Laser excited confocol microscope fluorescence method

0001This invention relates generally to a fluorescence scanner and more particularly to a laser excited fluorescence gel scanner employing a confocal microscopic detection system.

0002There is a great deal of interest in the development of automated DNA mapping and sequencing methodologies which is particularly important, in view of the recent interest in sequencing the human genome. The successful completion of this ambitious project will require improved automation. Sequence data are presently being added to data banks at a rate of 10⁶ bases/year but the human genome contains 3x10⁹ base pairs.

0003The detection system presently used by most workers in DNA sequencing or mapping involves using radioisotope labeled DNA. The slab gels in which the radioactive DNA fragments have been separated are placed against an x-ray film for overnight exposure of the film. After the exposure and development of the x-ray film, the sequence or size of the separated DNA fragments are read directly from the images on the film.

0004The autoradiographic detection method described above is not only slow but also requires handling and disposal of hazardous radioactive materials. The reason autoradiography is still so widely used is because it uniquely provides the necessary sensitivity.

0005There has been great interest in automating the sequence determination procedures using recent advances in optical, electronic and computer technology. Autoradiographic films can now be digitized by a scanning transmission densitometer or video cameras and the digitized images can be computer processed to determine DNA sequences. These digitizing and automated sequence determination systems use autoradiography as the primary detection method.

0006In 1986, L. M. Smith, J. Z. Sanders, R. J. Kaiser, P. Hughes, C. Dodd, C.R. Connell, C. Heiner, S. B. H. Kent and L.E. Hood, <u>Nature</u>, vol.321, pp. 674-679, developed a method for detecting fluorescently labeled DNA on gels which they believe is capable of sequencing approximately 15,000 base pairs per day. They state that one of the three areas needing development is "increasing the detection sensitivity of the system thereby allowing less material to be used per reaction which in turn allows the use of thinner gels having higher resolution. "An apparatus developed by W. Ansorge, A. Rosenthal, B. Sproat, C. Schwager, J. Stegemann, and H. Voss, <u>Nuc. Acids Res.</u>, voL 16, pp. 2203-2207 (1988), using a slightly different protocol, was able to sequence 500 base pairs in 5 hours with a sensitivity per band of 10^-18 mole or 6x10⁵ molecules. An analogous approach with similar capabilities was developed by J.M. Prober, G.L. Trainor, R.J. Dam, F.W. Hobbs, C.W. Robertson, R.J. Zagursky, A.J. Cocuzza, M.A. Jensen and K. Baumeister, <u>Science</u>, vol. 238, pp. 336-341 (1987).

0007The development of a high sensitivity detection system would obviously be very important. If very small amounts of fluorescently labeled DNA can be detected on gels, then less labeled DNA is required and the thickness of the gel can be reduced. A thinner gel will have higher resolution so it will not have to be run out as far to resolve the bands. This could result in a major saving in time. Also, the available fluorescence DNA sequencing systems require a detection system that is dedicated to the electrophoresis system during the entire approximate 10 hour run. The detection system would be more efficiently used if it detected gels off-line from the electrophoresis. This could also result in a major saving of time and increase in throughput.

0008One reference, DE 3,742,806, shows an optical system in a confocal arrangement. US Patent No. 4,833,332 (issued to Robertson, Jr. et al.) shows the use of an optical device with a column gel.

0009A confocal scanning microscope is described in G. J. Brakenhoff et al. : "Three-dimensional chromatin distribution in neuroblastoma nuclei shown by confocal scanning laser microscopy", Nature, Vol. 317 (1985), pages 748 - 749.

0010According to the present invention there is provided a gel scanner as set out in claim 1.

0011Also, according to the present invention, there is provided a method of detecting fluorescence from DNA fragments in a gel, as set out in claim 5.

0012Examples of embodiments of the present invention will now be described with reference to the drawings, in which:- <ul id="ul0001" list-style="none" compact="compact"><li>FIGURE 1 shows a laser excited fluorescence gel confocal microscope scanner in accordance with one embodiment of the invention;</li><li>FIGURE 2 is a schematic enlarged view of an objective lens assembly, the gel, gel support, gel objective interface and the volume from which fluorescence is gathered;</li><li>FIGURE 3 is a schematic enlarged view of another assembly of the type shown in Figure 2;</li><li>FIGURE 4 is a block diagram of a suitable data acquisition circuit;</li><li>FIGURE 5 is a block diagram of another data acquisition circuit;</li><li>Figure 6 shows a typical image formed by the gel scanner of an embodiment of the present invention; and</li><li>Figure 7 shows another laser excited fluorescence gel scanner in accordance with an embodiment of the present Invention.</li></ul>

0013Reference will now be made in detail to the preferred embodiments of the invention, examples of which are illustrated in the accompanying drawings. While the invention will be described in conjunction with the preferred embodiments, it Will be understood that they are not intended to limit the invention to those embodiments. On the contrary, the invention is intended to cover alternatives, modifications and equivalents, which may be included within the invention as defined by the appended claims.

0014Increasing the fluorescence emission rate from a sample above that from the background depends on the ability to focus the excitation light to a very small spot or volume, and to gather the light from the spot or volume while rejecting background and scattered light. In fluorescence spectroscopy, it is difficult to illuminate a large area uniformly or to focus the light to a small spot with conventional light sources such as arc lamps. When mapping nucleic acids or their derivatives they are either separated by polyacrylamide or agarose gel or other gel like separation matrices with thickness from 100 µm to several millimeters. To detect nucleic acids in the gel directly by fluorescence emission, one must get rid of or reduce the scattered light from the surface of the gel, scattered light from the substrates, and background emission from the substrates.

0015In an embodiment of the present invention, a confocal microscope forms an illuminated volume in the gel. The light comprises a polarized laser beam oriented so that the background scattering can be minimized as much as possible by the polarization characteristics of the scattered light. An oil immersion objective may be used to match the refractive index of the gel and the objective lens of the optical microscope so as to reduce the scattering. It is to be understood that an air gapped objective lens may also be employed. A confocal optical arrangement is used to reject stray scattering and emission from unwanted regions of the gel or sample carrier. Dichroic beam splitters may be used in the optical system to reject the scattered light by its spectral characteristics. A spatial filter or beam stop can be used to filter out background and scattered light.

0016Referring to Figure 1, a laser excited confocal microscope scanner is illustrated. A laser (not shown) is used as the excitation source. The laser beam 11 is first collimated and focused onto a spatial filter 12 by an 160-mm lens (not shown). After passing through spatial filter 12, the laser beam is reflected by dichroic beam splitter 13 through a 100X, N.A. 1.3 oil immersion objective 14 such as a Rolyn Optics 80.3610 100 NA 1.3. The dichroic beam splitter reflects light at the wavelength of the excitation laser beam, but transmits fluorescence light, which is Stokes shifted to longer wavelengths by the fluorescent sample. The objective 14 serves both as focusing lens and collection lens with very high collection efficiency. The position of the probe, volume 15, in the gel 16 supported by plate 17, Figure 2, can be scanned either by translating the objective and the spatial filter 18 or by translating the sample holder as shown by the arrows 19. The depth of the probe column is adjusted by moving the same elements up and down. The fluorescence emission with Stoke's shifted wavelength is collected by the objective 14 and passed through the dichroic beam splitter 13 which passes Stoke's shifted emission. This reduces scattering because it will not pass scattered light at the laser wavelength.

0017The light is reflected to spatial filter or image stop 18 by a second dichroic beam splitter 20. The spatial filter 18 spatially filters the emitted light and passes it to the phototube detector 21 while rejecting stray, background and scattered light from the various surfaces. The second dichroic beam splitter 20 reflects only the Stoke's shifted fluorescence and lets the scattered light pass through thus providing a second rejection of the background light. It also rejects scattered or reflected light because its polarization direction is such as to pass the reflected and scattered polarized light. The emitted light Is detected by a phototransducer such as a phototube detector 21.

0018The use of 160 mm focusing lens, illumination stop or spatial filter 12, and image stop or spatial filter 18 at 160mm away from the objective lens gives this detection system a confocal arrangement which allows depth profiling of the gel. The depth of view of the detection system with a 100X objective is estimated to be on the order of micrometers. By using this confocal arrangement, one can selectively probe a DNA sample volume 15 in the gel. The scattering from the surfaces of the gel is rejected by the image stop or pinhole 18. Also, the scattering and fluorescence background from the substrates will be rejected by the spatial filter. The fluorescence photons can be either directly detected by the phototube detector 21 or be passed through a bandpass filter 22 to further reject background emissions before detection by the phototube detector 21.

0019The sample is separated by electrophoresis on a slab gel. For an immersion objective the slab gel is covered with nonfluorescent immersion oil 23, Figure 2 right after electrophoresis to prevent it from drying and cracking. The gel is then placed on a computer controlled DC servo motor driven XY translation stage 24 to translate or scan the sample gel past the focused laser volume 15.

0020Figure 3 shows a non-immersion objective lens assembly in which the gel is covered by a thin glass plate 25 which prevents drying out of the gel.

0021A microcomputer with an analog-to-digital board or a frame grabber board is used to digitize data from the data acquisition circuit. The data acquisition circuit of Figure 4 consists of a preamplifier 26 to amplify signal from photomultiplier tube 21 a discriminator 27 to reject thermal noises and other low amplitude electronic noises introduced by the photomultiplier and the preamplifier. A frequency to voltage converter 28 converts counts to analog signal for processing with analog-to-digital converter 29. This photon counting and analog signal conversion method has the fast and relatively easy processing advantage of analog circuits while it also has the digital photon counting sensitivity that DC measurements lack. A more inexpensive version would simply use a photomultiplier tube 21, pre-amplifier 26 and analog-to-digital converter 29 as in Figure 5.

0022The data can also be processed digitally, in which mode, the counts from the phototube detector 21 are processed by a timer/counter 31, Figure 1, or frequency counter or multichannel scaler directly without the frequency to voltage converter and the digital-to-analog converter. Data acquisition circuit 32 provides data to a computer 33. The computer controls the XY translation stage 24 and displays the acquired image in real time.

0023Figure 6 shows an example of a DNA sequencing gel image obtained by this embodiment of the invention. Each band in the image represents one DNA fragment of a particular length. The averaged quantity per band in this image is about 10⁵ molecules. The fluorescence images are contrast-stretched with a histogram equalization method to enhance the images. The direct imaging of DNA or RNA in the gel by fluorescence emission has much better linearity than densitometric scanning of autoradiographic films which usually has a logarithmic response.

0024Figure 7 shows another embodiment of a fluorescence gel scanner incorporating the present invention. Reference numbers have been applied to parts previously described. In this embodiment, a collimated laser beam is directly applied through the lens assembly to a small volume of the gel. The fluorescence from the sample at the small volume is collected by the objective and focused through a spatial filter by a lens (40) to a detector (photomultiplier tube). In other respects, the scanner operates as described above. The location of the sensed volume within the gel may be selected by moving the gel, or by moving the lens assembly and spatial filter.

0025It is important to point out that these configurations are fundamentally better than an imaging charge coupled device (CCD) or charge injection device (CID) coupled to a fluorescence microscope. A fluorescence microscope is designed to image a very tiny area; however, the entire field is illuminated so that the incident intensity in any given small area is low. Furthermore, to image a large area like an electrophoresis slab gel, one has to use a lens that can project the whole image onto the camera at one time. This means using a large F-number lens with low collection efficiency. Despite the high quantum efficiency of charge coupled devices, the detection system as a whole is not as sensitive as a photon counting photomultiplier tube in this kind of application.

0026It is also worth pointing out that preferred embodiments of this invention have better sensitivity over the fluorescence detection system described by Smith et al., <u>Nature</u> (1986) simply due to the better collection efficiency offered by the microscope objective lens and the background rejection methods intrinisic to the confocal spatial filtering of the detected light.

0027In a preliminary experiment the detection limits of a specific embodiment of this invention for DNA sequencing gel reached about 1x10⁵ molecules per band on the average with a 250 µm thick gel and 3 mm wide sample well. Although the on-line detection method described by Smith, et al. (1986) has advantages, the off-line detection method taught in various embodiments of this invention do not require a laser and detection system dedicated to every electrophoresis system. This allows several gels being run simultaneously to have higher throughput and is more economical.

0028In summary, the laser excited confocal fluorescence scanning system taught herein is a very sensitive method for detecting DNA and RNA in gels. A preferred embodiment of this invention employs a confocal microscope with a high numerical aperture objective to achieve the highest collection efficiency possible. Preferred embodiments of the invention teach polarization, spectral filtering, spatial filtering and refractive index matching principles to effectively reduce background in order to obtain optimum detection limits. The electronic gating of noises by photon counting with frequency to voltage conversion provides further improvement in signal-to-noise. The translation of the gel across the laser beam provides a means to image a large electrophoresis gel with high sensitivity and spatial resolution. The ultimate spatial resolution in this fluorescence imaging system is determined by the spot size of the laser beam which can be as small as 1-2µm in diameter using the optical elements described in this embodiment of the invention. The combination of high spatial resolution and low detection limits of this fluorescence imaging system means that very low detection limits can be easily achieved which approach the limits of autoradiography.

0029As an improved instrument for fluorescence detection and imaging of electrophoresis gels, this invention should be of interest to biological or biochemical researchers, particularly those working in DNA sequencing and mapping. Preferred embodiments of this invention can detect DNA samples that cannot be detected by conventional fluorescence detection methods, and it provides a faster and safer way to do DNA sequencing without handling radioactive materials.