Portable biochip scanner device

The United States Government has rights in this invention pursuant to Contract No. W-31-109-ENG-38 between the United States Department of Energy (DOE) and the University of Chicago representing Argonne National Laboratory.

The present invention relates to a portable biochip scanner device used to detect and acquire fluorescence signal data from biological microchips (biochips), in particular oligonucleotide biochips.

A related U.S. Pat. No. 6,329,661, entitled “A BIOCHIP SCANNER DEVICE”, by Alexander Perov, Alexander I. Belgovskiy and Andrei D. Mirzabekov is being filed on the same day as the present patent application.

At the present time, biochips, after being incubated with a sample solution containing fluorescently labeled target molecules are assayed using either a microscope equipped with a charge coupled device (CCD) camera or a laser scanner. To acquire large volume of digital data (1-100 MB per image) in a reasonable time these devices employ sophisticated optical, mechanical, and electronic components which results in high cost of the hardware used. Regardless of the technique of fluorescence measurement used, all known biochip analyzers are high-resolution imaging instruments. This means that their output data is essentially a digital image of the chip composed of approximately 1000N elementary data points, where N represents the number of biochip immobilization sites. As a biochip user is typically interested in relative fluorescence intensities of the immobilization sites, an image as the output data format is highly redundant and requires further processing before the data can be analyzed. This may include signal integration over the immobilization sites, background subtraction, and normalization. The image processing is especially difficult in the case of analyzers based on wide-field microscopes, in which both the sensitivity and the image background are inherently non-uniform. With increasing complexity of biochips, the software for processing the fluorescence data becomes increasing intricate and rather demanding in terms of computer memory and processor speed.

The above identified related application discloses a novel technique of reading biochips that we refer to as Discrete Scanning (or Row Scanning) and a laser scanner that embodies this principle in practice. In contrast to the imaging scanners, this device scans exclusively the rows of a biochip array, the beam focal spot being adjusted to match the size of the array elements. The scanner employs a HeNe laser emitting at 594 nm to excite Texas Red-labeled target molecules, an optical system with a fiber-optic output for delivery of the excitation light to a miniature scanning head, and a low-noise photodiode as a fluorescence detector. A computer-controlled positioning system is used to move the scanning head in both X and Y directions to monitor the intensity of fluorescence for each element of a 2D biochip array. The-above setup provides a detection threshold and dynamic range close to those of commercially available biochip readers. In the same time, it is much less demanding in terms of the amplifiers bandwidth, analog-to-digital conversion rate, optical resolution, and scanning mechanics parameters.

There is, however, a need for even simpler and portable biochip reader device. These requirements are typical for applications in which the number of biochip array elements sufficient to assure adequate analytical capability is relatively small, for example, a few hundred or even less.

A principal object of the present invention is to provide a portable biochip scanner device used to detect and acquire fluorescence signal data from biological microchips (biochips) and method of use. Other important objects of the present invention are to provide such method and portable biochip scanner device substantially without sacrificing the sensitivity and dynamic range; and to overcome some disadvantages of prior art arrangements.

In brief, a portable biochip scanner device used to detect and acquire fluorescence signal data from biological microchips (biochips) is provided. The portable biochip scanner device employs a laser for emitting an excitation beam. An optical fiber delivers the laser beam to a portable biochip scanner. A lens collimates the laser beam, the collimated laser beam is deflected by a dichroic mirror and focused by an objective lens onto a biochip. The fluorescence light from the biochip is collected and collimated by the objective lens. The fluorescence light is delivered to a photomultiplier tube (PMT) via an emission filter and a focusing lens. The focusing lens focuses the fluorescence light into a pinhole. A signal output of the PMT is processed and displayed.

The present invention together with the above and other objects and advantages may best be understood from the following detailed description of the preferred embodiments of the invention illustrated in the drawings, wherein:

FIG. 1 is a schematic and block diagram illustrating a portable biochip scanner device in accordance with the preferred embodiment;

FIGS. 2A and 2B are diagrams illustrating a linear biochip array in accordance with the preferred embodiment; and

FIG. 3 is a diagram illustrating a LCD display of the portable biochip scanner device in accordance with the preferred embodiment.

Having reference now to the drawings, in FIG. 1, there is shown a portable biochip scanner device in accordance with the preferred embodiment generally designated by the reference character 100 . Portable biochip scanner device 100 is used to detect and acquire fluorescence signal data from biochips, such as oligonucleotide biochips.

In accordance with features of the invention, scanner 100 can include compact photodetectors, such as photodiodes or miniature photomultiplier tubes and low-power lasers and provide the performance characteristics necessary for reliable detection of fluorescence at the level of 100,000 fluorescent molecules/gel pad. Using the discrete scanning technique allows for considerably relaxed hardware characteristics, such as bandwidth, analog-to-digital conversion rate, optical resolution, and scanning mechanics parameters without sacrificing sensitivity and dynamic range of the instrument.

Portable biochip scanner device 100 is particularly effective for applications in which the number of biochip array elements required to assure adequate analytical capability is relatively small (few hundreds or even less), whereas low cost and portability of the reader device are highly desirable. The discrete portable biochip scanner device 100 is designed to meet these requirements.

Portable biochip scanner device 100 employs a compact solid-state laser 102 emitting at a wavelength matching the excitation band of a particular flurophore. In one embodiment, this laser 102 would be a 5 mW diode laser emitting at 635 nm, which falls close enough to the absorption maximums of such fluorescent labels as “Bodipy 650” and Cy5. Laser 102 also could be a frequency-doubled diode-pumped Nd:YAG laser emitting at 532 nm which suitable for exciting such labels as tetramethylrodamine, Cy3, and Lissamine.

Laser 102 operates in a continuous-wave mode. A lens 104 focuses the laser beam into an optical fiber 106 which delivers the light to a filter compartment 108 . Here, a lens 110 collimates the beam. The collimated beam is next deflected by a dichroic mirror 112 and focused by an objective lens 114 onto the biochip 116 mounted on a scanning stage 134 . The ratio of the focal lengths of the lenses 110 and 114 is chosen to have the beam diameter on the biochip equal to the size of the biochip array elements. The fluorescence light emerging from the biochip array elements is collected and collimated by the lens 114 . Then the light passes in sequence the dichroic mirror 112 , an emission interference filter 118 and a lens 120 which focuses the fluorescence light into a pinhole 122 . The pinhole 122 rejects the stray light that otherwise would contribute to the background. A photomultiplier tube (PMT) 124 serves as a light detector. In the embodiment described here the photomultiplier is an integral part of a miniature detector module that also includes a high-voltage power supply for the PMT and a transimpedance amplifier 126 that converts the signal photocurrent into voltage. Such photomultiplier detector modules are commercially available, for example from Hamamatsu Corp. of Bridgewater, N.J. Next, the signal is digitized with an analog-to-digital converter (ADC) 128 and processed by a microprocessor board 130 . The processing may include digital filtering and integration of the signal. The microprocessor can also be used as a driver of a compact liquid-crystal display (LCD) 132 employed for monitoring the scanner output.

In practical use, the operator initiates a scan by sending an appropriate signal, for example by pressing a button on the instrument's front panel to the controller of scanning stage 134 . When the scanning stage 134 arrives in a certain position designated as a “Start Scan” position, a position sensor located close to the stage sends a signal to the microprocessor board 130 that controls the data acquisition and the ADC 128 starts periodical sampling of the PMT amplifier output. On the stage arrival at a second, “End Scan”, position, another position sensor stops the data acquisition in a similar manner. The digital data obtained is processed and displayed on the LCD screen 132 , for instance, as a bar diagram, each bar representing the integral fluorescence intensity of a particular biochip array element.

A lens part number C220-TM-B sold by Thorlabs of Newton, N.J. can be used for the first lens 110 . A lens part number C230-TM-B sold by Thorlabs of Newton, N.J. can be used for the objective lens 114 . A lens part number C220-TM-B sold by Thorlabs of Newton, N.J. can be used for lens 104 and lens 120 . For 635 nm excitation wavelength, a diode laser module part number DLM 3604-635 sold by Optima Precision of West Linn, Oreg., can be used as laser 102 , and a filter part number 670DF40 and a dichroic mirror part number 640DRLP, both sold by Omega Optical of Brattleboro, Vt. can serve as emission filter 118 and dichroic mirror 112 , respectively.

For 532 nm excitation wavelength, a diode pumped solid state laser part number BR-LPC-3-X sold by Brimrose of Baltimore, Md., can be used as laser 102 , and a filter part number 565EFLP and a dichroic mirror part number 670DRLP, both sold by Omega Optical of Brattleboro, Vt. can serve as emission filter 118 and dichroic mirror 112 , respectively.

Pinhole 122 can be implemented with a part number 04 PPM 017 sold by Melles Griot of Irvine, Calif. The ADC 128 can be implemented with a data acquisition card number LabPC 1200 sold by National Instruments of Austin, Tex. The scanning mechanics 126 can be implemented with a linear scanning stage part number 402002LN-MP-DL3CRM1 sold by Daedal of Harrison City, Pa.

FIGS. 2A and 2B are diagrams illustrating a linear biochip array in accordance with the preferred embodiment. Referring to FIG. 2A, the size of a laser beam spot 102 A substantially matches the immobilization site of the linear biochip array 116 . FIG. 2B illustrates the linear biochip array 116 .

FIG. 3 illustrates an exemplary display on the LCD display 132 of the portable biochip scanner device 100 in accordance with the preferred embodiment. As shown, as a bar diagram, each bar represents the integral fluorescence intensity of a particular element of biochip array 116 .