACCAtCGgATCGTGGTGT

AaGGgCTGCAaAAGATCCTcAACGTGCAaAAGAAGCTaCCgATCATaCAa

AGtAGtGGCAGtACCGGatTgCCcAAGGGCGTaGCCCTaCCgCACCGCAC

AGATtCAatctGCCCTGCTGGTGCCCACaCTaTTtAGcTTCTTCGCtAAG

tGGtGTtGTGTTCGTGGACGAGGTGCCtAAaGGaCTGACcGGCAAGtTGG

ATCGCCGTGTAATAATTCTAGA.

For the second approach, firefly luciferase luc+codons were optimized for mammalian expression, and the number of consensus transcription factor binding site, and CG dinucleotides (CG islands, potential methylation sites) was reduced. The second approach yielded: versions hluc+ver2BF1 through hluc+ver2BF5. hluc+ver2BF1 is codon-optimized, hluc+ver2BF2 is a sequence obtained after a first round of removal of identified undesired sequences including transcription factor binding sites, hluc+ver2BF3 was obtained after a second round of removal of identified undesired sequences including transcription factor binding sites, hluc+ver2BF4 was obtained after a third round of removal of identified undesired sequences including transcription factor binding sites, hluc+ver2BF5 was obtained after a fourth round of removal of identified undesired sequences including transcription factor binding sites, hluc+ver2BF6 was obtained after removal of promoter modules and RBS, hluc+ver2BF7 was obtained after further removal of identified undesired sequences including transcription factor binding sites, and hluc+ver2BF8 was obtained after modifying a restriction enzyme recognition site.

hluc+ver2B1-B5 have the following sequences (SEQ ID Nos. 24-28):

hluc + ver2B1 AAAGCCACCATGGAGGATGCTAAGAATATTAAGAAGGGGCCTGCTCCTTT TTATCCTCTGGAGGATGGGACAGCTGGGGAGCAGCTGCATAAGGCTATGA AGAGATATGCTCTGGTGCCTGGGACAATTGCTTTTACAGATGCTCATATT GAGGTGGATATTACATATGCTGAGTATTTTGAGATGTCTGTGAGACTGGC TGAGGCTATGAAGAGATATGGGCTGAATACAAATCATAGAATTGTGGTGT GTTCTGAGAATTCTCTGCAGTTTTTTATGCCTGTGCTGGGGGCTCTGTTT ATTGGGGTGGCTGTGGCTCCTGCTAATGATATTTATAATGAGAGAGAGCT GCTGAATTCTATGGGGATTTCTCAGCCTACAGTGGTGTTTGTGTCTAAGA AGGGGCTGCAGAAGATTCTGAATGTGCAGAAGAAGCTGCCTATTATTCAG AAGATTATTATTATGGATTCTAAGACAGATTATCAGGGGTTTCAGTCTAT GTATACATTTGTGACATCTCATCTGCCTCCTGGGTTTAATGAGTATGATT TTGTGCCTGAGTCTTTTGATAGAGATAAGACAATTGCTCTGATTATGAAT TCTTCTGGGTCTACAGGGCTGCCTAAGGGGGTGGCTCTGCCTCATAGAAC AGCTTGTGTGAGATTTTCTCATGCTAGAGATCCTATTTTTGGGAATCAGA TTATTCCTGATACAGCTATTCTGTCTGTGGTGCCTTTTCATCATGGGTTT GGGATGTTTACAACACTGGGGTATCTGATTTGTGGGTTTAGAGTGGTGCT GATGTATAGATTTGAGGAGGAGCTGTTTCTGAGATCTCTGCAGGATTATA AGATTCAGTCTGCTCTGCTGGTGCCTACACTGTTTTCTTTTTTTGCTAAG TCTACACTGATTGATAAGTATGATCTGTCTAATCTGCATGAGATTGCTTC TGGGGGGGCTCCTCTGTCTAAGGAGGTGGGGGAGGCTGTGGCTAAGAGAT TTCATCTGCCTGGGATTAGACAGGGGTATGGGCTGACAGAGACAACATCT GCTATTCTGATTACACCTGAGGGGGATGATAAGCCTGGGGCTGTGGGGAA GGTGGTGCCTTTTTTTGAGGCTAAGGTGGTGGATCTGGATACAGGGAAGA CACTGGGGGTGAATCAGAGAGGGGAGCTGTGTGTGAGAGGGCCTATGATT ATGTCTGGGTATGTGAATAATCCTGAGGCTACAAATGCTCTGATTGATAA GGATGGGTGGCTGCATTCTGGGGATATTGCTTATTGGGATGAGGATGAGC ATTTTTTTATTGTGGATAGACTGAAGTCTCTGATTAAGTATAAGGGGTAT CAGGTGGCTCCTGCTGAGCTGGAGTCTATTCTGCTGCAGCATCCTAATAT TTTTGATGCTGGGGTGGCTGGGCTGCCTGATGATGATGCTGGGGAGCTGC CTGCTGCTGTGGTGGTGCTGGAGCATGGGAAGACAATGACAGAGAAGGAG ATTGTGGATTATGTGGCTTCTCAGGTGACAACAGCTAAGAAGCTGAGAGG GGGGGTGGTGTTTGTGGATGAGGTGCCTAAGGGGCTGACAGGGAAGCTGG ATGCTAGAAAGATTAGAGAGATTCTGATTAAGGCTAAGAAGGGGGGGAAG ATTGCTGTGTAATAATTCTAGA hluc + ver2B2 AAAGCCACCATGGAAGATGCTAAAAACATTAAGAAGGGGCCTGCTCCTTT CTACCCTCTGGAGGATGGGACTGCCGGGGAGCAGCTGCATAAAGCTATGA AGCGGTATGCTCTGGTGCCAGGCACAATTGCGTTCACGGATGCTCACATT GAGGTGGACATTACATACGCTGAGTATTTTGAGATGTCGGTGCGGCTGGC TGAGGCTATGAAGCGATATGGGCTGAATACAAACCATAGAATTGTAGTGT GCTCTGAGAACTCGTTGCAGTTTTTTATGCCTGTGCTGGGGGCTCTCTTC ATCGGGGTGGCTGTGGCTCCTGCTAACGACATTTACAATGAGAGAGAGCT TTTGAACTCGATGGGGATTTCTCAGCCTACAGTGGTGTTTGTGAGTAAGA AAGGGCTTCAAAAGATTCTCAATGTGCAAAAGAAGCTGCCTATTATTCAA AAGATTATTATTATGGACTCTAAGACAGACTACCAGGGGTTTCAGTCTAT GTATACATTTGTGACATCTCATCTGCCTCCTGGGTTCAACGAGTATGACT TTGTGCCCGAGTCTTTCGACAGAGATAAGACAATTGCTCTGATTATGAAT TCATCTGGGTCTACCGGGCTGCCTAAGGGTGTAGCTCTGCCACATAGAAC AGCTTGTGTGAGATTTTCTCATGCTAGGGACCCTATTTTTGGGAATCAGA TTATTCCTGATACTGCTATTCTGTCGGTTGTGCCCTTTCATCATGGGTTT GGGATGTTTACAACACTGGGCTACCTGATATGTGGGTTTAGAGTGGTGCT CATGTATAGGTTTGAGGAGGAGCTTTTTTTGCGCTCTCTGCAAGATTATA AGATTCAGTCTGCTCTGCTGGTGCCTACACTGTTTTCTTTTTTTGCTAAG TCTACCCTGATCGATAAGTATGATCTGTCCAACCTGCACGAGATTGCTTC TGGGGGGGCTCCTCTGTCTAAGGAGGTAGGTGAGGCTGTGGCTAAGCGCT TTCATCTGCCTGGAATCAGACAGGGGTATGGGCTAACAGAAACAACATCT GCTATTCTGATTACACCAGAGGGGGATGATAAGCCCGGGGCTGTAGGGAA AGTGGTGCCCTTTTTTGAAGCTAAAGTAGTTGATCTTGATACCGGTAAGA CACTGGGGGTGAATCAGCGAGGGGAACTGTGTGTGAGAGGGCCTATGATT ATGTCGGGGTATGTGAACAACCCTGAGGCTACAAATGCTCTGATTGATAA GGATGGGTGGCTGCATTCGGGCGATATTGCTTACTGGGATGAGGATGAGC ATTTCTTCATCGTGGACAGACTGAAGTCGTTGATCAAATATAAGGGGTAT CAAGTAGCTCCTGCTGAGCTGGAGTCCATTCTGCTTCAACATCCTAACAT TTTCGATGCTGGGGTGGCTGGGCTGCCTGATGATGATGCTGGGGAGCTGC CTGCTGCTGTAGTGGTGCTGGAGCACGGTAAGACAATGACAGAGAAGGAG ATTGTGGATTATGTGGCTTCACAAGTGACAACAGCTAAGAAACTGAGAGG TGGCGTTGTGTTTGTGGATGAGGTGCCTAAAGGGCTGACAGGCAAGCTGG ATGCTAGAAAAATTCGAGAGATTCTGATTAAGGCTAAGAAGGGTGGAAAG ATTGCTGTGTAATAGTTCTAGA hluc + ver2B3 AAAGCCACCATGGAAGATGCTAAAAACATTAAGAAGGGGCCTGCTCCTTT CTACCCTCTTGAAGATGGGACTGCTGGCGAGCAACTTCACAAAGCTATGA AGCGGTATGCTCTTGTGCCAGGCACAATTGCGTTCACGGATGCTCACATT GAGGTGGACATCACATACGCTGAGTATTTTGAGATGTCGGTGCGGCTGGC AGAAGCTATGAAGCGCTATGGGCTGAATACAAACCATAGAATTGTAGTGT GCAGTGAGAACTCGTTGCAGTTCTTTATGCCCGTGCTGGGGGCTCTCTTC ATCGGGGTGGCTGTGGCTCCTGCTAACGACATCTACAACGAGCGAGAGCT GTTGAACTCGATGGGGATTTCTCAGCCTACAGTGGTGTTTGTGAGTAAGA AAGGGCTTCAAAAGATTCTCAATGTGCAAAAGAAGCTGCCTATTATTCAA AAGATTATTATTATGGACTCTAAGACCGACTACCAGGGGTTTCAGTCTAT GTATACATTTGTGACATCTCATCTGCCTCCTGGCTTCAACGAGTACGACT TCGTGCCCGAGTCTTTCGACAGAGATAAGACAATTGCTCTGATCATGAAT TCATCCGGGTCTACCGGGCTGCCTAAGGGTGTAGCTCTGCCCCATAGAAC AGCTTGTGTGAGATTTTCTCATGCTAGGGACCTATTTTTGGGAATCAGAT TATTCCTGACACTGCTATTCTGTCGGTGGTGCCCTTTCATCATGGGTTTG GGATGTTTACAACACTGGGCTACCTAATATGTGGGTTTAGAGTGGTGCTC ATGTATAGGTTTGAAGAAGAGCTGTTCTTACGCTCTTTGCAAGATTATAA GATTCAGTCTGCTCTGCTGGTGCCAACACTATTCTCTTTTTTTGCTAAGT CTACGCTCATAGACAAGTATGACTTGTCCAACTTGCACGAGATTGCTTCT GGCGGAGCACCTCTGTCTAAGGAGGTAGGTGAGGCTGTGGCTAAGCGCTT TCATCTGCCTGGTATCAGACAGGGGTATGGGCTAACAGAAACAACATCTG CTATTCTGATTACACCAGAGGGGGATGATAAGCCCGGGGCTGTAGGGAAA GTGGTGCCCTTTTTTGAAGCCAAAGTAGTTGATCTTGATACCGGTAAGAC ACTAGGGGTGAACCAGCGTGGTGAACTGTGTGTGAGAGGGCCTATGATTA TGTCGGGGTACGTTAACAACCCCGAAGCTACAAATGCTCTGATTGATAAG GATGGCTGGCTGCATTCGGGCGACATTGCTTACTGGGATGAGGATGAGCA TTTCTTCATCGTGGACAGACTGAAGTCGTTGATCAAATACAAGGGGTATC AAGTAGCTCCTGCTGAGCTGGAATCCATTCTGCTTCAACATCCCAACATT TTCGATGCTGGGGTGGCTGGGCTGCCTGATGATGATGCTGGGGAGTTGCC TGCTGCTGTAGTGGTGCTTGAGCACGGTAAGACAATGACAGAGAAGGAGA TCGTGGATTATGTGGCTTCACAAGTGACAACAGCTAAGAAACTGAGAGGT GGCGTTGTGTTTGTGGATGAGGTGCCTAAAGGGCTCACTGGCAAGCTGGA TGCTAGAAAAATTCGAGAGATTCTGATTAAGGCTAAGAAGGGTGGAAAGA TTGCTGTGTAATAGTTCTAGA hluc + ver2B4 AAAGCCACCATGGAAGATGCTAAAAACATTAAGAAGGGGCCTGCTCCCTT CTACCCTCTTGAAGATGGGACTGCTGGCGAGCAACTTCACAAAGCTATGA AGCGGTATGCTCTTGTGCCAGGCACAATTGCGTTCACGGATGCTCACATT GAGGTGGACATCACATACGCTGAGTATTTTGAGATGTCGGTGCGGCTGGC AGAAGCTATGAAGCGCTATGGGCTGAATACAAACCATAGAATTGTAGTGT GCAGTGAGAACTCGTTGCAGTTCTTTATGCCCGTGCTGGGGGCTCTCTTC ATCGGGGTGGCTGTGGCTCCTGCTAACGACATCTACAACGAGCGAGAGCT GTTGAACTCGATGGGGATCTCTGAGCCTACAGTGGTGTTTGTGAGTAAGA AAGGGCTTCAAAAGATTCTCAATGTGCAAAAGAAGCTGCCTATTATTCAA AAGATTATTATTATGGACTCTAAGACAGACTACCAGGGGTTTCAGTCCAT GTATACATTTGTGACATCTCATCTGCCTCCTGGCTTCAACGAGTACGACT TCGTGCCCGAGTCTTTCGACAGAGATAAGACAATTGCTCTGATCATGAAT TCATCCGGGTCTACCGGGCTGCCTAAGGGTGTAGCTCTGCCCCATCGAAC AGCTTGTGTGAGATTCTCTCATGCCAGGGACCCGATCTTTGGGAATCAGA TTATTCCTGACACTGCTATTCTGTCGGTGGTGCCCTTTCATCATGGGTTT GGGATGTTTACAACACTGGGATACCTAATATGTGGGTTTAGAGTGGTGCT CATGTATAGGTTTGAAGAAGAACTGTTCTTACGCTCTTTGCAAGATTATA AGATTCAGTCTGCTCTGCTGGTGCCAACACTATTCTCTTTTTTTGCTAAG TCTACGCTCATAGACAAGTATGACTTGTCCAACTTGCACGAGATTGCTTC TGGCGGAGCACCTCTGTCTAAGGAGGTAGGTGAGGCTGTGGCTAAGCGCT TTCATCTGCCTGGTATCAGACAGGGGTACGGGCTAACAGAAACAACTTCT GCTATTCTGATTACACCAGAGGGCGATGACAAGCCCGGGGCTGTAGGGAA AGTGGTGCCCTTTTTTGAAGCCAAAGTAGTTGATCTTGATACCGGTAAGA CACTAGGGGTGAACCAGCGTGGTGAACTGTGTGTGCGGGGCCCTATGATT ATGTCGGGGTACGTTAACAACCCCGAAGCTACAAATGCTCTTATTGATAA GGATGGCTGGTTGCATTCGGGCGACATTGCCTACTGGGATGAGGATGAGC ATTTCTTCATCGTGGACAGACTGAAGTCGTTGATCAAATACAAGGGGTAT CAAGTAGCTCCTGCTGAGCTGGAATCCATTCTGCTTCAACATCCAAACAT TTTCGATGCTGGGGTGGCTGGGCTGCCTGATGATGATGCTGGAGAGTTGC CTGCTGCTGTAGTAGTGCTTGAGCACGGTAAGACAATGACAGAGAAGGAG ATCGTGGATTATGTGGCTTCACAAGTGACAACAGCTAAGAAACTGAGAGG TGGCGTTGTGTTTGTGGATGAGGTGCCTAAAGGGCTCACTGGCAAGCTGG ATGCCAGAAAAATTCGAGAGATTCTCATTAAGGCTAAGAAGGGTGGAAAG ATTGCTGTGTAATAGTTCTAGA hluc + ver2B5 AAAGCCACCATGGAAGATGCTAAAAACATTAAGAAGGGGCCTGCTCCCTT CTACCCTCTTGAAGATGGGACTGCTGGCGAGCAACTTCACAAAGCTATGA AGCGGTATGCTCTTGTGCCAGGCACAATTGCGTTCACGGATGCTCACATT GAGGTGGACATCACATACGCTGAGTATTTTGAGATGTCGGTGCGGCTGGC AGAAGCTATGAAGCGCTATGGGCTGAATACAAACCATAGAATTGTAGTGT GCAGTGAGAACTCGTTGCAGTTCTTTATGCCCGTGCTGGGGGCTCTCTTC ATCGGGGTGGCTGTGGCTCCTGCTAACGACATCTACAACGAGCGAGAGCT GTTGAACTCGATGGGGATCTCTCAGCCTACAGTGGTGTTTGTGAGTAAGA AAGGGCTTCAAAAGATTCTCAATGTGCAAAAGAAGCTGCCTATTATACAA AAGATTATTATTATGGACTCTAAGACCGACTACCAGGGGTTTCAGTCCAT GTACACATTTGTAACCTCTCATCTGCCTCCTGGCTTCAACGAGTACGACT TCGTGCCCGAGTCTTTCGACAGGGACAAAACGATTGCTCTGATCATGAAC TCATCCGGGTCTACCGGGCTGCCTAAGGGTGTAGCTCTGCCCCATCGAAC AGCTTGTGTGAGATTCTCTCATGCCAGGGACCCGATCTTTGGGAATCAGA TTATTCCTGACACTGCTATTCTGTCGGTGGTGCCCTTTCATCATGGGTTT GGGATGTTCACAACACTGGGATACCTCATTTGCGGGTTTAGAGTGGTGCT CATGTATAGGTTTGAAGAAGAACTATTCCTACGCTCTTTGCAAGATTATA AGATTCAGTCTGCTCTGCTGGTGCCAACACTATTCTCTTTTTTTGCTAAG TCTACGCTCATAGACAAGTATGACTTGTCCAACTTGCACGAGATTGCTTC TGGCGGAGCACCTCTGTCTAAGGAGGTAGGTGAGGCTGTGGCTAAGCGCT TTCATCTGCCTGGTATCAGACAGGGGTACGGGCTAACAGAAACAACTTCT GCTATTCTGATTACACCAGAGGGCGATGACAAACCCGGGGCTGTAGGGAA AGTGGTGCCCTTTTTTGAAGCCAAAGTAGTTGATCTTGATACCGGTAAGA CACTAGGGGTGAACCAGCGTGGTGAACTGTGTGTGCGGGGCCCTATGATT ATGTCGGGGTACGTTAACAACCCCGAAGCTACAAATGCTCTTATTGATAA GGATGGCTGGTTGCATTCGGGCGACATTGCCTACTGGGATGAGGATGAGC ATTTCTTCATCGTGGACAGACTGAAGTCGTTGATCAAATACAAGGGGTAT CAAGTAGCTCCTGCTGAGCTGGAATCCATTCTGCTTCAACATCCTAACAT TTTCGATGCTGGGGTGGCTGGGCTGCCTGATGATGATGCTGGAGAGTTGC CTGCTGCTGTAGTAGTGCTTGAGCACGGTAAGACAATGACAGAGAAGGAG ATCGTGGATTATGTGGCTTCACAAGTGACAACAGCTAAGAAACTGAGAGG TGGCGTTGTGTTTGTGGATGAGGTGCCTAAAGGGCTCACTGGCAAGCTGG ATGCCAGAAAAATTCGAGAGATTCTCATTAAGGCTAAGAAGGGTGGAAAG ATTGCTGTGTAATAGTTCTAGA

hluc+ver2B6 has the following sequence:

(SEQ ID NO: 29) AAAGCCACCATGGAaGATGCcAAaAAcATTAAGAAGGGGCCTGCTCCcTT cTAcCCTCTtGAaGATGGGACtGCtGGcGAGCAaCTtCAcAAaGCTATGA AGcGgTATGCTCTtGTGCCaGGcACAATTGCgTTcACgGATGCTCAcATT GAaGTaGAcATcACATAcGCTGAGTATTTTGAGATGTCgGTGcGgCTGGC aGAaGCTATGAAGcGcTATGGGCTGAATACAAAcCATAGAATTGTaGTGT GcagTGAGAAcTCgtTGCAGTTcTTTATGCCcGTGCTGGGGGCTCTcTTc ATcGGGGTGGCTGTGGCTCCTGCTAAcGAcATcTAcAAcGAGcGAGAGCT gtTGAAcTCgATGGGGATcTCTCAGCCTACAGTGGTGTTTGTGagTAAGA AaGGGCTtCAaAAGATTCTcAATGTGCAaAAGAAGCTGCCTATTATaCAa AAGATTATTATTATGGAcTCtAAGACcGAcTAcCAGGGGTTTCAGTCcAT GTAcACATTTGTaACcTCTCATCTGCCTCCTGGcTTcAAcGAGTAcGAcT TcGTGCCcGAGTCTTTcGAcAGgGAcAAaACgATTGCTCTGATcATGAAc agcTCcGGGTCTACcGGGCTGCCTAAGGGtGTaGCTCTGCCcCATcGAAC AGCTTGTGTGAGATTcTCTCATGCcAGgGAcCCgATcTTtGGaAAcCAGA TcATcCCTGAcACtGCTATTCTGTCgGTgGTGCCcTTTCATCATGGGTTT GGGATGTTcACAACACTGGGaTAccTcATtTGcGGGTTTAGAGTGGTGCT cATGTATAGgTTTGAaGAaGAaCTaTTccTacGcTCTtTGCAaGATTATA AGATTCAGTCTGCTCTGCTGGTGCCaACACTaTTcTCTTTTTTTGCTAAG TCTACgCTcATaGAcAAGTATGActTGTCcAActTGCAcGAGATTGCTTC TGGcGGaGCaCCTCTGTCTAAGGAGGTaGGtGAGGCTGTGGCTAAGcGcT TTCATCTGCCTGGtATcAGACAGGGGTAcGGGCTaACAGAaACAACtTCT GCTATTCTGATTACACCaGAGGGcGATGAcAAaCCcGGGGCTGTaGGGAA aGTGGTGCCcTTTTTTGAaGCcAAaGTaGTtGATCTtGATACcGGtAAGA CACTaGGGGTGAAcCAGcGtGGtGAaCTGTGTGTGcGgGGcCCTATGATT ATGTCgGGGTAcGTtAAcAAcCCcGAaGCTACAAATGCTCTcATaGAcAA GGAcGGgTGGcTtCATagcGGcGAcATTGCcTAcTGGGAcGAGGATGAGC ATTTcTTcATcGTGGAcAGACTGAAGTCgtTGATcAAaTAcAAGGGGTAT CAaGTaGCTCCTGCTGAGCTGGAaTCcATTCTGCTtCAaCAcCCcAAtAT cTTcGATGCTGGGGTGGCTGGGCTGCCTGATGATGATGCTGGaGAGcTGC CTGCTGCTGTaGTaGTGCTtGAGCAcGGtAAGACAATGACAGAGAAGGAG ATcGTGGATTATGTGGCTTCaCAaGTGACAACAGCTAAGAAaCTGAGAGG tGGcGTtGTGTTTGTGGATGAGGTGCCTAAaGGGCTcACtGGcAAGCTGG ATGCcAGAAAaATTcGAGAGATTCTcATTAAGGCTAAGAAGGGtGGaAAG ATTGCTGTGTAATAgTTCTAGA.

hluc+ver2BF8 was created by removing a Ptx1 consensus transcription factor binding site from hluc+ver2BF7.

hluc+ver2B7 has the following sequence:

(SEQ ID NO: 94) AAAGCCACCATGGAAGATGCCAAAAACATTAAGAAGGGGCCTGCTCCCTT CTACCCTCTTGAAGATGGGACTGCTGGCGAGCAACTTCACAAAGCTATGA AGCGGTATGCTCTTGTGCCAGGGACAATTGCGTTCACGGATGCTCACATT GAAGTAGACATCACATACGCTGAGTATTTTGAGATGTCGGTGCGGCTGGC AGAAGCTATGAAGCGCTATGGGCTGAATACAAACCATAGAATTGTAGTGT GCAGTGAGAACTCGTTGCAGTTCTTTATGCCCGTGCTGGGGGCTCTCTTC ATCGGGGTGGCTGTGGCTCCTGCTAACGACATCTACAACGAGCGAGAGCT GTTGAACTCGATGGGGATCTCTCAGCCTACAGTGGTGTTTGTGAGTAAGA AAGGGCTTCAAAAGATTCTCAATGTGCAAAAGAAGCTGCCTATTATACAA AAGATTATTATTATGGACTCTAAGACAGACTACCAGGGGTTTCAGTCCAT GTACACATTTGTAACCTCTCATCTGCCTCCTGGCTTCAACGAGTACGACT TCGTGCCCGAGTCTTTCGACAGGGACAAAACGATTGCTCTGATCATGAAC AGCTCCGGGTCTACCGGGCTGCCTAAGGGTGTAGCTCTGCCCCATCGAAC AGCTTGTGTGAGATTCTCTCATGCCAGGGACCCGATCTTTGGAAACCAGA TCATCCCTGACACTGCTATTCTGTCGGTGGTGCCCTTTCATCATGGGTTT GGGATGTTCACAACACTGGGATACCTCATTTGCGGGTTTAGAGTGGTGCT CATGTATAGGTTTGAAGAAGAACTATTCCTACGCTCTTTGCAAGATTATA AGATTCAGTCTGCTCTGCTGGTGCCAACACTATTCTCTTTTTTTGCTAAG TCTACGCTCATAGACAAGTATGACTTGTCCAACTTGCACGAGATTGCTTC TGGCGGAGCACCTCTGTCTAAGGAGGTAGGTGAGGCTGTGGCTAAGCGCT TTCATCTGCCTGGTATCAGACAGGGGTACGGGCTAACAGAAACAACTTCT GCTATTCTGATTACACCAGAGGGCGATGACAAACCCGGGGCTGTAGGGAA AGTGGTGCCCTTTTTTGAAGCCAAAGTAGTTGATCTTGATACCGGTAAGA CACTAGGGGTGAACCAGCGTGGTGAACTGTGTGTGCGGGGCCCTATGATT ATGTCGGGGTACGTTAACAACCCCGAAGCTACAAATGCTCTCATAGACAA GGACGGGTGGCTTCATAGCGGCGACATTGCCTACTGGGACGAGGATGAGC ATTTCTTCATCGTGGACAGACTGAAGTCGTTGATCAAATACAAGGGGTAT CAAGTAGCTCCTGCCGAGCTTGAGTCCATTCTGCTTCAACACCCCAATAT CTTCGATGCTGGGGTGGCTGGGCTGCCTGATGATGATGCTGGAGAGCTGC CTGCTGCTGTAGTAGTGCTTGAGCATGGTAAGACAATGACAGAGAAGGAG ATCGTGGATTATGTGGCTTCACAAGTGACAACAGCTAAGAAACTCCGAGG TGGCGTTGTGTTTGTGGATGAGGTGCCTAAAGGGCTCACTGGCAAGCTGG ATGCCAGAAAAATTCGAGAGATTCTCATTAAGGCTAAGAAGGGTGGAAAG ATTGCTGTGTAATAGTTCTAGA

hluc+ver2B8 has the following sequence

(SEQ ID NO: 31) AAAGCCACCATGGAaGATGCcAAaAAcATTAAGAAGGGGCCTGCTCCcTT cTAcCCTCTtGAaGATGGGACtGCtGGcGAGCAaCTtCAcAAaGCTATGA AGcGgTATGCTCTtGTGCCaGGgACAATTGCgTTcACgGATGCTCAcATT GAaGTaGAcATcACATAcGCTGAGTATTTTGAGATGTCgGTGcGgCTGGC aGAaGCTATGAAGcGcTATGGGCTGAATACAAAcCATAGAATTGTaGTGT GcagTGAGAAcTCgtTGCAGTTcTTTATGCCcGTGCTGGGGGCTCTcTTc ATcGGGGTGGCTGTGGCTCCTGCTAAcGAcATcTAcAAcGAGcGAGAGCT gtTGAAcTCgATGGGGATcTCTCAGCCTACAGTGGTGTTTGTGagTAAGA AaGGGCTtCAaAAGATTCTcAATGTGCAaAAGAAGCTaCCgATcATaCAa AAGATcATcATcATGGAtagcAAGACcGAcTAcCAGGGGTTTCAGTCcAT GTAcACATTTGTaACcTCTCATCTGCCTCCTGGcTTcAAcGAGTAcGAcT TcGTGCCcGAGTCTTTcGAcAGgGAcAAaACgATTGCTCTGATcATGAAc agcTCcGGGTCTACcGGGCTGCCTAAGGGtGTaGCTCTGCCcCATcGAAC AGCTTGTGTGAGATTcTCTCATGCcAGgGAcCCgATcTTtGGaAAcCAGA TcATcCCTGAcACtGCTATTCTGTCgGTgGTGCCcTTTCATCATGGGTTT GGGATGTTcACAACACTGGGaTAccTcATtTGcGGGTTTAGAGTGGTGCT cATGTATAGgTTTGAaGAaGAaCTaTTccTacGcTCTtTGCAaGATTATA AGATTCAGTCTGCTCTGCTGGTGCCaACACTaTTcTCTTTTTTTGCTAAG TCTACgCTcATaGAcAAGTATGActTGTCcAActTGCAcGAGATTGCTTC TGGcGGaGCaCCTCTGTCTAAGGAGGTaGGtGAGGCTGTGGCTAAGcGcT TTCATCTGCCTGGtATcAGACAGGGGTAcGGGCTaACAGAaACAACtTCT GCTATTCTGATTACACCaGAGGGcGATGAcAAaCCtGGGGCTGTaGGGAA aGTGGTGCCcTTTTTTGAaGCcAAaGTaGTtGATCTtGATACcGGtAAGA CACTaGGGGTGAAcCAGcGtGGtGAaCTGTGTGTGcGgGGcCCTATGATT ATGTCgGGGTAcGTtAAcAAcCCcGAaGCTACAAATGCTCTcATaGAcAA GGAcGGgTGGcTtCATagcGGcGAcATTGCcTAcTGGGAcGAGGATGAGC ATTTcTTcATcGTGGAcAGACTGAAGTCgtTGATcAAaTAcAAGGGGTAT CAaGTaGCTCCTGCcGAGCTtGAgTCcATTCTGCTtCAaCAcCCcAAtAT cTTcGATGCTGGGGTGGCTGGGCTGCCTGATGATGATGCTGGaGAGcTGC CTGCTGCTGTaGTaGTGCTtGAGCAtGGtAAGACAATGACAGAGAAGGAG ATcGTGGATTATGTGGCTTCaCAaGTGACAACAGCTAAGAAaCTccGAGG tGGcGTtGTGTTTGTGGATGAGGTGCCTAAaGGGCTcACtGGcAAGCTGG ATGCcAGAAAaATTcGAGAGATTCTcATTAAGGCTAAGAAGGGtGGaAAG ATTGCTGTGTAATAgTTCTAGA.

hluc+ver2BF8 was modified to yield hluc+ver2BF9.

hluc+ver2B9 has the following sequence

(SEQ ID NO: 32)

cTAcCCTCTtGAaGATGGGACtGCtGGcGAGCAaCTtCAcAAaGCTATGA

AGcGgTATGCTCTtGTGCCaGGgACAATTGCgTTcACgGATGCTCAcATT

GAaGTaGAcATcACATAcGCTGAGTATTTTGAGATGTCgGTGcGgCTGGC

GcagTGAGAAcTCgtTGCAGTTcTTTATGCCcGTGCTGGGGGCTCTcTTc

gtTGAAcagtATGGGGATcTCTCAGCCTACAGTGGTGTTTGTGagTAAGA

AaGGGCTtCAaAAGATTCTcAATGTGCAaAAGAAGCTaCCgATcATaCAa

AAGATcATcATcATGGAtagcAAGACcGAcTAcCAGGGGTTTCAGTCcAT

GTAcACATTTGTaACcTCTCATCTGCCTCCTGGcTTcAAtGAGTAtGAcT

TcGTGCCcGAGTCTTTcGAcAGgGAcAAaACgATTGCTCTGATcATGAAc

agcagtGGGTCTACcGGGCTGCCTAAGGGtGTaGCTCTGCCcCATcGAAC

AGCTTGTGTGAGATTcTCTCATGCcAGgGAcCCgATcTTtGGaAAcCAGA

cATGTATAGgTTTGAaGAaGAaCTaTTccTacGcTCTtTGCAaGATTATA

TCTACgCTcATaGAcAAGTATGActTGTCcAActTGCAcGAGATTGCTTC

aGTGGTGCCcTTTTTTGAaGCcAAaGTaGTtGATCTtGATACcGGtAAGA

CACTaGGGGTGAAcCAGaGaGGtGAatTGTGTGTGaGgGGcCCTATGATT

ATGTCgGGGTAcGTtAAcAAcCCcGAaGCTACAAATGCTCTcATaGAcAA

GGAcGGgTGGcTtCATagtGGaGAtATTGCcTAcTGGGAtGAaGATGAGC

ATTTcTTcATcGTGGAcAGACTGAAGTCgtTGATcAAaTAcAAGGGGTAT

CAaGTaGCTCCTGCcGAGCTtGAgTCcATTCTGCTtCAaCAcCCcAAtAT

ATTGCTGTGTAATAgTTCTAGA.

The BglI sequence in hluc+ver2BF9 was removed resulting in hluc+ver2BF10. hluc+ver2BF10 demonstrated poor expression.

hluc+ver2B10 has the following sequence

Synthetic Selectable Polypeptide Genes

Design Process

Define Sequences

Protein sequence that should be maintained:

Neo: from neo gene of pCI-neo (Promega) (SEQ ID NO:1) Hyg: from hyg gene of pcDNA3.1/Hygro (Invitrogen) (SEQ ID NO:6)

DNA flanking regions for starting sequence:

5′ end: Kozak sequence from neo gene of pCI-neo ( GCCACCATGA ; SEQ ID NO:34)), PflMI site (CCANNNNNTGG; SEQ ID NO:35), add Ns at end (to avoid search algorithm errors & keep ORF1): neo/hyg: NNNNNCCAnnnnnTG GCCACC-ATG-G (SEQ ID NO:36) Change: replace PflMI with SbfI (CCTGCAGG) 3′ end: two stop codons (at least one TAA), PflMI site (not compatible with that at 5′ end to allow directional cloning), add Ns at end (to avoid search algorithm errors): neo/hyg: TAATAACCAnnnnnTGGNNN (SEQ ID NO:37) Change: replace PflMI with AflII (CTTAAG)

Define Codon Usage

Codon Usage was Obtained from the Codon Usage Database (http://www.kazusa.or.ip/codon/):

Based on: GenBank Release 131.0 [15 Aug. 2002] (Nakamura et al., 2000).

Codon Usage Tables were Downloaded for:

HS: Homo sapiens [gbpri] 50,031 CDS's (21,930,294 codons)

MM: Mus musculus [gbrod] 23,113 CDS's (10,345,401 codons)

EC: Escherichia coli [gbbct] 11,985 CDS's (3,688,954 codons)

EC K12 : Escherichia coli K12 [gbbct] 4,291 CDS's (1,363,716 codons)

HS and MM were compared and found to be closely similar, use HS table

EC and EC K12 were compared and found to be closely similar, use EC K12 table

Codon Selection Strategy:

Generate Starting Gene Sequences

Use Custom Codon Usage Table in Vector NTI 8.0 (Informax) (“Strategy A”) Back-Translate neo and hyg Protein Sequences Neo (Based on Neomycin Gene from Promega's pCI-neo)

(SEQ ID NO: 2) MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRPVLFVK TDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQ DLLSSHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEA GLVDQDDLDEEHQGLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVEN GRFSGFIDCGRLGVADRYQDIALATRDIAEELGGEWADRFLVLYGIAAPD SQRIAFYRLLDEFF and encoded by (SEQ ID NO: 1) Atgattgaacaagatggattgcacgcaggttctccggccgcttgggtgga gaggctattcggctatgactgggcacaacagacaatcggctgctctgatg ccgccgtgttccggctgtcagcgcaggggcgcccggttctttttgtcaag accgacctgtccggtgccctgaatgaactgcaggacgaggcagcgcggct atcgtggctggccacgacgggcgttccttgcgcagctgtgctcgacgttg tcactgaagcgggaagggactggctgctattgggcgaagtgccggggcag gatctcctgtcatctcaccttgctcctgccgagaaagtatccatcatggc tgatgcaatgcggcggctgcatacgcttgatccggctacctgcccattcg accaccaagcgaaacatcgcatcgagcgagcacgtactcggatggaagcc ggtcttgtcgatcaggatgatctggacgaagagcatcaggggctcgcgcc agccgaactgttcgccaggctcaaggcgcgcatgcccgacggcgaggatc tcgtcgtgacccatggcgatgcctgcttgccgaatatcatggtggaaaat ggccgcttttctggattcatcgactgtggccggctgggtgtggcggaccg ctatcaggacatagcgttggctacccgtgatattgctgaagagcttggcg gcgaatgggctgaccgcttcctcgtgctttacggtatcgccgctcccgat tcgcagcgcatcgccttctatcgccttcttgacgagttcttctga

Hyg (Based on Hygromycin Gene from Invitrogen's pcDNA3.1/Hygro)

Create Starting (Codon-Optimized) Gene Sequences:

hneo (Humanized Starting Gene Sequence without Flanking Regions in hneo-F)

(SEQ ID NO: 3)

AGTTCTTCTAATAACCAGTCTCTGG.

hhyg (Humanized Starting Gene Sequence without Flanking Regions)

(SEQ ID NO: 8) CCACTCAGTGGCCACCATGAAGAAGCCCGAGCTGACCGCCACCAGCGTGG AGAAGTTCCTGATCGAGAAGTTCGACAGCGTGAGCGACCTGATGCAGCTG AGCGAGGGCGAGGAGAGCCGCGCCTTCAGCTTCGACGTGGGCGGCCGCGG CTACGTGCTGCGCGTGAACAGCTGCGCCGACGGCTTCTACAAGGACCGCT ACGTGTACCGCCACTTCGCCAGCGCCGCCCTGCCCATCCCCGAGGTGCTG GACATCGGCGAGTTCAGCGAGAGCCTGACCTACTGCATCAGCCGCCGCGC CCAGGGCGTGACCCTGCAGGACCTGCCCGAGACCGAGCTGCCCGCCGTGC TGCAGCCCGTGGCCGAGGCCATGGACGCCATCGCCGCCGCCGACCTGAGC CAGACCAGCGGCTTCGGCCCCTTCGGCCCCCAGGGCATCGGCCAGTACAC CACCTGGCGCGACTTCATCTGCGCCATCGCCGACCCCCACGTGTACCACT GGCAGACCGTGATGGACGACACCGTGAGCGCCAGCGTGGCCCAGGCCCTG GACGAGCTGATGCTGTGGGCCGAGGACTGCCCCGAGGTGCGCCACCTGGT GCACGCCGACTTCGGCAGCAACAACGTGCTGACCGACAACGGCCGCATCA CCGCCGTGATCGACTGGAGCGAGGCCATGTTCGGCGACAGCCAGTACGAG GTGGCCAACATCTTCTTCTGGCGCCCCTGGCTGGCCTGCATGGAGCAGCA GACCCGCTACTTCGAGCGCCGCCACCCCGAGCTGGCCGGCAGCCCCCGCC TGCGCGCCTACATGCTGCGCATCGGCCTGGACCAGCTGTACCAGAGCCTG GTGGACGGCAACTTCGACGACGCCGCCTGGGCCCAGGGCCGCTGCGACGC CATCGTGCGCAGCGGCGCCGGCACCGTGGGCCGCACCCAGATCGCCCGCC GCAGCGCCGCCGTGTGGACCGACGGCTGCGTGGAGGTGCTGGCCGACAGC GGCAACCGCCGCCCCAGCACCCGCCCCCGCGCCAAGGAGTAATAACCAGC TCTTGG.

Programs and Databases Used for Identification and Removal of Sequence Motifs

All from Genomatix Software GmbH (Munich, Germany, http://www.genomatix.de):

GEMS Launcher Release 3.5.2 (June 2003) MatInspector professional Release 6.2.1 June 2003 Matrix Family Library Ver 3.1.2 June 2003 (incl. 318 vertebrate matrices in 128 families) ModelInspector professional Release 4.8 October 2002 Model Library Ver 3.1 March 2003 (226 modules) SequenceShaper tool User Defined Matrices

Sequence Motifs to Remove from Starting Gene Sequences

(In Order of Priority)

Restriction Enzyme Recognition Sequences:

See user-defined matrix subset neo and hyg. Same as those used for design of hluc+version 2.0 Generally includes those required for cloning (pGL4) or commonly used for cloning Change: also SbfI, AflI, AccIII

Transcription Factor Binding Sequences:

Promoter modules (2 TF binding sites with defined orientation) with default score or greater Vertebrate TF binding sequences with score of at least core=0.75/matrix=optimized

Eukaryotic Transcription Regulatory Sites:

Kozak sequence Splice donor/acceptor sequences in (+) strand PolyA addition sequences in (+) strand

Prokaryotic Transcription Regulatory Sequences:

E. coli promoters E. coli RBS (if less than 20 bp upstream of Met codon)

User-defined Matrix Subset “neo+hyg”

Format: Matrix name (core similarity threshold/matrix similarity threshold)

U$AatII (0.75/1.00) U$BamHI (0.75/1.00) U$BglI (0.75/1.00) U$BglII (0.75/1.00) U$BsaI (0.75/1.00) U$BsmAI (0.75/1.00) U$BsmBI (0.75/1.00) U$BstEII (0.75/1.00) U$BstXI (0.75/1.00) U$Csp45I (0.75/1.00) U$CspI (0.75/1.00) U$EC-P-10 (1.00/Optimized) U$EC-P-35 (1.00/Optimized) U$EC-Prom (1.00/Optimized) U$EC-RBS (0.75/1.00) U$EcoRI (0.75/1.00) U$HindIII (0.75/1.00) U$Kozak (0.75/Optimized) U$KpnI (0.75/1.00) U$MluI (0.75/1.00) U$NcoI (0.75/1.00) U$NdeI (0.75/1.00) U$NheI (0.75/1.00) U$NotI (0.75/1.00) U$NsiI (0.75/1.00) U$PflMI (0.75/1.00) U$PmeI (0.75/1.00) U$PolyAsig (0.75/1.00) U$PstI (0.75/1.00) U$SacI (0.75/1.00) U$SacII (0.75/1.00) U$SalI (0.75/1.00) U$SfiI (0.75/1.00) U$SgfI (0.75/1.00) U$SmaI (0.75/1.00) U$SnaBI (0.75/1.00) U$SpeI (0.75/1.00) U$Splice-A (0.75/Optimized) U$Splice-D (0.75/Optimized) U$XbaI (0.75/1.00) U$XcmI (0.75/1.00) U$XhoI (0.75/1.00) ALL vertebrates.lib (0.75/Optimized)

User-defined Matrix Subset “neo+hyg-EC”

Format: Matrix name (core similarity threshold/matrix similarity threshold)

U$AatII (0.75/1.00) U$BamHI (0.75/1.00) U$BglI (0.75/1.00) U$BglII (0.75/1.00) U$BsaI (0.75/1.00) U$BsmAI (0.75/1.00) U$BsmBI (0.75/1.00) U$BstEII (0.75/1.00) U$BstXI (0.75/1.00) U$Csp45I (0.75/1.00) U$CspI (0.75/1.00) U$EcoRI (0.75/1.00) U$HindIII (0.75/1.00) U$Kozak (0.75/Optimized) U$KpnI (0.75/1.00) U$MluI (0.75/1.00) U$NcoI (0.75/1.00) U$NdeI (0.75/1.00) U$NheI (0.75/1.00) U$NotI (0.75/1.00) U$NsiI (0.75/1.00) U$PflMI (0.75/1.00) U$PmeI (0.75/1.00) U$PolyAsig (0.75/1.00) U$PstI (0.75/1.00) U$SacI (0.75/1.00) U$SacII (0.75/1.00) U$SalI (0.75/1.00) U$SfiI (0.75/1.00) U$SgfI (0.75/1.00) U$SmaI (0.75/1.00) U$SnaBI (0.75/1.00) U$SpeI (0.75/1.00) U$Splice-A (0.75/Optimized) U$Splice-D (0.75/Optimized) U$XbaI (0.75/1.00) U$XcmI (0.75/1.00) U$XhoI (0.75/1.00) ALL vertebrates.lib (0.75/Optimized)

User-defined Matrix Subset “pGL4-072503”

Format: Matrix name (core similarity threshold/matrix similarity threshold)

U$AatII (0.75/1.00) U$AccIII (0.75/1.00) U$AflII (0.75/1.00) U$BamHI (0.75/1.00) U$BglI (0.75/1.00) U$BglII (0.75/1.00) U$BsaI (0.75/1.00) U$BsmAI (0.75/1.00) U$BsmBI (0.75/1.00) U$BstEII (0.75/1.00) U$BstXI (0.75/1.00) U$Csp45I (0.75/1.00) U$CspI (0.75/1.00) U$EC-P-10 (1.00/Optimized) U$EC-P-35 (1.00/Optimized) U$EC-Prom (1.00/Optimized) U$EC-RBS (0.75/1.00) U$EcoRI (0.75/1.00) U$HindIII (0.75/1.00) U$Kozak (0.75/Optimized) U$KpnI (0.75/1.00) U$MluI (0.75/1.00) U$NcoI (0.75/1.00) U$NdeI (0.75/1.00) U$NheI (0.75/1.00) U$NotI (0.75/1.00) U$NsiI (0.75/1.00) U$PflMI (0.75/1.00) U$PmeI (0.75/1.00) U$PolyAsig (0.75/1.00) U$PstI (0.75/1.00) U$SacI (0.75/1.00) U$SacII (0.75/1.00) U$SalI (0.75/1.00) U$SbfI (0.75/1.00) U$SfiI (0.75/1.00) U$SgfI (0.75/1.00) U$SmaI (0.75/1.00) U$SnaBI (0.75/1.00) U$SpeI (0.75/1.00) U$Splice-A (0.75/Optimized) U$Splice-D (0.75/Optimized) U$XbaI (0.75/1.00) U$XcmI (0.75/1.00) U$XhoI (0.75/1.00) ALL vertebrates.lib

Strategy for Removal of Sequence Motifs

The undesired sequence motifs specified above were removed from the starting gene sequence by selecting alternate codons that allowed retention of the specified protein and flanking sequences. Alternate codons were selected in a way to conform to the overall codon selection strategy as much as possible.

General Steps:

Identify undesired sequence matches with MatInspector using matrix family subset “neo+hyg” or “neo+hyg-EC” and with ModelInspector using default settings.

Identify possible replacement codons to remove undesired sequence matches with SequenceShaper (keep ORF).

Incorporate changes into a new version of the synthetic gene sequence and re-analyze with MatInspector and ModelInspector.

Specific Steps:

First try to remove undesired sequence matches using subset “neo+hyg-EC” and SequenceShaper default remaining thresholds (0.70/Opt-0.20).

For sequence matches that cannot be removed with this approach use lower SequenceShaper remaining thresholds (e.g. 0.70/Opt-0.05).

For sequence matches that still cannot be removed, try different combinations of manually chosen replacement codons (especially if more than 3 base changes might be needed). If that introduces new sequence matches, try to remove those using the steps above (a different starting sequence sometimes allows a different removal solution).

Use subset “neo+hyg” to check whether problematic E. coli sequence matches were introduced, and if so try to remove them using an analogous approach to that described above for non E. coli sequences.

Use an analogous strategy for the flanking (non-ORF) sequences. Final check with subset “pGL4-072503” after change in flanking cloning sites

After codon optimizing neo and hyg, hneo and hhyg were obtained. Regulatory sequences were removed from hneo and hhyg yielding hneo-1F and hhyg-1F (the corresponding sequences without flanking regions are SEQ ID Nos. 38 and 30, respectively). Regulatory sequences were removed from hneo-1F and hhyg-1F yielding hneo-2F and hhyg-2F (the corresponding sequences without flanking regions are SEQ ID Nos. 39 and 42, respectively). Regulatory sequences were removed from hneo-2F and hhyg-2F yielding hneo-3F and hhyg-3F. Hneo-3F and hhyg-3F were further modified by altering 5′ and 3′ cloning sites yielding hneo-3FB and hhyg-3FB:

hneo-3 (after 3rd round of sequence removal, subset neo+hyg) has the following sequence:

(SEQ ID NO: 4)

ATCGGaTGtAGCGAtGCgGCCGTGTTCCGtCTaAGCGCtCAaGGCCGgCC

CCgGACGGtGAGGACCTGGTtGTGACaCAtGGtGAtGCCTGCCTcCCtAA

AGTTCTTtTAATGACCAGgCTCTGG;

hneo-3FB (change PflMI sites to SbfI at 5′ end and AflII at 3′ end) has the following sequence:

(SEQ ID NO: 5)

cctgcaggCCACCATGATCGAACAAGACGGCCTCCATGCTGGCAGTCCCG

TCTTTTAATGAgcttaag;

hhyg-3 (after 3rd round of sequence removal, subset neo+hyg) has the following sequence:

(SEQ ID NO: 9)

tcgGAGGGCGAaGAgAGCCGaGCCTTCAGCTTCGAtGTcGGCGGaCGCGG

CCAaGGCGTtACtCTcCAaGACCTcCCCGAaACaGAGCTGCCtGCtGTGt

TaCAGCCtGTcGCCGAaGCtATGGAtGCtATtGCCGCCGCCGACCTcAGt

aACCTGGCGgGAtTTCATtTGCGCCATtGCtGAtCCCCAtGTcTACCACT

GGCAACCGCCGgCCCAGtACaCGaCCgCGCGCtAAGGAGTAgTAACCAGg

ctcTGG;

and

hhyg-3FB (change PflMI sites to SbfI at 5′ end and AflII at 3′ end) has the following sequence:

(SEQ ID NO: 10) cctgcaggCCACCATGAAGAAGCCCGAGCTGACCGCTACCAGCGTTGAAA AATTTCTCATCGAGAAGTTCGACAGTGTGAGCGACCTGATGCAGTTGTCG GAGGGCGAAGAGAGCCGAGCCTTCAGCTTCGATGTCGGCGGACGCGGCTA TGTACTGCGGGTGAATAGCTGCGCTGATGGCTTCTACAAAGACCGCTACG TGTACCGCCACTTCGCCAGCGCTGCACTACCCATCCCCGAAGTGTTGGAC ATCGGCGAGTTCAGCGAGAGCCTGACATACTGCATCAGTAGACGCGCCCA AGGCGTTACTCTCCAAGACCTCCCCGAAACAGAGCTGCCTGCTGTGTTAC AGCCTGTCGCCGAAGCTATGGATGCTATTGCCGCCGCCGACCTCAGTCAA ACCAGCGGCTTCGGCCCATTCGGGCCCCAAGGCATCGGCCAGTACACAAC CTGGCGGGATTTCATTTGCGCCATTGCTGATCCCCATGTCTACCACTGGC AGACCGTGATGGACGACACCGTGTCCGCCAGCGTAGCTCAAGCCCTGGAC GAACTGATGCTGTGGGCCGAAGACTGTCCCGAGGTGCGCCACCTCGTCCA TGCCGACTTCGGCAGCAACAACGTCCTGACCGACAACGGGCGCATGACCG CCGTAATCGACTGGTCCGAAGCTATGTTCGGGGACAGTCAGTACGAGGTG GCCAACATCTTCTTCTGGCGGCCCTGGCTGGCTTGCATGGAGCAGCAGAC TCGCTACTTCGAGCGCCGGCATCCCGAGCTGGCCGGCAGCCCTCGTCTGC GAGCCTACATGCTGCGCATCGGCCTGGATCAGCTCTACCAGAGCCTCGTG GACGGCAACTTCGACGATGCTGCCTGGGCTCAAGGCCGCTGCGATGCCAT CGTCCGCAGCGGGGCCGGCACCGTCGGTCGCACACAAATCGCTCGCCGGA GCGCCGCCGTATGGACCGACGGCTGCGTCGAGGTGCTGGCCGACAGCGGC AACCGCCGGCCCAGTACACGACCGCGCGCTAAGGAGTAGTAActtaag.

Analysis of hneo-3FB and hhyg-3FB

hneo-3FB had no transcription factor binding sequence, including promoter module, matches (GEMS release 3.5.2 June 2003; vertebrate TF binding sequence families (core similarity: 0.75/matrix similarity: opt); and promoter modules (default parameters: optimized threshold or 80% of maximum score)), while hhyg-3FB had 4 transcription factor binding sequence matches remaining but no promoter modules (Table 10). The following transcription factor binding sequences were found in hhyg-3FB:

1) V$MINI Family: Muscle Initiators (2 members) Best match: Muscle Initiator Sequence 1 Ref: Laura L. Lopez & James W. Fickett “Muscle-Specific Regulation of Transcription: A Catalog of Regulatory Elements” http://www.cbil.upenn.edu/MTIR/HomePage.html

Position in ORF: −7 to 11

2) V$PAX5

Family: PAX-5/PAX-9 B-cell-specific activating proteins (4 members)

Best match: B-cell-specific activating protein

Ref: MEDLINE 94010299

Position in ORF: 271 to 299

3) V$AREB

Family: Atp1a1 regulatory element binding (4 members)

Best match: AREB6

Ref: MEDLINE 96061934

Position in ORF: 310 to 322

4) V$VMYB

Family: AMV-viral myb oncogene (2 members)

Best match: v-Myb

Ref: MEDLINE 94147510

Position in ORF: 619 to 629

Other sequences remaining in hneo-3F included one E. coli RBS 8 bases upstream of Met (ORF position 334 to 337); hneo-3FB included a splice acceptor site (+) and PstI site as part of a 5′ cloning site for SbfI, and one E. coli RBS 8 bases upstream of Met (ORF position 334 to 337); hhyg-3F had no other sequence matches; and hhyg-3FB included a splice acceptor site (+) and PstI site as part of a 5′ cloning site for SbfI.

Subsequently, regulatory sequences were removed from hneo-3F and hhyg-3F yielding hneo-4 and hhyg-4. Then regulatory sequences were removed from hneo-4 yielding hneo-5.

Table 15 summarizes the identity of various genes.

An expression cassette (hNeo-cassette) with a synthetic neomycin gene flanked by a SV40 promoter and a synthetic poly(A) site is shown below.

(SEQ ID NO: 44) GGATCCGTTTGCGTATTGGGCGCTCTTCCGCTGATCTGCGCAGCACCATG GCCTGAAATAACCTCTGAAAGAGGAACTTGGTTAGCTACCTTCTGAGGCG GAAAGAACCAGCTGTGGAATGTGTGTCAGTTAGGGTGTGGAAAGTCCCCA GGCTCCCCAGCAGGCAGAAGTATGCAAAGCATGCATCTCAATTAGTCAGC AACCAGGTGTGGAAAGTCCCCAGGCTCCCCAGCAGGCAGAAGTATGCAAA GCATGCATCTCAATTAGTCAGCAACCATAGTCCCGCCCCTAACTCCGCCC ATCCCGCCCCTAACTCCGCCCAGTTCCGCCCATTCTCCGCCCCATGGCTG ACTAATTTTTTTTATTTATGCAGAGGCCGAGGCCGCCTCTGCCTCTGAGC TATTCCAGAAGTAGTGAGGAGGCTTTTTTGGAGGCCTAGGCTTTTGCAAA AAGCTCGATTCTTCTGACACTAGCGCCACCATGATCGAACAAGACGGCCT CCATGCTGGCAGTCCCGCAGCTTGGGTCGAACGCTTGTTCGGGTACGACT GGGCCCAGCAGACCATCGGATGTAGCGATGCGGCCGTGTTCCGTCTAAGC GCTCAAGGCCGGCCCGTGCTGTTCGTGAAGACCGACCTGAGCGGCGCCCT GAACGAGCTTCAAGACGAGGCTGCCCGCCTGAGCTGGCTGGCCACCACCG GCGTACCCTGCGCCGCTGTGTTGGATGTTGTGACCGAAGCCGGCCGGGAC TGGCTGCTGCTGGGCGAGGTCCCTGGCCAGGATCTGCTGAGCAGCCACCT TGCCCCCGCTGAGAAGGTTTCTATCATGGCCGATGCAATGCGGCGCCTGC ACACCCTGGACCCCGCTACCTGCCCCTTCGACCACCAGGCTAAGCATCGG ATCGAGCGTGCTCGGACCCGCATGGAGGCCGGCCTGGTGGACCAGGACGA CCTGGACGAGGAGCATCAGGGCCTGGCCCCCGCTGAACTGTTCGCCCGAC TGAAAGCCCGCATGCCGGACGGTGAGGACCTGGTTGTCACACACGGAGAT GCCTGCCTCCCTAACATCATGGTCGAGAATGGCCGCTTCTCCGGCTTCAT CGACTGCGGTCGCCTAGGAGTTGCCGACCGCTACCAGGACATCGCCCTGG CCACCCGCGACATCGCTGAGGAGCTTGGCGGCGAGTGGGCCGACCGCTTC TTAGTCTTGTACGGCATCGCAGCTCCCGACAGCCAGCGCATCGCCTTCTA CCGCTTGCTCGACGAGTTCTTTTAATGATCTAGAACCGGTCATGGCCGCA ATAAAATATCTTTATTTTCATTACATCTGTGTGTTGGTTTTTTGTGTGTT CGAACTAGATGCTGTCGAC.

An expression cassette (hPuro-cassette) with a synthetic puromycin gene flanked by a SV40 promoter and a synthetic poly(A) site is shown below.

(SEQ ID NO: 11) GGATCCGTTTGCGTATTGGGCGCTCTTCCGCTGATCTGCGCAGCACCATG GCCTGAAATAACCTCTGAAAGAGGAACTTGGTTAGCTACCTTCTGAGGCG GAAAGAACCAGCTGTGGAATGTGTGTCAGTTAGGGTGTGGAAAGTCCCCA GGCTCCCCAGCAGGCAGAAGTATGCAAAGCATGCATCTCAATTAGTCAGC AACCAGGTGTGGAAAGTCCCCAGGCTCCCCAGCAGGCAGAAGTATGCAAA GCATGCATCTCAATTAGTCAGCAACCATAGTCCCGCCCCTAACTCCGCCC ATCCCGCCCCTAACTCCGCCCAGTTCCGCCCATTCTCCGCCCCATGGCTG ACTAATTTTTTTTATTTATGCAGAGGCCGAGGCCGCCTCTGCCTCTGAGC TATTCCAGAAGTAGTGAGGAGGCTTTTTTGGAGGCCTAGGCTTTTGCAAA AAGCTCGATTCTTCTGACACTAGCGCCACCATGACCGAGTACAAGCCTAC CGTGCGCCTGGCCACTCGCGATGATGTGCCCCGCGCCGTCCGCACTCTGG CCGCCGCTTTCGCCGACTACCCCGCTACCCGGCACACCGTGGACCCCGAC CGGCACATCGAGCGTGTGACAGAGTTGCAGGAGCTGTTCCTGACCCGCGT CGGGCTGGACATCGGCAAGGTGTGGGTAGCCGACGACGGCGCGGCCGTGG CCGTGTGGACTACCCCCGAGAGCGTTGAGGCCGGCGCCGTGTTCGCCGAG ATCGGCCCCCGAATGGCCGAGCTGAGCGGCAGCCGCCTGGCCGCCCAGCA GCAAATGGAGGGCCTGCTTGCCCCCCATCGTCCCAAGGAGCCTGCCTGGT TTCTGGCCACTGTAGGAGTGAGCCCCGACCACCAGGGCAAGGGCTTGGGC AGCGCCGTCGTGTTGCCCGGCGTAGAGGCCGCCGAACGCGCCGGTGTGCC CGCCTTTCTCGAAACAAGCGCACCAAGAAACCTTCCATTCTACGAGCGCC TGGGCTTCACCGTGACCGCCGATGTCGAGGTGCCCGAGGGACCTAGGACC TGGTGTATGACACGAAAACCTGGCGCCTAATGATCTAGAACCGGTCATGG CCGCAATAAAATATCTTTATTTTCATTACATCTGTGTGTTGGTTTTTTGT GTGTTCGAACTAGATGCTGTCGAC; hpuro: (SEQ ID NO: 91) GCTAGCGCCACCATGACCGAGTACAAGCCCACCGTGCGCCTGGCCACCCG CGACGACGTGCCCCGCGCCGTGCGCACCCTGGCCGCCGCCTTCGCCGACT ACCCCGCCACCCGCCACACCGTGGACCCCGACCGCCACATCGAGCGCGTG ACCGAGCTGCAGGAGCTGTTCCTGACCCGCGTGGGCCTGGACATCGGCAA GGTGTGGGTGGCCGACGACGGCGCCGCCGTGGCCGTGTGGACCACCCCCG AGAGCGTGGAGGCCGGCGCCGTGTTCGCCGAGATCGGCCCCCGCATGGCC GAGCTGAGCGGCAGCCGCCTGGCCGCCCAGCAGCAGATGGAGGGCCTGCT GGCCCCCCACCGCCCCAAGGAGCCCGCCTGGTTCCTGGCCACCGTGGGCG TGAGCCCCGACCACCAGGGCAAGGGCCTGGGCAGCGCCGTGGTGCTGCCC GGCGTGGAGGCCGCCGAGCGCGCCGGCGTGCCCGCCTTCCTGGAGACCAG CGCCCCCCGCAACCTGCCCTTCTACGAGCGCCTGGGCTTCACCGTGACCG CCGACGTGGAGGTGCCCGAGGGCCCCCGCACCTGGTGCATGACCCGCAAG CCCGGCGCCTAATGATCTAGA; hpuro-1: (SEQ ID NO: 92) gctagcgccaccatgaccgagtacaagcctaccgtgcgcctggccactcg cgatgatgtgccccgcgccgtccgcactctggccgccgctttcgccgact accccgctacccggcacaccgtggaccccgaccggcacatcgagcgtgtg acagagttgcaggagctgttcctgacccgcgtcgggctggacatcggcaa ggtgtgggtagccgacgacggcgcggccgtggccgtgtggactacccccg agagcgttgaggccggcgccgtgttcgccgagatcggcccccgaatggcc gagctgagcggcagccgcctggccgcccagcagcaaatggagggcctgct tgccccccatcgtcccaaggagcccgcctggtttctggccactgtaggag tgagccccgaccaccagggcaagggcttgggcagcgccgtcgtgttgccc ggcgtagaggccgccgaacgcgccggtgtgcccgcctttctggagacaag cgctccgcgtaaccttccattctacgagcgcctgggcttcaccgtgaccg ccgatgtcgaggtgcccgagggaccccggacctggtgcatgactcgcaag cctggcgcctaatgatctaga; and hpuro-2 (SEQ ID NO: 93) GCTAGCGCCACCATGACCGAGTACAAGCCTACCGTGCGCCTGGCCACTCG CGATGATGTGCCCCGCGCCGTCCGCACTCTGGCCGCCGCTTTCGCCGACT ACCCCGCTACCCGGCACACCGTGGACCCCGACCGGCACATCGAGCGTGTG ACAGAGTTGCAGGAGCTGTTCCTGACCCGCGTCGGGCTGGACATCGGCAA GGTGTGGGTAGCCGACGACGGCGCGGCCGTGGCCGTGTGGACTACCCCCG AGAGCGTTGAGGCCGGCGCCGTGTTCGCCGAGATCGGCCCCCGAATGGCC GAGCTGAGCGGCAGCCGCCTGGCCGCCCAGCAGCAAATGGAGGGCCTGCT TGCCCCCCATCGTCCCAAGGAGCCTGCCTGGTTTCTGGCCACTGTAGGAG TGAGCCCCGACCACCAGGGCAAGGGCTTGGGCAGCGCCGTCGTGTTGCCC GGCGTAGAGGCCGCCGAACGCGCCGGTGTGCCCGCCTTTCTCGAAACAAG CGCACCAAGAAACCTTCCATTCTACGAGCGCCTGGGCTTCACCGTGACCG CCGATGTCGAGGTGCCCGAGGGACCTAGGACCTGGTGTATGACACGAAAA CCTGGCGCCTAATGATCTAGA.

The starting puro sequence (from psi STRIKE) has SEQ ID NO:15

(atgaccgagt acaagcccac ggtgcgcctc gccacccgcg acgacgtccc ccgggccgta  cgcaccctcg ccgccgcgtt cgccgactac cccgccacgc gccacaccgt cgacccggac  cgccacatcg agcgggtcac cgagctgcaa gaactcttcc tcacgcgcgt cgggctcgac  atcggcaagg tgtgggtcgc ggacgacggc gccgcggtgg cggtctggac cacgccggag  agcgtcgaag cgggggcggt gttcgccgag atcggcccgc gcatggccga gttgagcggt  tcccggctgg ccgcgcagca acagatggaa ggcctcctgg cgccgcaccg gcccaaggag  cccgcgtggt tcctggccac cgtcggcgtg tcgcccgacc accagggcaa gggtctgggc  agcgccgtcg tgctccccgg agtggaggcg gccgagcgcg ccggggtgcc cgccttcctg  gagacctccg cgccccgcaa cctccccttc tacgagcggc tcggcttcac cgtcaccgcc  gacgtcgagg tgcccgaagg accgcgcacc tggtgcatga cccgcaagcc cggtgcc).

Other synthetic hyg and neo genes include

hneo-1: (SEQ ID NO: 38) CCACTCAGTGGCCACCATGATCGAGCAGGACGGCCTcCAtGCtGGCAGtC CCGCaGCCTGGGTcGAGCGCtTGTTCGGgTACGACTGGGCCCAGCAGACC ATCGGaTGtAGCGAtGCCGCaGTGTTCCGCCTGAGCGCtCAaGGCCGgCC CGTGCTGTTCGTGAAGACCGACCTGAGCGGCGCCCTGAACGAGCTtCAaG ACGAGGCtGCCCGCCTGAGCTGGCTGGCCACCACCGGtGTaCCCTGCGCC GCtGTGtTGGAtGTtGTGACCGAaGCCGGCCGCGACTGGCTGCTGCTGGG CGAGGTGCCtGGCCAGGACCTGCTGAGCAGCCACCTGGCCCCCGCtGAGA AGGTGAGCATCATGGCCGACGCCATGCGgCGCCTGCACACCCTGGACCCC GCtACaTGCCCCTTCGACCACCAGGCtAAGCACCGCATCGAGCGgGCtCG gACCCGCATGGAGGCCGGCCTGGTGGACCAGGACGACCTGGACGAGGAGC ACCAGGGCCTGGCCCCCGCtGAaCTGTTCGCCCGCCTGAAaGCCCGCATG CCgGACGGtGAGGACCTGGTtGTGACaCACGGCGACGCCTGCCTcCCtAA CATCATGGTcGAGAACGGgCGCTTCtcCGGCTTCATCGACTGCGGCCGCC TGGGCGTtGCCGACCGCTACCAGGACATCGCCCTGGCCACCCGCGACATC GCCGAGGAGCTGGGCGGCGAGTGGGCCGACCGCTTCCTGGTctTGTACGG CATCGCaGCtCCCGACAGCCAGCGCATCGCCTTCTACCGCCTGCTGGACG AGTTCTTCTAgTAACCAGgCTCTGG; hneo-2 (SEQ ID NO: 39) CCACTCcGTGGCCACCATGATCGAaCAaGACGGCCTcCAtGCtGGCAGtC CCGCaGCtTGGGTcGAaCGCtTGTTCGGgTACGACTGGGCCCAGCAGACC ATCGGaTGtAGCGAtGCgGCCGTGTTCCGtCTaAGCGCtCAaGGCCGgCC CGTGCTGTTCGTGAAGACCGACCTGAGCGGCGCCCTGAACGAGCTtCAaG ACGAGGCtGCCCGCCTGAGCTGGCTGGCCACCACCGGtGTaCCCTGCGCC GCtGTGtTGGAtGTtGTGACCGAaGCCGGCCGgGACTGGCTGCTGCTGGG CGAGGTcCCtGGCCAGGAtCTGCTGAGCAGCCACCTtGCCCCCGCtGAGA AGGTttcCATCATGGCCGAtGCaATGCGgCGCCTGCACACCCTGGACCCC GCtACaTGCCCCTTCGACCACCAGGCtAAGCAtCGgATCGAGCGtGCtCG gACCCGCATGGAGGCCGGCCTGGTGGACCAGGACGACCTGGACGAGGAGC AtCAGGGCCTGGCCCCCGCtGAaCTGTTCGCCCGCCTGAAaGCCCGCATG CCgGACGGtGAGGACCTGGTtGTGACaCAtGGaGAtGCCTGCCTcCCtAA CATCATGGTcGAGAAtGGcCGCTTCtcCGGCTTCATCGACTGCGGtCGCC TaGGaGTtGCCGACCGCTACCAGGACATCGCCCTGGCCACCCGCGACATC GCtGAGGAGCTtGGCGGCGAGTGGGCCGACCGCTTCtTaGTctTGTACGG CATCGCaGCtCCCGACAGCCAGCGCATCGCCTTCTACCGCCTGCTcGACG AGTTCTTtTAATGACCAGgCTCTGG; hhyg-1 (SEQ ID NO: 30) CCACTCAGTGGCCACCATGAAGAAGCCCGAGCTGACCGCTACCAGCGTTG AGAAGTTCCTGATCGAGAAGTTCGACAGCGTGAGCGACCTGATGCAGTTA AGCGAGGGCGAGGAAAGCCGCGCCTTCAGCTTCGATGTCGGCGGACGCGG CTATGTACTGCGGGTGAATAGCTGCGCTGATGGCTTCTACAAAGACCGCT ACGTGTACCGCCACTTCGCCAGCGCTGCACTGCCCATCCCCGAGGTGCTG GACATCGGCGAGTTCAGCGAGAGCCTGACATACTGCATCAGCCGCCGCGC TCAAGGCGTGACTCTCCAAGACCTGCCCGAGACAGAGCTGCCCGCTGTGC TACAGCCTGTCGCCGAGGCTATGGACGCTATTGCCGCCGCCGACCTGAGC CAGACCAGCGGCTTCGGCCCATTCGGGCCCCAAGGCATCGGCCAGTACAC CACCTGGCGCGACTTCATCTGCGCCATTGCTGATCCCCATGTCTACCACT GGCAGACCGTGATGGACGACACCGTGAGCGCCAGCGTAGCTCAAGCCCTG GACGAGCTGATGCTGTGGGCCGAGGACTGCCCCGAGGTGCGCCATCTCGT CCATGCCGACTTCGGCAGCAACAACGTCCTGACCGACAACGGCCGCATCA CCGCCGTAATCGACTGGAGCGAGGCCATGTTCGGGGACAGTCAGTACGAG GTGGCCAACATCTTCTTCTGGCGGCCCTGGCTGGCCTGCATGGAGCAGCA AACCCGCTACTTCGAGCGCCGCCATCCCGAGCTGGCCGGCAGCCCCCGTC TGCGAGCCTACATGCTGCGCATCGGCCTGGATCAGCTCTACCAGAGCCTC GTGGACGGCAACTTCGACGATGCTGCCTGGGCTCAAGGCCGCTGCGATGC CATCGTCCGCAGCGGGGCCGGCACCGTCGGTCGCACACAAATCGCTCGCC GGAGCGCCGCCGTATGGACCGACGGCTGCGTCGAGGTGCTGGCCGACAGC GGCAACCGCCGGCCCAGTACACGACCGCGCGCTAAGGAGTAGTAACCAGC TCTTGG; hhyg-2: (SEQ ID NO: 42) CCACTCCGTGGCCACCATGAAGAAGCCCGAGCTGACCGCTACCAGCGTTG AAAAATTTCTCATCGAGAAGTTCGACAGTGTGAGCGACCTGATGCAGTTG TCGGAGGGCGAAGAGAGCCGAGCCTTCAGCTTCGATGTCGGCGGACGCGG CTATGTACTGCGGGTGAATAGCTGCGCTGATGGCTTCTACAAAGACCGCT ACGTGTACCGCCACTTCGCCAGCGCTGCACTACCCATCCCCGAAGTGTTG GACATCGGCGAGTTCAGCGAGAGCCTGACATACTGCATCAGTAGACGCGC CCAAGGCGTTACTCTCCAAGACCTCCCCGAAACAGAGCTGCCTGCTGTGT TACAGCCTGTCGCCGAAGCTATGGATGCTATTGCCGCCGCCGACCTCAGT CAAACCAGCGGCTTCGGCCCATTCGGGCCCCAAGGCATCGGCCAGTACAC AACCTGGCGGGATTTCATTTGCGCCATTGCTGATCCCCATGTCTACCACT GGCAGACCGTGATGGACGACACCGTGTCCGCCAGCGTAGCTCAAGCCCTG GACGAACTGATGCTGTGGGCCGAAGACTGTCCCGAGGTGCGCCACCTCGT CCATGCCGACTTCGGCAGCAACAACGTCCTGACCGACAACGGCCGCATCA CCGCCGTAATCGACTGGAGCGAGGCTATGTTCGGGGACAGTCAGTACGAG GTGGCCAACATCTTCTTCTGGCGGCCCTGGCTGGCTTGCATGGAGCAGCA GACTCGCTACTTCGAGCGCCGGCATCCCGAGCTGGCCGGCAGCCCTCGTC TGCGAGCCTACATGCTGCGCATCGGCCTGGATCAGCTCTACCAGAGCCTC GTGGACGGCAACTTCGACGATGCTGCCTGGGCTCAAGGCCGCTGCGATGC CATCGTCCGCAGCGGGGCCGGCACCGTCGGTCGCACACAAATCGCTCGCC GGAGCGCCGCCGTATGGACCGACGGCTGCGTCGAGGTGCTGGCCGACAGC GGCAACCGCCGGCCCAGTACACGACCGCGCGCTAAGGAGTAGTAACCAGC TCTTGG;

hHygro (SacI site in ORF near 5′ end, insert in-frame linker coding for 12 amino acids at 3′ end, and SnaBI site added at 3′ end in ORF)

(SEQ ID NO: 70)

aagcttgctagcgccaccatgaagaagcccgagctcaccgctaccagcgt

tgaaaaatttctcatcgagaagttcgacagtgtgagcgacctgatgcagt

tgtcggagggcgaagagagccgagccttcagcttcgatgtcggcggacgc

ggctatgtactgcgggtgaatagctgcgctgatggcttctacaaagaccg

ctacgtgtaccgccacucgccagcgctgcactacccatccccgaagtgtt

ggacatcggcgagttcagcgagagcctgacatactgcatcagtagacgcg

cccaaggcgttactctccaagacctccccgaaacagagctgcctgctgtg

ttacagcctgtcgccgaagctatggatgctattgccgccgccgacctcag

tcaaaccagcggcttcggcccattcgggccccaaggcatcggccagtaca

caacctggcgggatttcatttgcgccattgctgatccccatgtctaccac

tggcagaccgtgatggacgacaccgtgtccgccagcgtagctcaagccct

ggacgaactgatgctgtgggccgaagactgtcccgaggtgcgccacctcg

tccatgccgacttcggcagcaacaacgtcctgaccgacaacggccgcatc

accgccgtaatcgactggtccgaagctatgttcggggacagtcagtacga

ggtggccaacatcttcttctggcggccctggctggcttgcatggagcagc

agactcgctacttcgagcgccggcatcccgagctggccggcagccctcgt

ctgcgagcctacatgctgcgcatcggcctggatcagctctaccagagcct

cgtggacggcaacttcgacgatgctgcctgggctcaaggccgctgcgatg

ccatcgtccgcagcggggccggcaccgtcggtcgcacacaaatcgctcgc

cggagcgccgccgtatggaccgacggctgcgtcgaggtgctggccgacag

cggcaaccgccggcccagtacacgaccgcgcgctaaggagggtggcggag

ggagcggtggcggaggttcctacgtatagtctagactcgag;

hhyg-4

(SEQ ID NO: 71)

atgaagaagcccgagctcaccgctaccagcgttgaaaaamctcatcgaga

agttcgacagtgtgagcgacctgatgcagttgtcggagggcgaagagagc

cgagccttcagcttcgatgtcggcggacgcggctatgtactgcgggtgaa

tagctgcgctgatggcttctacaaagaccgctacgtgtaccgccacttcg

ccagcgctgcactacccatccccgaagtgttggacatcggcgagttcagc

gagagcctgacatactgcatcagtagacgcgcccaaggcgttactctcca

agacctccccgaaacagagctgcctgctgtgttacagcctgtcgccgaag

ctatggatgctattgccgccgccgacctcagtcaaaccagcggcttcggc

ccattcgggccccaaggcatcggccagtacacaacctggcgggatttcat

ttgcgccattgctgatccccatgtctaccactggcagaccgtgatggacg

acaccgtgtccgccagcgtagctcaagccctggacgaactgatgctgtgg

gccgaagactgtcccgaggtgcgccacctcgtccatgccgacttcggcag

caacaacgtcctgaccgacaacggccgcatcaccgccgtaatcgactggt

ccgaagctatgttcggggacagtcagtacgaggtggccaacatcttcttc

tggcggccctggctggcttgcatggagcagcagactcgctacttcgagcg

ccggcatcccgagctggccggcagccctcgtctgcgagcctacatgctgc

gcatcggcctggatcagctctaccagagcctcgtggacggcaacttcgac

gatgctgcctgggctcaaggccgctgcgatgccatcgtccgcagcggggc

cggcaccgtcggtcgcacacaaatcgctcgccggagcgcagccgtatgga

ccgacggctgcgtcgaggtgctggccgacagcggcaaccgccggcccagt

acacgaccgcgcgctaaggaaggcggtggaggtagtggtggcggaggtag

ctacgta;

hneo-4:

(SEQ ID NO: 72)

CTTTTAATCTAGA;

and

hneo-5:

(SEQ ID NO: 73)

CTTTTAATGATCTAGA.

The synthetic nucleotide sequence of the invention may be employed in fusion constructs. For instance, a synthetic sequence for a selectable polypeptide may be fused to a wild-type sequence or to another synthetic sequence which encodes a different polypeptide. For instance, the neo sequence in the following examples of a synthetic Renilla luciferase-neo sequence may be replaced with a synthetic neo sequence of the invention:

(hrl-neo fusion; SEQ ID NO: 12)

atggcttccaaggtgtacgaccccgagcaacgcaaacgcatgatcactgg

gcctcagtggtgggctcgctgcaagcaaatgaacgtgctggactccttca

tcaactactatgattccgagaagcacgccgagaacgccgtgatttttgca

tggtaacgctgcctccagctacctgtggaggcacgtcgtgcctcacatcg

agcccgtggctagatgcatcatccctgatctgatcggaatgggtaagtcc

ggcaagagcgggaatggctcatatcgcctcctggatcactacaagtacct

caccgcttggttcgagctgctgaaccttccaaagaaaatcatctttgtgg

gccacgactggggggcttgtctggcctttcactactcctacgagcaccaa

gacaagatcaaggccatcgtccatgctgagagtgtcgtggacgtgatcga

gtcctgggacgagtggcctgacatcgaggaggatatcgccctgatcaaga

gcgaagagggcgagaaaatggtgcttgagaataacttcttcgtcgagacc

atgctcccaagcaagatcatgcggaaactggagcctgaggagttcgctgc

ctacctggagccattcaaggagaagggcgaggttagacggcctaccctct

cctggcctcgcgagatccctctcgttaagggaggcaagcccgacgtcgtc

cagattccgcaactacaacgcctaccttcgggccagcgacgatctgccta

agatgttcatcgagtccgaccctgggttcttttccaacgctattgtcgag

ggagctaagaagttccctaacaccgagttcgtgaaggtgaagggcctcca

cttcagccaggaggacgctccagatgaaatgggtaagtacatcaagagct

tcgtggagcgcgtgctgaagaacgagcagaccggtggtgggagcggaggt

ggcggatcaggtggcggaggctccggagggattgaacaagatggattgca

cgcaggttctccggccgcttgggtggagaggctattcggctatgactggg

cacaacagacaatcggctgctctgatgccgccgtgttccggctgtcagcg

caggggcgcccggttctttttgtcaagaccgacctgtccggtgccctgaa

tgaactgcaggacgaggcagcgcggctatcgtggctggccacgacgggcg

ttccttgcgcagctgtgctcgacgttgtcactgaagcgggaagggactgg

ctgctattgggcgaagtgccggggcaggatctcctgtcatctcaccttgc

tcctgccgagaaagtatccatcatggctgatgcaatgcggcggctgcata

cgcttgatccggctacctgcccattcgaccaccaagcgaaacatcgcatc

gagcgagcacgtactcggatggaagccggtcttgtcgatcaggatgatct

ggacgaagagcatcaggggctcgcgccagccgaactgttcgccaggctca

aggcgcgcatgcccgacggcgaggatctcgtcgtgacccatggcgatgcc

tgcttgccgaatatcatggtggaaaatggccgcttttctggattcatcga

ctgtggccggctgggtgtggcggaccgctatcaggacatagcgttggcta

cccgtgatattgctgaagagcttggcggcgaatgggctgaccgcttcctc

gtgctttacggtatcgccgctcccgattcgcagcgcatcgccttctatcg

ccttcttgacgagttcttctaa

and

(neo-hrl-fusion; SEQ ID NO: 13)

atgattgaacaagatggattgcacgcaggttctccggccgcttgggtgga

gaggctattcggctatgactgggcacaacagacaatcggctgctctgatg

ccgccgtgttccggctgtcagcgcaggggcgcccggttctttttgtcaag

accgacctgtccggtgccctgaatgaactgcaggacgaggcagcgcggct

atcgtggctggccacgacgggcgttccttgcgcagctgtgctcgacgttg

tcactgaagcgggaagggactggctgctattgggcgaagtgccggggcag

gatctcctgtcatctcaccttgctcctgccgagaaagtatccatcatggc

tgatgcaatgcggcggctgcatacgcttgatccggctacctgcccattcg

accaccaagcgaaacatcgcatcgagcgagcacgtactcggatggaagcc

ggtcttgtcgatcaggatgatctggacgaagagcatcaggggctcgcgcc

agccgaactgttcgccaggctcaaggcgcgcatgcccgacggcgaggatc

tcgtcgtgacccatggcgatgcctgcttgccgaatatcatggtggaaaat

ggccgcttttctggattcatcgactgtggccggctgggtgtggcggaccg

ctatcaggacatagcgttggctacccgtgatattgctgaagagcttggcg

gcgaatgggctgaccgcttcctcgtgctttacggtatcgccgctcccgat

tcgcagcgcatcgccttctatcgccttcttgacgagttcttcaccggtgg

tgggagcggaggtggcggatcaggtggcggaggctccggaggggcttcca

aggtgtacgaccccgagcaacgcaaacgcatgatcactgggcctcagtgg

tgggctcgctgcaagcaaatgaacgtgctggactccttcatcaactacta

tgattccgagaagcacgccgagaacgccgtgatttttctgcatggtaacg

ctgcctccagctacctgtggaggcacgtcgtgcctcacatcgagcccgtg

gctagatgcatcatccctgatctgatcggaatgggtaagtccggcaagag

cgggaatggctcatatcgcctcctggatcactacaagtacctcaccgctt

ggttcgagctgctgaaccttccaaagaaaatcatctttgtgggccacgac

tggggggcttgtctggcctttcactactcctacgagcaccaagacaagat

caaggccatcgtccatgctgagagtgtcgtggacgtgatcgagtcctggg

acgagtggcctgacatcgaggaggatatcgccctgatcaagagcgaagag

ggcgagaaaatggtgcttgagaataacttcttcgtcgagaccatgctccc

aagcaagatcatgcggaaactggagcctgaggagttcgctgcctacctgg

agccattcaaggagaagggcgaggttagacggcctaccctctcctggcct

cgcgagatccctctcgttaagggaggcaagcccgacgtcgtccagattcc

gcaactacaacgcctaccttcgggccagcgacgatctgcctaagatgttc

atcgagtccgaccctgggttcttttccaacgctattgtcgagggagctaa

gaagttccctaacaccgagttcgtgaaggtgaagggcctccacttcagcc

aggaggacgctccagatgaaatgggtaagtacatcaagagcttcgtggag

cgcgtgctgaagaacgagcagtaa.