An Apparatus for the Detection of Laser-induced Epifluorescence
Field of the Invention
The present invention involves detection methods and an apparatus to detect laser-induced epifluorescence - a system that comprises collecting and detecting fluorescence, by employing an elliptical, a spherical or a cylindrical reflector, emitted by biological samples placed on a transparent or semi-transparent substrate when the sample is irradiated either by a laser or any other electromagnetic radiation.
Background of the Invention
Laser- induced fluorescence detection methods are most widely used at the present time to detect fluorescence from a DNA chip or a protein chip based on membrane layer. With this method, a laser is used to excite the fluorescent sample to an excited state, which then returns to the ground state, emitting fluorescence in the downward transition process, and the intensity of this fluorescence is utilized as an indicator of the relative amount of the fluorescing molecules. By affixing fluorescent materials to a DNA or protein sample, one can obtain quantitative information on the relative amounts of analytes.
The confocal laser scanning system configuration is most widely adopted in laser-induced fluorescence detection systems. Here, the laser is used as the source of illumination and the fluorescence from each illuminated spot on the sample goes through a corresponding spatial filter to reach the
detector, such as a photomultiplier tube, and then is converted into a digital image.
As shown in Fig 1, the laser light (11) with a wavelength appropriate for the excitation of the fluorescing material in the sample is focused onto a spot on the sample, inducing fluorescence emission. This fluorescence radiation emanating from a spot of a few hundred microns in diameter eventually ends up at the photodetector (17) after passing through the spatial filter (16), eliminating all other sources of unwanted radiation originating from points other than the point under consideration. (12), (14) and (15) represent the spatial filter for incident light, the objective lens and the sample, respectively.
This confocal geometry demands proper combinations of cover glass, objective lens and the mounting medium, but has a definite advantage of eliminating the background light from the fore- and background of the spot under measurement. Yet the confocal system has the following drawbacks.
First of all, the focusing efficiency is extremely low.
The light collection (hereinafter referred to as "focusing") efficiency in the conventional system can not be higher than 8% when the collection angle is as large as 60°. The portion of the fluorescence energy as captured by the objective lens is proportional to the solid angle extended by the objective to the illuminated point, which sets the ceiling on the collection efficiency at about 8%. This means that more than 90% of the fluorescence generated by the sample is not utilized to generate an electric signal. With a device that is capable of increasing this collection efficiency, one might be able to utilize
low cost photo-detecting devices.
Next, the fluorescence yield is low.
The amount of fluorescence is primarily determined by the amount of fluorescing elements in the sample and is proportional to the incident light intensity. However, over a certain threshold, the amount of emitted fluorescence plateaus and a higher intensity of the incident light may damage the sample and the fluorescence generating mechanism. This sets the limit of the incident energy on the sample. Of the incident light, the major portion goes through the substrate to get trapped and lost by the beam dump or the beam trap. These devices are used to prevent the unused light from being reflected by any surfaces that happens to be in its path, thus degrading the signal-to-noise ratio at the detecting element. With these devices, one can prevent the undesirable effects caused by the scattered light, yet it would be more efficient if a method were available that would recycle the transmitted light to increase the fluorescence yield.
Summary of Invention
Based on the problems described above, the present invention intends to provide a laser-induced epifluorescence detection apparatus employing an elliptical, spherical or a cylindrical reflector. Also, the present invention further provides a new apparatus with greatly enhanced focusing efficiency and fluorescence yield that recycles the light transmitted through the sample-mounted substrate.
In an embodiment, the present invention provides an apparatus for the detection of laser-induced epifluorescence, consisting of a light source that emits laser light; an excitation filter that trims the bandwidth of the emitted light from the light source; a sample control system that controls the position of the sample on which the light passed through the excitation filter scans; an elliptical reflector that reflects the fluorescence emitted from the sample and the scattered light of incident light; a focusing system that collects light transmitted through the sample; a spatial filter that eliminates noise component from the light reflected from the elliptical reflector and output light from the light collecting system; a collimator that converts the light passed through the spatial filter to parallel light; a fluorescence filter that filters only the fluorescence from the combination of fluorescence and the scattered light; and a photodetector system that converts the output light from the fluorescence filter into an electrical signal. In another embodiment, the present invention provides an apparatus for the detection of laser-induced epifluorescence, consisting of a light source that emits laser light; an excitation filter that trims the bandwidth of the emitted light from the light source; a sample control system that controls the position of the sample on which the light passed through the excitation filter scans; a spherical reflector that reflects the fluorescence emitted from the sample and the scattered light of incident light; a focusing system that collects light transmitted through the sample; a spatial filter that eliminates noise component from the light reflected from the spherical reflector and output light from the light collecting system; a collimator that converts the light passed through the spatial filter to parallel light; a fluorescence filter that filters only the fluorescence from the combination of fluorescence and the scattered light; and a photodetector system that converts the output light from the fluorescence
filter into the electric signal.
In another embodiment, the present invention provides an apparatus for the detection of laser-induced epifluorescence, consisting of a light source that emits 1 -dimensional (1-D) laser light; an excitation filter that trims the bandwidth of the emitted light from the light source; a sample control system that controls the position of the sample on which the 1-D light passed through the excitation filter scans; a cylindrical reflector that reflects the fluorescence emitted from the sample and the scattered light of incident light; a focusing system that collects 1-D light transmitted through the sample; a spatial filter that eliminates noise component from the light reflected from the cylindrical reflector and output light from the 1-D light collecting system; a collimator that converts the light passed through the spatial filter to parallel light; a fluorescence filter that filters only the fluorescence from the combination of fluorescence and the scattered light; an 1-D imaging lens that images the fluorescence distribution from each point of the sample on an 1-D arrayed photodetector and a photodetector system that converts the 1-D output light from the imaging lens into the electric signal.
In another embodiment, the present invention provides an apparatus for the detection of laser-induced epifluorescence, consisting of a light source that emits laser light; an excitation filter that trims the bandwidth of the emitted light from the light source; a sample control system that controls the position of the sample on which the light passed through the excitation filter scans; a reflector that reflects the fluorescence emitted from the sample and the scattered light of incident light; an optical feedback system that is placed in the rear of the sample and sends the transmitted excitation light back to the sample; a spatial filter that has a pinhole for eliminating noise component from the light reflected from the reflector; a collimator that converts the light passed
through the spatial filter to parallel light; a fluorescence filter that filters only the fluorescence from the combination of fluorescence and the scattered light; and a photodetector system that converts the output light from the fluorescence filter into an electrical signal.
Brief Description of the Drawings
Fig 1 : a configuration diagram of a conventional apparatus for the detection of laser-induced epifluorescence. Fig 2: a configuration diagram of an apparatus for the detection of laser-induced epifluorescence using an elliptical reflector according to the present invention.
Fig 3: a configuration diagram of an apparatus for the detection of laser-induced epifluorescence using a spherical reflector according to the present invention.
Fig 4: a configuration diagram of an apparatus for the detection of laser-induced epifluorescence using a cylindrical reflector according to the present invention.
Fig 5: a state diagram of scanning the sample by the apparatus as described in Fig. 4.
Fig 6: a configuration diagram of the apparatus for the detection of laser-induced epifluorescence using an optical feedback system according to the present invention.
< Legends for figures >
21,31,41 : light source 22,32,42: excitation filter
23: elliptical reflector 33: spherical reflector
43: cylindrical reflector 24,34,44: sample substrate
25,35(A,B),45: focusing system 26,36,46: spatial filter
27,37,47: collimator 28,38,48: fluorescence filter
29,'39,49: photodetector 30,40,50: computer terminal 51 : imaging lens 60: optical feedback system
Detailed Description of the Invention
The term "epifluorescence" as applied with respect to the laser-induced epifluorescence detecting apparatus of the present invention means the fluorescence emitted from the analytes affixed to a biochip such as a DNA chip or a protein chip based on a membrane.
A DNA chip is a detection system that is made of up to a few hundred thousand DNA molecules immobilized in a very limited area. In other words, a DNA chip is a biological microchip having DNA strands fixed on top of a (semi-)transparent substrate of a material such as glass or silica so that gene expression, gene combination, protein distribution and reaction status can be investigated. Depending on the genetic materials used, the DNA chip can be classified either as a cDNA chip or an oligonucleotide chip. Full-length open reading frames of over 500bp can be contained on the cDNA chip, and oligonucleotides of 15 ~ 25 bases can be contained on the oligonucleotide chip.
There exist two techniques for fabricating a DNA chip utilizing the target DNA; one of synthesizing an oligonucleotide on the substrate and the other of transplanting already synthesized or amplified target DNAs onto the substrate. The former technique is inherited from the semiconductor photolithographic techniques and can achieve higher density integration, yet the length of the target DNA cannot exceed 20 nucleotides. These DNA chips
are suitable for diagnosis of diseases or analysis of single nucleotide polymorphisms (SNPs). DNA chips by the latter technique find many applications in areas as differential gene expression, and target DNAs are transplanted on substrates coated with poly L-lysine, amine or aldehydes. In another embodiment, the apparatus according to the present invention detects the epifluorescence emitted from the membrane-based protein chips. The manufacturing technique and application thereof of these protein chips are widely known and well described in many scientific journals and patent documents. A protein chip for example will provide an integrated array of antibodies against disease-related proteins, and the analytes prepared from the patients' body fluid is used as the biochemical marker to determine the existence and the progress of the disease at its early stage. Such a small substrate can be fabricated by affixing desired protein with agents such as avidin. Polystyrene can also be used as the substrate, which has high affinity for proteins. Also, depending on properties of proteins, polyvinylchloride and polypropylene are also available.
The process of integrating proteins onto a (semi-)transparent substrate is well known to persons with ordinary skill in the art. In case of polystyrene substrate, one would make 8 grooves 1 mm apart, 1mm W x 2mm L x 1.5mm D in a 1 .5cm W x 1.5cm L polystyrene substrate. If the proteins are spotted on each groove with 400 nm diameter 500 nm apart, one can integrate 10 different kinds of proteins over a distance of 1cm. Therefore, a test chip for 80 different proteins on a single substrate can be realized.
Fluorescing agents used for marking analytic samples in the laser-induced epifluorescence detection method and the apparatus according to
the present invention have a "Stokes shift" of 20 nm or more. Most representative fluorescing agents are fluorescent particles, quantum dots, lanthanide chelates such as Samarium, Europeum, Terbium and fluoescent dyes including FITC, Rhodamine green, thiadicarbocyanin, Cy2, Cy3, Cy5, Cy5.5, Alexa 488, Alexa 546, Alexa 594 and Alexa 647. Dyes Cy3 and Cy5 are most desirable dyes for detection of DNA fluorescence. The strength of fluorescence in general is proportional to the intensity of the excitation light, within a certain threshold.
The laser-induced epifluorescence detection method and the apparatus according to the present invention can include He-Ne laser and diode lasers. Examples of representative He-Ne lasers may include compact portable precision iodine-stabilized He-Ne laser from National Research Laboratory of Metrology (NRLM), Agency of Industrial Science and Technology (AIST), Ministry of International Trade and Industry (MITI)(Model NEO-92SI), and 05 LYR 173 from Melles Griot in Irvine California, USA. The diode laser is more compact and portable and comes in IR or red colors.
The apparatus according to the present invention includes a reflector that reflects and focuses the fluorescence emitted from the sample. In case of the elliptical reflector, the sample will be located on the first focal point of the mirror where the incident light is focused after passing through the excitation filter, and the light reflected from the reflector and output from the focusing system will be focused on the second focal point. In case of the spherical reflector, the sample will be located on the center of the mirror where the incident light is focused after passing through the excitation filter. Also, in case of using the 1-D laser source, the sample will be located on the first focal point of the cylindrical reflector where the incident light is focused after
passing through the excitation filter.
The present invention also includes an optical feedback system that is placed in the rear of the sample and returns the transmitted light back to the sample. The preferred optical feedback system can be a spherical reflector.
Hereinafter, the laser-induced epifluorescence detection method and the apparatus according to the present invention are described in detail with reference to the accompanying figures.
Example 1
Figure 2 shows a configuration diagram of the laser-induced epifluorescence detection method and the apparatus using an elliptical reflector according to example 1, which consists of a light source (21) that emits laser light; an excitation filter (22) that trims the bandwidth of the emitted light from the light source; a sample control system (24) that controls the position of the sample on which the light passed through the excitation filter scans; an elliptical reflector (23) that reflects the fluorescence emitted from the sample (ex., DNA chip or protein chip) and the scattered light of incident laser light; an objective lens as a focusing system (25) that collects light passed through the substrate and the sample control system; a spatial filter (26) that is located on the second focal point of the elliptical reflector (23) and has a pinhole for eliminating the noise component from the light reflected from the elliptical reflector (23) and output light from the focusing system (25); a collimator (27) that converts the light passed through the spatial filter (26) to parallel light; a fluorescence filter (28) that filters out the non-fluorescent laser light from the parallel light output from the collimator (27); a photodetector (29) that converts the output light from the fluorescence filter (28) to an electrical
signal; and a computer terminal unit(30) that analyzes and displays the electrical signal obtained from the photo detector (29).
The sample control system (24) that has a sample substrate having samples arranged in a regular pattern, uses transparent or semi-transparent substrates as sample substrate, and uses the elliptical reflector (23) as a reflector, wherein the sample is positioned at the first focal point of the elliptical reflector (23) by the sample control system (24).
Laser used as a light source in the present invention is a 2 mW He-Ne laser that emits radiation at 638 nm, which lies close to the maximum absorption peak of the fluorescence dye.
In the laser-induced epifluorescence detection method and the apparatus according to Example 1 of the present invention, the radiation from the laser source (21), after passing through the excitation filter (22), crosses the elliptical reflector through the hole at the center of the reflector. It is recommended that the light source (21), the excitation filter (22) and the elliptical reflector (23) be aligned in a straight line.
The light having passed through the elliptical reflector (23) is brought to a focus on the surface of the sample (DNA chip or protein chip) mounted on the sample control system (24) that can move the sample in any direction within a preset range. The focusing point coincides with the first focal point of the elliptical reflector (23).
The fluorescence emitted from the excitation light of the sample radiates in all directions including the front part and the rear part of the sample control system (24). The light (A) that is directed to the front part is reflected by the elliptical reflector (23) toward the rear part of the sample control system (24), and the light (B) that is directed to the rear part is focused to the pinhole
of the spatial filter (26) by the focusing system (25). In this time, the light (A) that is reflected by the elliptical reflector (23) toward the rear part is also focused to the pinhole of the spatial filter (26).
The light that passes through the spatial filter (26) in this way is filtered to eliminate the noise component caused by dust located on the surface of the sample, and converted to parallel light by the collimator (27). The parallel light formed by passing through the collimator (27) is filtered to eliminate the excitation light and thus only fluorescence is introduced to the photodetector (29) wherein the fluorescence is converted into an electrical signal, and the on-board computer (30) analyzes the data and stores the results appropriately.
After the data are taken and the result stored on the computer memory, the sample is moved to a new location by the sample control system (24) and the same process is repeated to measure the fluorescence component of the next target point of sample.
Example 2
Figure 3 shows the configuration of the laser-induced epifluorescence detection method and the apparatus using a spherical reflector according to example 2, which is equipped with a sample control system (34) having transparent and semi-transparent sample substrate, and uses a spherical reflector as a reflector wherein the sample is located in the center of the spherical reflector (33) by the sample control system (34).
The apparatus consists of a light source (31) that emits laser light; an excitation filter (32) that trims the bandwidth of the emitted light from the light source; a sample control system (34) that controls the position of the sample on which the light passed through the excitation filter scans; a spherical
reflector (33) that reflects the fluorescence emitted from the sample (ex. a DNA chip or protein chip) and the scattered light of incident laser light; an objective lens (35 A, 35B) as a focusing system (35) that collects light passed through the sample control system; a spatial filter (36) that has a pinhole to eliminate the noise component from output light from the focusing system (35); a collimator (37) that converts the light passed through the spatial filter (36) to parallel light; a fluorescence filter (38) that filters out the non-fluorescent laser light from the parallel light output from the collimator (37); a photodetector (39) that converts the output light from the fluorescence filter (38) to an electrical signal; and a computer terminal unit(40) that analyzes and displays the electrical signal obtained from the photo detector (39).
In the laser-induced epifluorescence detection method and the apparatus according to Example 2 of the present invention, the light from the laser source (31), after passing through the excitation filter (32), crosses the spherical reflector (33) through the hole at the center of the reflector. The light having passed through the spherical reflector (33) is brought to a focus on the surface of the sample (a DNA chip or protein chip) to cause emission of fluorescence, wherein the fluorescence caused by the incident light radiates to the front part and the rear part of the sample. The light (D) that is directed to the front part is precisely reflected back to the position of the sample after being radiated to the spherical reflector (33) at a right angle, wherein the spherical reflector is located in a distance equal to the radius of the reflector from the sample. Since only a portion of fluorescence reflected to the sample is absorbed into the sample, most of fluorescence passes through the sample without reacting.
The light (E) that is directed to the rear of sample and the light (D) that is reflected by the spherical reflector (34) are introduced to a focusing system
(35). Objective lenses (35 A) and (35B) are used as the focusing system (35) in this example, but various combinations of concave and convex spherical lenses also are available.
The light that passes through the focusing system (35) in this way is filtered via the pinhole of a spatial filter (36) to eliminate the noise component caused by dust located on the surface of the sample, and is converted to parallel light by the collimator (37). The parallel light formed by passing through the collimator (37) is filtered to eliminate the excitation light and thus only fluorescence is introduced to the photodetector (39) wherein the fluorescence is converted into an electrical signal, and the on-board computer (40) analyzes the data and stores the results appropriately.
After the data are taken and the result is stored on the computer memory, the sample is moved to a new location by the sample control system (34) and the same process is repeated to measure the fluorescence component of the sample.
Example 3 The figure 4 shows the configuration diagram of the laser-induced epifluorescence detection method and the apparatus using a cylindrical reflector (43) according to Example 3 in the present invention, which uses a cylindrical reflector (43) as a reflector, wherein the sample is located in the center of cylindrical reflector (43) by the sample control system (44). The apparatus consists of a light source (41) that emits 1-dimensional
(1-D) laser light; an excitation filter (32) that trims the bandwidth of the light emitted from the light source (41); a sample control system (44) that controls
the position of the sample on which the 1-D light passed through the excitation filter scans; a cylindrical reflector (43) that reflects the fluorescence emitted from the sample and the scattered light of incident laser light; an objective lens as a focusing system (45) that collects light passed through the sample; a spatial filter (46) that eliminates the noise component from the light reflected by the cylindrical reflector (43) and the light passed through the sample; a collimator (47) that converts the light passed through the spatial filter (46) to parallel light; a fluorescence filter (48) that filters out the non-fluorescent laser light from the parallel light output from the collimator (47); an imaging lens (51) that images the fluorescence distribution form each point of the sample (44) on a 1-D arrayed photodetector (49); a photodetector (49) that converts the output light from the imaging lens (51) to an electrical signal; and a computer terminal unit (50) that analyzes and displays the electric signal obtained from the photo detector (49). In the laser-induced epifluorescence detection method and the apparatus according to example 3 of the present invention, 1-D excitation light from laser source (41) passes through the excitation filter (42) and is irradiated to the sample in the center of the cylindrical reflector (43) to induce fluorescence. This fluorescence and the scattered light from the excitation light are reflected by the cylindrical reflector (43) to be focused on the spatial filter (46), while the light penetrating the sample is focused via the focusing system (45) to the spatial filter (46).
The light passed through the spatial filter (46) in the focused state is converted to parallel light by the collimator (47) and the converted parallel light passes through the fluorescence filter (48) and the imaging lens (51) in turn to be introduced to 1-D arrayed photodetector (49). Finally, an electrical signal generated by the photodetector is transferred and analyzed in the
computer terminal unit (50).
After the data are taken and the result is stored on the computer memory for the one arrangement of the sample, the sample is moved to a new location by the sample control system and the process is repeated to measure the fluorescence component of the sample.
The focusing system (45) and the collimator (47) can be independently a cylindrical or a half-cylindrical lens, as described in figure 4.
Figure 5 shows a state diagram of scanning steps of the biochip substrate as described in figure 4.
Since the incident light linearly expanded in to a thin band is irradiated onto the sample substrate (44A) arrayed in a 2-dimensional pattern, multiple samples (44B) can be scanned simultaneously, with replacing the 1-D scan process with the 2-D scan process.
Example 4
Figure 6 shows the configuration diagram of the laser-induced epifluorescence detection method and the apparatus using an optical feedback system according to example 4 of the present invention, which contains a reflector to improve the focusing efficiency and a light recycling system to increase the fluorescence quantum yield which sends the transmitted excitation light back to the sample.
A spherical reflector (33) was used in the case of the example 4, but it can be replaced with an elliptical one. The apparatus consists of a light source (31) that emits laser light; an excitation filter (32) that trims the bandwidth of the emitted light from the light source; a sample control system (34) that controls the position of the
sample on which the light passed through the excitation filter (32) scans; a spherical reflector (33) that reflects the emitting fluorescence from the sample and the scattered light of incident light; a secondary spherical reflector as an optical feedback system (60) that is placed in the rear of the sample and returns the fluorescence light (I) from the sample and the paraxial scattering light (H) back to the sample; an objective lens as a focusing system (35) that is placed in the rear of the optical feedback system (60) and collects the light passed through the sample control system (34); a spatial filter (36) that has a pinhole for eliminating noise component from the output light from the focusing system (35); a collimator (37) that converts the light passed through the spatial filter to parallel light; a fluorescence filter (38) that filters only the fluorescence from the combination of fluorescence and the excitation light output from the collimator (37); a photodetector (39) that converts the output light from the fluorescence filter (38) into an electrical signal; and a computer terminal unit (40) that analyzes and displays the electrical signal obtained from the photodetector (39).
In example 4 of the present invention, a secondary spherical mirror is located in a distance equal to the radius of the reflector from the sample, so as to reflect fluorescence light (I) from the sample and the paraxial scattering light (H) back to the sample so as to be recycled as excitation energy. Light passing through the sample is collected by the focusing system (35) located in the rear of the optical feedback system (60) and is brought to the spatial filter
(4).
In Example 4 of the present invention, the sample is located in the center of the spherical reflector (33) and the light with an appropriate wavelength is focused on the sample to produce the fluorescence, which then propagates to the front part and the rear part of the sample.
Therefore, the light (D) that is directed to the front part is precisely reflected back to the position of the sample after being radiated to the spherical reflector (33) at a right angle, wherein the spherical reflector is located in a distance equal to the radius of the reflector from the sample. Since only a portion of fluorescence reflected to the sample is absorbed into the sample because the fluorescence has wavelength quite different from the excitation energy, most of fluorescence passes through the sample without reacting.
Meanwhile, fluorescence directed to the rear part of the sample and the paraxial scattering light (H) are reflected by the secondary spherical reflector as an optical feedback system (60), to be introduced back to the sample. As a result, the light emission efficiency of the bio-sample will be enhanced.
After this, light passed through the sample is focused to the pinhole of the spatial filter (36) located in the rear of optical feedback system (60), undergoes suitable processing via the collimator (37), passes through the fluorescence filter (38) to be introduced to the photodetector (39), and is finally sent to a computer terminal unit (40) that analyzes and displays the electrical signal obtained from the photodetector (39).
Industrial Applicability
The apparatus for the detection of laser-induced epifluorescence according to the present invention is able to provide higher light focusing efficiency and improved utilization of the incident light energy by recycling the transmitted light to increase the fluorescence yield, compared to the conventional system.