CA2179710C - Improved real-time scanning fluorescence electrophoresis apparatus for the analysis of polynucleotide fragments - Google Patents
Improved real-time scanning fluorescence electrophoresis apparatus for the analysis of polynucleotide fragments Download PDFInfo
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- CA2179710C CA2179710C CA002179710A CA2179710A CA2179710C CA 2179710 C CA2179710 C CA 2179710C CA 002179710 A CA002179710 A CA 002179710A CA 2179710 A CA2179710 A CA 2179710A CA 2179710 C CA2179710 C CA 2179710C
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
- G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
- G01N27/416—Systems
- G01N27/447—Systems using electrophoresis
- G01N27/44704—Details; Accessories
- G01N27/44717—Arrangements for investigating the separated zones, e.g. localising zones
- G01N27/44721—Arrangements for investigating the separated zones, e.g. localising zones by optical means
Abstract
This invention relates to an improved real-time scanning fluorescence electrophoresis apparatus for the electrophoretic analysis of fluorescently-labeled polynucleotide fragments. The apparatus is characterized by having an electrophoresis chamber containing an electrophoretic separation medium capable of accommodating multiple electrophoresis lanes arranged in a planar array. a fluorescence detector mounted on a translatable stage, a light source for exciting fluorescent molecules, and a computer for collecting data consisting of time, location, fluorescence wavelength and fluorescent intensity information. The improvements herein disclosed include (i) using a spectral-array detector for detecting the emission light from said fluorescently-labeled polynucleotide fragments including the simultaneous detection of multiple fluorescent labels, and (ii) a temperature control means to control the temperature of the electrophoretic separation medium during electrophoresis.
Description
W0 95/21377 217 9 710 PCTrt-S~Sl~13i3 IMPROVED REALrTINIE SCANNING FLUORESCENCE
ELECTROPHORESIS APPARATUS FOR TFIE ANALYSIS OF
POLYNUCLEOTTDE FRAGMENTS
This invention relates to improved apparatus for performing electrophoresis, and more particularly io an improved real-time scanning fluorescence electrophoresis apparatus for polynucleotide fragment analysis.
$ACKCiROUND OF THE INVENTION
Electrophoretic polynucleotide fragment analysis methods are used to characterize mixtures of poIynucleotide fi-agments based on their migration velocity through a polymer network under the influence of an electric field, i.e. their electrophoretic mobility, in combination with single or multi-color fluorescence detection. Typically these methods are applied subsequent to amplification of the target polynucleotide using a method such as PCR, e.g. Mullis, U.S. patent 4,683,202. Examples of such methods include polynucleotide sequencing, e.g. Trainor, Anal.Chem., 62: 418-426 (I990), restriction fi-agment length polymorphisim (RFLP) analysis, e.g. Watkins, Biotechniques, 6: 310-319 (1988), and variable number of tandem repeat (VNT'R) or microsateilite analysis, e.g_ Ziegle et ai., Genomics, 14: 1026-1031. Each of these methods can provide valuable genetic information about t:.~ target polynucleotide.
Current electrophoretic potynucleotide fiagment analysis systems are characterized by multiple electrophoresis lanes arranged in a planar array, e.g. a multi-lane slab gel, in combination with a real-time-scanning fluorescence detector, e.g. Hunkapiller et al., U.S.
patent 4,8I 1,218. Multiple lanes are used to increase the overall throughput of the analyzer. In order to collect data during the electrophoresis from multiple lanes, the optical detector system is scanned across the w' : ofthe electrophoresis chamber perpendicular to the direction of migration of the labeled polynucleotides.
Preferably, multi-color fluorescence detection is used to increase the information density per lane, e.g.
for DNA sequencing, four Label colors are used, one color for each base. A
light source, e.g. a laser, excites the fluorescent labels attached to the polvnucIeotide fraQrnents, and multiple emission filters discriminate between labels having different spectral properties.
In addition, a computer is used to collect data consisting of time, lane number, and ~
W'O 95/213 r' 217 9 710 PCT;2S95i0I353 fluorescence emission wavelength information, and transform it into useful information, e.g. DNA sequence.
A significant limitation on the speed and resolution of current polynucleotide fragment analysis systems is the ability to dissipate the Joule heat that is generated as a result of the electric current passing through the electrophoresis medium.
Because of problems caused by Joule heating, current systems are limited to low, e.g. 25 V/cm, electrical fields, resulting in long analysis times, e.g. 8 hrs. Joule heating and the resulting temperature gradient across the gel can negatively impact the quality of the separation in two ways. Fuss, because heat is generated throughout the electrophoresis medium but only dissipated at its' outside surfaces, a parabolic temperature profile is establish across the depth of the channel. Since electrophoretic velocity is a strong function of temperature, approximately 2% per oC, this temperature profile leads to a parabolic velocity profile for the migrating analyzes. This spatial dependence of velocity causes a broadening of the ttligrating zones, leading to reduced separation performance. The extent of the temperature profile can be reduced by making the electrophoresis channel thinner, e.g. Bromley et al., Nucleic Acids Research, 19: 4121~I25 (1991); Stegettlann et al., Methods in Molecular and Cellular Biology, 2: 182-184 ( 1991 ). Therefore, as automated system which incorporates thin electrophoresis channels would be desirable.
Second, if the average temperature of the electrophoresis medium becomes too high, the structural integrity of the medium can be compromised. In the case of polymer gel media, e.g. crossIinked polyacrylamide gels, the elevated temperature can lead to complete destruction of the gel. The average temperature of the electrophoresis medium can be controlled by increasing the rate of heat transfer from the electrophoresis channel to the surrounding environment. Therefore, a system which more efficiently transfers the Joule heat generated as a result of the electrophoresis to the surrounding environment would be desirable.
A fiuther limitation on the speed and resolution of eiectrophoretic separations is the rate at which the detector can acquire data from fast moving analyte bands. The most desirable form of detection for polynucleotide fragment analysis would be simultaneous multi-color detection. However, current approaches, i.e. an indexable filter wheel in combination with a photomultiplier tube (PMT) detector, are not ideal because the filter - wheel must be,indexed rapidly enough to observe each color before it moves out of the detector region. This is problematic due to the high elecirophoretic velocity of the _2_ W0 95/2137% 217 9 710 PCTIU595/01353 polynucleotide fragments in high-speed systems. If a sufficient number of data points are not collected for each analyte band, e.g. 10 points per band, the ability to discriminate between adjacent bands is lost. One way to increase the rate of data acquisition for a multi-color system is to collect signals from all the colors simultaneously rather than serially. Therefore, a detection system which acquires all colors simultaneously would be desirable.
In light of the above, what was needed was an improved electrophoresis apparatus capable of accommodating high electric fields through enhanced heat dissipation characteristics and detector performance.
SUMMARY OF THE IrIVENTION
The present invention is directed to improvements to an apparatus for electrophoretic polynucleotide analysis, said improvements leading to increased I S throughput of the system. The improvements include ~) incorporating a spectral-array detector to increase the rate of data acquisition, and (ii) incorporating an improved means to control the temperature of the electrophoresis medium. The analyzer system of the present invention is comprised o~ in combination, An improved real-time scanning fluorescence electrophoresis apparazirs for the electrophoretic analysis of ffuorescently-labeled polynucleotide fragments of the type having an electrophoresis chamber containing an electrophoretic separation medium capable of accommodating multiple electrophoresis lanes arranged in a planar array, a fluorescence detector mounted on a translatable stage, a light source for exciting fluorescent molecules, and a computer for collecting data consisting of time, location, fluorescence wavelength and fluorescent intensity information wherein the improvement comprises:
(a) a spectral-array detector for detecting the emission light from said fluorescently-labeled p ~lynucleotide fragments including the simultaneous detection of multiple fluorescent labels, (b) a temperature control means to control the temperature of the electrophoretic separation medium during electrophoresis.
g~F DESCRIPTION OF THE DRAWfir'GS
Figure I shows a vertically oriented slab gel.
_ 3 _ W'O 95/213'7 217 9 710 PCT'L'S95/013i3 Figure Z shows a schematic diagram of the fight path in a preferred embodiment of the spectral-array detection system of the present invention.
Figures 3 shows a plate holder according to a prefered embodiment of the invention.
Figure 4 shows a plate locating mechanism according to a prefered embodiment of the invention. .
Figure S shows a temperature control mechanism according to a prefered embodiment of the invention.
The term "polynucleotide" as used herein refers to linear polymers of natural or modified nucleoside monomers, including double and single stranded deoxyribonucleosides, I S n'bonucleosides, a-anomeric forms thereof, and the like. Usually the nucleoside monomers are linked by phosphodiester bonds or analogs thereof to form polynucleotides ranging in siae from a few monomeric units, e.g. 8-40, to several thousands of monomeric units.
Whenever a polynucleotide is represented by a sequence of letters, such as "ATGCCTG," it will be understood that the nucleotides are in 5'-3' order from left to right and that "A"
denotes deoxyadenosine, "C" denotes deoxycytidine, "G" denotes deoxyguanosine, and "T"
denotes thymidine, unless otherwise noted. Analogs of phosphodiester linkages include phosphorothioate, phosphorodithioate, phosphoroseienoate, phosphorodiselenoate, phosphoroanilothioate, phosphotaniIidate, phosphoramidate, and the like.
As used herein, "nucleoside" includes the natural nucleosides, including 2'-deoxy and 2'-hydroxyl forms, e.g. as described in Kornberg and Baker, DNA
Replication, 2nd Ed. (Freeman, San Francisco, 1992). "Analogs" in reference to nucleosides includes synthetic nucleosides having modified base moieties and/or modified sugar moieties, e.g.
described generally by Scheit, Nucleotide Analogs (John Wiley, New York, 1980).
As used herein, the term "electrophoretic separation medium" refers to a material through which the polynucleotides are electrophoresed and which imparts a size-dependent eIectrophoretic velocity to the polynucleotides. Typically, such material is a porous network formed by linear or branched polymer molecules, or she like, e.g.
crossiinked polyacrylamide.
_.1 _ W095I213'i 217 9 710 PCTIhS9sID1353 As used herein, the term "elecuophoresis chamber" refers to the container in which the electrophorertic separation is contained. Typically, this container is formed by two rectangular glass plates which are separated by thin polymer sheets, spacers, located between the plates at the edge regions of the plates. This is traditionally referred to as slab electrophoresis. When the electrophoretic separation medium is a rigid crosslinked gel, this format is referred to as slab gel dearophoresis.
DESCRIPTION OF THE PREFERRED EMBODIIvtENTS
Figure 1 shows polynucieotide fragment samples (2) which have been labeled with one of several ffuorophores loaded into loading wells {4) of vertically oriented slab gel (8), said gel motmted in the analyzer of the present invention. The fragments are electrophoresed through gel (8) where they are separated based on their relative size.
Following separation, the fragments pass through laser excitation and defection region (12) where the fluorescently labeled polynucieotide fragments are detected.
The fluorophores emit light at a specific wavelength based upon the particular dye used, thereby facilitating the identification of each fragment.
After the polynucleotide fragments have been separated, they are detected by a simultaneous multi-color detection means. An important feattue of the polynucleotide analyzer of the present invention is the "spectral-array fluorescence detector". As used herein, the term "spectral- array fluorescence detector" refers to a detector which employs [) a means to spectrally separate the fluorescence emission light, such as a diffraction grating, or a prism, or the like, (ii) an array of detector elements sensitive to light radiation, such as a diode array, a charged coupled device (CCD) system, an array of photomultiplier tubes, or the like, (iii) an excitation light source, such as an incandescent bulb, an arc lamp, a laser, a laser diode, or the like, and (iv) associated optics capable of directing and conditioning both the excitation and emission light. The output of a spectral-array detector is light intensity as a function of array location, wherein the array location can be directly related to the wavelength of the light falling on that location. One example of such a detector is given by Karger et al., Nucleic Acids Research 19: 4955-4962 {1991).
One preferred method of treating the output of a spectral-array detector is to create a "virtual filter". As used herein, the term "virtual filter" refers to a method of manipulating data from a spectral-array detector such that a plurality of discrete WO 95/21377 ~ 17 9 710 pCTli'S95/013;3 wavelength ranges are sampled, wherein the location and bandwidth ofeach wavelength range can be dynamically changed using software. The virtual filter can mimic a physical interference or absorbence filter, however it has several important advantages. First, virtual-filters can be programmed to interrogate multiple emission wavelengths simultaneously, malting possible the e~cient mufti-color detection of fast-moving analytes without the need to rapidly index a multiplicity of filters. Second, virtual filters can be programmed to detect a range of emission bandwidths. This is important because for any application, there exists an optimum bandwidth which results in an optimum combination of sensitivity and color discrimination: as the detection band width is made wider, the detector collects more light, hereby increasing sensitivity, however, at the same time, the broader bandwidth decreases the ability to discriminate between closely related colors. Third, virtual filters have essentially perfect transmission curves, i.e. the filter ran discriminate between very closely related colors. Forth, the selected wavelength ranges of the virtual filter can be easily adjusted using software to match the characteristics of various excitation light sources and dye sets. Therefore, changing dye chemistries is a simple matter of changing the virtual filter with software, whereas a mechanical modification of the system is required when physical filters are used.
Moreover, the selected wavelength ranges and band widths of the virtual filter can be changed dynamically, i.e. doting the course of a rua, to compensate for any spectral changes in the dye labels which occur during a tun.
Figure 2 is a schematic diagram of the light path in a preferred embodiment of the spectral-array detection system of the present invention. Preferably, the analyzer system of the invention uses a laser as a fluorescence excitation light source, e.g.
an argon ion laser that emits a 40 mW, 0.67 mm diameter polarized light beam having intensity tttaxima at wavelengths of 488 and 514 nm. Light from laser (66) is reflected off of adjustabiy-mounted turning mirrors (68) which direct the laser light to the desired location.
Telescope lenses (70) then reduce the beam diameter to approximately 100 Elm, and bending mirror (72) directs the light into electrophoresis medium (104) at right angles.
Light emitted from the laser-excited fluorescent label is collected by aspheric collection lens (74) which collimates the light in the direction of the detector. The emitted light then passes around bending mirror (72) and through laser rejection filter (76), thereby reducing the level of scattered laser fight entering the detector. Because the excitation laser light passes through the center of aspheric collection lens (74), a certain amount of laser light will be reflected directly back from the lens surface in the direction of the detection, causing unwanted background signal. Bending mirror (72), which is mounted in the center of laser rejection filter (76), acts to deflect this reflected light away from the colletion path thus reducing the amount of reflected light entering the detector. The collected emission light then passes through plano-convex lens (78) which focuses the emission light at slit (80) mounted on the entrance to spectrograph (82). (Spectrograph (82) utilizes a 405 g/mm, 450 nm blaze grating with a dispersion of 17 nm/mm.) After passing through spectrograph (82), the light then falls onto CCD (90). The output signal from CCD (90) is transmitted to electronic computer (64) for subsequent data analysis and presentation.
To further increase the emission light signal and decrease background light scatter, a nonconductive mirror coating is applied to the inside surface (102) of front gel plate (108). This surface reflects emission light back to the cllection lenses rather than allowing it to be lost to the surroundings through the front gel plate.
In addition, when the primary laser light strikes this mirrored surface it is reflected back through the gel, thereby exciting additonal fluorophores resulting in more emission light.
Furthermore, this mirrored surface decreases unwanted background light generated by the fluorescence of the front glass plate itself.
In order to interrogate all of the electrophoresis lanes on a real-time basis, the optical system described above, less turning mirrors (68) and computer (90), is scanned across the width of the electrophoresis chamber.
Another important feature of the present invention is the novel means used to mount the electrophoresis chamber onto the analyzer. Preferably, the electrophoresis chamber is formed by two glass plates separated by two spacers located at the left and right edges of the plates. The glass plates are mounted into a plate holder which acts to support and secure the glass plates along with an upper buffer reservoir in a convenient manner. See Figure 3. The plate holder consists of rectangular frame (200) onto which is attached plurality of twist clamps (204). (Note that only one twist clamp is indicated in Figure 3, as (204), in order to retain the clarity of the drawing.) When twist clamps (204) are in the horizontal orientation, they service to secure the glass plates in the holder, and, when twist clamps (204) are in a vertical orientation, they allow the glass plates to be conveniently inserted or removed from the plate holder. The rectangular frame includes two locational registration notices (208) to insure the proper positioning of the plate holder in the analyzer. Beam stop (212) is -7a-positioned so as to protect the user from direct W'O 95121377 - - PCT/US95/01353 exposure to the excitation laser light. The frame also includes two handles (202) to facilitate transportation of the plate holder assembly. The plate holder provides a means for detachably mounting upper buffer reservoir (216). A protrusion (228) on each side of upper buffer reservoir (216) is positioned such that when the uppermost twist clamps are in the horizontal position, the upper buffer reservoir (216) is forced against the front glass plate, thereby creating a liquid-tight seal between the upper buffer chamber and the front glass plate. Upper buffer reservoir (216) contains electrode (220) and electrical cable (224) for connecting electrode (220) to an electrophoresis power supply. The plate holder is designed to secure glass plates of varying lengths. For applications requiring less separation and/or a shorter atlalysis time, a shorter length would be used, and for applications requiring more separation and for which longer analysis times can be tolerated, a longer length would be used.
A fiuther important aspect of the present invention is the plate locating mechanism. In order to efficiently collect the fluorescence emission light, the detection region of the electrophoresis chamber must be properly positioned with respect to the collection optics. Specifically, the detection region must be aligned such that the focal point of the collection optics is Located within the separation medium, and not in the wall of the electrophoresis chamber. The plate locating mechanism insures that this positioning is reproducibly achieved. The mechanism will be described with reference to Figure 4.
When a thin electrophoresis chamber is being used, i.e. less than 0.2 mm, preadjusted locating pins (300) fit through notches (304) in back glass plate (308) and push front glass plate (312) against front tip (324) oflocating pins (300). When a thick electrophoresis cfiamber is being used, i.e. greater than 0.2 mm, step-portion (320) of locating pins (300) is forced against back glass plate (312). Locating pins (300) are preadjusted such that the interior of the electrophoresis chamber is at the focal point ofthe collection optics. Glass plates (308 and 312) are forced against locating pins (300) by twist clamps (330).
While increasing the electric freId across the electrophoresis chamber increases the speed of the electrophoretic separation, it also leads to increased Joule heat generated within the electrophoresis medium, which in turn can lead to destruction of the electrophoresis medium. To remove the heat generated by running "fast"
electrophoresis, a temperature control mechanism (Figure 5 ) has been developed. The temperature control mechanism includes a back heat transfer plate (400) against which back glass plate (404) is mounted to the instrument. Preferably, heat transfer plate (400) is made from coated aluminum. The coating acts as an electrical insulator to inhibit arcing _g_ WO 95/213TT 21 l 9 710 PCT~2'S951DI353 between back glass plate (404) and the rest of the instrument. Within back cooling plate (400) are channels through which a flowable heat transfer medium can be circulated.
Front heat transfer plate (408), also containing channels capable of being &lled with a flowable heat transfer medium, is contacted with front glass plate (412). Pump (416) circulates the flowable heat transfer medium from reservoir (420) through front and back heat transfer plates (400 and 408). Heat is removed from the circulating flowable heat transfer medium by passing it through heat exchanger (424), thereby cooling the flowable heat transfer medium to ambient temperature. If superambient heating or subambient cooling of the gels is desired for a specific application, the ffowable heat transfer medium passes through a heater or cooler (not shown) before flowing through the heat transfer plates. Active temperature control of the gel is effected by means of temperature sensors (430) mounted to the heat transfer plates in combination with computer (434) which regulates the temperature of the plates by controlling the flow rate of the flowable heat transfer medium through the heat transfer plates.
Although the invention has been illustrated by the foregoing description it is not to be construed as being limited to the materials employed therein but rather the invention is directed to the generic area as hereinbefore disclosed. Various modifications and embodiments thereof can be made without departing from the spirit or scope thereof.
ELECTROPHORESIS APPARATUS FOR TFIE ANALYSIS OF
POLYNUCLEOTTDE FRAGMENTS
This invention relates to improved apparatus for performing electrophoresis, and more particularly io an improved real-time scanning fluorescence electrophoresis apparatus for polynucleotide fragment analysis.
$ACKCiROUND OF THE INVENTION
Electrophoretic polynucleotide fragment analysis methods are used to characterize mixtures of poIynucleotide fi-agments based on their migration velocity through a polymer network under the influence of an electric field, i.e. their electrophoretic mobility, in combination with single or multi-color fluorescence detection. Typically these methods are applied subsequent to amplification of the target polynucleotide using a method such as PCR, e.g. Mullis, U.S. patent 4,683,202. Examples of such methods include polynucleotide sequencing, e.g. Trainor, Anal.Chem., 62: 418-426 (I990), restriction fi-agment length polymorphisim (RFLP) analysis, e.g. Watkins, Biotechniques, 6: 310-319 (1988), and variable number of tandem repeat (VNT'R) or microsateilite analysis, e.g_ Ziegle et ai., Genomics, 14: 1026-1031. Each of these methods can provide valuable genetic information about t:.~ target polynucleotide.
Current electrophoretic potynucleotide fiagment analysis systems are characterized by multiple electrophoresis lanes arranged in a planar array, e.g. a multi-lane slab gel, in combination with a real-time-scanning fluorescence detector, e.g. Hunkapiller et al., U.S.
patent 4,8I 1,218. Multiple lanes are used to increase the overall throughput of the analyzer. In order to collect data during the electrophoresis from multiple lanes, the optical detector system is scanned across the w' : ofthe electrophoresis chamber perpendicular to the direction of migration of the labeled polynucleotides.
Preferably, multi-color fluorescence detection is used to increase the information density per lane, e.g.
for DNA sequencing, four Label colors are used, one color for each base. A
light source, e.g. a laser, excites the fluorescent labels attached to the polvnucIeotide fraQrnents, and multiple emission filters discriminate between labels having different spectral properties.
In addition, a computer is used to collect data consisting of time, lane number, and ~
W'O 95/213 r' 217 9 710 PCT;2S95i0I353 fluorescence emission wavelength information, and transform it into useful information, e.g. DNA sequence.
A significant limitation on the speed and resolution of current polynucleotide fragment analysis systems is the ability to dissipate the Joule heat that is generated as a result of the electric current passing through the electrophoresis medium.
Because of problems caused by Joule heating, current systems are limited to low, e.g. 25 V/cm, electrical fields, resulting in long analysis times, e.g. 8 hrs. Joule heating and the resulting temperature gradient across the gel can negatively impact the quality of the separation in two ways. Fuss, because heat is generated throughout the electrophoresis medium but only dissipated at its' outside surfaces, a parabolic temperature profile is establish across the depth of the channel. Since electrophoretic velocity is a strong function of temperature, approximately 2% per oC, this temperature profile leads to a parabolic velocity profile for the migrating analyzes. This spatial dependence of velocity causes a broadening of the ttligrating zones, leading to reduced separation performance. The extent of the temperature profile can be reduced by making the electrophoresis channel thinner, e.g. Bromley et al., Nucleic Acids Research, 19: 4121~I25 (1991); Stegettlann et al., Methods in Molecular and Cellular Biology, 2: 182-184 ( 1991 ). Therefore, as automated system which incorporates thin electrophoresis channels would be desirable.
Second, if the average temperature of the electrophoresis medium becomes too high, the structural integrity of the medium can be compromised. In the case of polymer gel media, e.g. crossIinked polyacrylamide gels, the elevated temperature can lead to complete destruction of the gel. The average temperature of the electrophoresis medium can be controlled by increasing the rate of heat transfer from the electrophoresis channel to the surrounding environment. Therefore, a system which more efficiently transfers the Joule heat generated as a result of the electrophoresis to the surrounding environment would be desirable.
A fiuther limitation on the speed and resolution of eiectrophoretic separations is the rate at which the detector can acquire data from fast moving analyte bands. The most desirable form of detection for polynucleotide fragment analysis would be simultaneous multi-color detection. However, current approaches, i.e. an indexable filter wheel in combination with a photomultiplier tube (PMT) detector, are not ideal because the filter - wheel must be,indexed rapidly enough to observe each color before it moves out of the detector region. This is problematic due to the high elecirophoretic velocity of the _2_ W0 95/2137% 217 9 710 PCTIU595/01353 polynucleotide fragments in high-speed systems. If a sufficient number of data points are not collected for each analyte band, e.g. 10 points per band, the ability to discriminate between adjacent bands is lost. One way to increase the rate of data acquisition for a multi-color system is to collect signals from all the colors simultaneously rather than serially. Therefore, a detection system which acquires all colors simultaneously would be desirable.
In light of the above, what was needed was an improved electrophoresis apparatus capable of accommodating high electric fields through enhanced heat dissipation characteristics and detector performance.
SUMMARY OF THE IrIVENTION
The present invention is directed to improvements to an apparatus for electrophoretic polynucleotide analysis, said improvements leading to increased I S throughput of the system. The improvements include ~) incorporating a spectral-array detector to increase the rate of data acquisition, and (ii) incorporating an improved means to control the temperature of the electrophoresis medium. The analyzer system of the present invention is comprised o~ in combination, An improved real-time scanning fluorescence electrophoresis apparazirs for the electrophoretic analysis of ffuorescently-labeled polynucleotide fragments of the type having an electrophoresis chamber containing an electrophoretic separation medium capable of accommodating multiple electrophoresis lanes arranged in a planar array, a fluorescence detector mounted on a translatable stage, a light source for exciting fluorescent molecules, and a computer for collecting data consisting of time, location, fluorescence wavelength and fluorescent intensity information wherein the improvement comprises:
(a) a spectral-array detector for detecting the emission light from said fluorescently-labeled p ~lynucleotide fragments including the simultaneous detection of multiple fluorescent labels, (b) a temperature control means to control the temperature of the electrophoretic separation medium during electrophoresis.
g~F DESCRIPTION OF THE DRAWfir'GS
Figure I shows a vertically oriented slab gel.
_ 3 _ W'O 95/213'7 217 9 710 PCT'L'S95/013i3 Figure Z shows a schematic diagram of the fight path in a preferred embodiment of the spectral-array detection system of the present invention.
Figures 3 shows a plate holder according to a prefered embodiment of the invention.
Figure 4 shows a plate locating mechanism according to a prefered embodiment of the invention. .
Figure S shows a temperature control mechanism according to a prefered embodiment of the invention.
The term "polynucleotide" as used herein refers to linear polymers of natural or modified nucleoside monomers, including double and single stranded deoxyribonucleosides, I S n'bonucleosides, a-anomeric forms thereof, and the like. Usually the nucleoside monomers are linked by phosphodiester bonds or analogs thereof to form polynucleotides ranging in siae from a few monomeric units, e.g. 8-40, to several thousands of monomeric units.
Whenever a polynucleotide is represented by a sequence of letters, such as "ATGCCTG," it will be understood that the nucleotides are in 5'-3' order from left to right and that "A"
denotes deoxyadenosine, "C" denotes deoxycytidine, "G" denotes deoxyguanosine, and "T"
denotes thymidine, unless otherwise noted. Analogs of phosphodiester linkages include phosphorothioate, phosphorodithioate, phosphoroseienoate, phosphorodiselenoate, phosphoroanilothioate, phosphotaniIidate, phosphoramidate, and the like.
As used herein, "nucleoside" includes the natural nucleosides, including 2'-deoxy and 2'-hydroxyl forms, e.g. as described in Kornberg and Baker, DNA
Replication, 2nd Ed. (Freeman, San Francisco, 1992). "Analogs" in reference to nucleosides includes synthetic nucleosides having modified base moieties and/or modified sugar moieties, e.g.
described generally by Scheit, Nucleotide Analogs (John Wiley, New York, 1980).
As used herein, the term "electrophoretic separation medium" refers to a material through which the polynucleotides are electrophoresed and which imparts a size-dependent eIectrophoretic velocity to the polynucleotides. Typically, such material is a porous network formed by linear or branched polymer molecules, or she like, e.g.
crossiinked polyacrylamide.
_.1 _ W095I213'i 217 9 710 PCTIhS9sID1353 As used herein, the term "elecuophoresis chamber" refers to the container in which the electrophorertic separation is contained. Typically, this container is formed by two rectangular glass plates which are separated by thin polymer sheets, spacers, located between the plates at the edge regions of the plates. This is traditionally referred to as slab electrophoresis. When the electrophoretic separation medium is a rigid crosslinked gel, this format is referred to as slab gel dearophoresis.
DESCRIPTION OF THE PREFERRED EMBODIIvtENTS
Figure 1 shows polynucieotide fragment samples (2) which have been labeled with one of several ffuorophores loaded into loading wells {4) of vertically oriented slab gel (8), said gel motmted in the analyzer of the present invention. The fragments are electrophoresed through gel (8) where they are separated based on their relative size.
Following separation, the fragments pass through laser excitation and defection region (12) where the fluorescently labeled polynucieotide fragments are detected.
The fluorophores emit light at a specific wavelength based upon the particular dye used, thereby facilitating the identification of each fragment.
After the polynucleotide fragments have been separated, they are detected by a simultaneous multi-color detection means. An important feattue of the polynucleotide analyzer of the present invention is the "spectral-array fluorescence detector". As used herein, the term "spectral- array fluorescence detector" refers to a detector which employs [) a means to spectrally separate the fluorescence emission light, such as a diffraction grating, or a prism, or the like, (ii) an array of detector elements sensitive to light radiation, such as a diode array, a charged coupled device (CCD) system, an array of photomultiplier tubes, or the like, (iii) an excitation light source, such as an incandescent bulb, an arc lamp, a laser, a laser diode, or the like, and (iv) associated optics capable of directing and conditioning both the excitation and emission light. The output of a spectral-array detector is light intensity as a function of array location, wherein the array location can be directly related to the wavelength of the light falling on that location. One example of such a detector is given by Karger et al., Nucleic Acids Research 19: 4955-4962 {1991).
One preferred method of treating the output of a spectral-array detector is to create a "virtual filter". As used herein, the term "virtual filter" refers to a method of manipulating data from a spectral-array detector such that a plurality of discrete WO 95/21377 ~ 17 9 710 pCTli'S95/013;3 wavelength ranges are sampled, wherein the location and bandwidth ofeach wavelength range can be dynamically changed using software. The virtual filter can mimic a physical interference or absorbence filter, however it has several important advantages. First, virtual-filters can be programmed to interrogate multiple emission wavelengths simultaneously, malting possible the e~cient mufti-color detection of fast-moving analytes without the need to rapidly index a multiplicity of filters. Second, virtual filters can be programmed to detect a range of emission bandwidths. This is important because for any application, there exists an optimum bandwidth which results in an optimum combination of sensitivity and color discrimination: as the detection band width is made wider, the detector collects more light, hereby increasing sensitivity, however, at the same time, the broader bandwidth decreases the ability to discriminate between closely related colors. Third, virtual filters have essentially perfect transmission curves, i.e. the filter ran discriminate between very closely related colors. Forth, the selected wavelength ranges of the virtual filter can be easily adjusted using software to match the characteristics of various excitation light sources and dye sets. Therefore, changing dye chemistries is a simple matter of changing the virtual filter with software, whereas a mechanical modification of the system is required when physical filters are used.
Moreover, the selected wavelength ranges and band widths of the virtual filter can be changed dynamically, i.e. doting the course of a rua, to compensate for any spectral changes in the dye labels which occur during a tun.
Figure 2 is a schematic diagram of the light path in a preferred embodiment of the spectral-array detection system of the present invention. Preferably, the analyzer system of the invention uses a laser as a fluorescence excitation light source, e.g.
an argon ion laser that emits a 40 mW, 0.67 mm diameter polarized light beam having intensity tttaxima at wavelengths of 488 and 514 nm. Light from laser (66) is reflected off of adjustabiy-mounted turning mirrors (68) which direct the laser light to the desired location.
Telescope lenses (70) then reduce the beam diameter to approximately 100 Elm, and bending mirror (72) directs the light into electrophoresis medium (104) at right angles.
Light emitted from the laser-excited fluorescent label is collected by aspheric collection lens (74) which collimates the light in the direction of the detector. The emitted light then passes around bending mirror (72) and through laser rejection filter (76), thereby reducing the level of scattered laser fight entering the detector. Because the excitation laser light passes through the center of aspheric collection lens (74), a certain amount of laser light will be reflected directly back from the lens surface in the direction of the detection, causing unwanted background signal. Bending mirror (72), which is mounted in the center of laser rejection filter (76), acts to deflect this reflected light away from the colletion path thus reducing the amount of reflected light entering the detector. The collected emission light then passes through plano-convex lens (78) which focuses the emission light at slit (80) mounted on the entrance to spectrograph (82). (Spectrograph (82) utilizes a 405 g/mm, 450 nm blaze grating with a dispersion of 17 nm/mm.) After passing through spectrograph (82), the light then falls onto CCD (90). The output signal from CCD (90) is transmitted to electronic computer (64) for subsequent data analysis and presentation.
To further increase the emission light signal and decrease background light scatter, a nonconductive mirror coating is applied to the inside surface (102) of front gel plate (108). This surface reflects emission light back to the cllection lenses rather than allowing it to be lost to the surroundings through the front gel plate.
In addition, when the primary laser light strikes this mirrored surface it is reflected back through the gel, thereby exciting additonal fluorophores resulting in more emission light.
Furthermore, this mirrored surface decreases unwanted background light generated by the fluorescence of the front glass plate itself.
In order to interrogate all of the electrophoresis lanes on a real-time basis, the optical system described above, less turning mirrors (68) and computer (90), is scanned across the width of the electrophoresis chamber.
Another important feature of the present invention is the novel means used to mount the electrophoresis chamber onto the analyzer. Preferably, the electrophoresis chamber is formed by two glass plates separated by two spacers located at the left and right edges of the plates. The glass plates are mounted into a plate holder which acts to support and secure the glass plates along with an upper buffer reservoir in a convenient manner. See Figure 3. The plate holder consists of rectangular frame (200) onto which is attached plurality of twist clamps (204). (Note that only one twist clamp is indicated in Figure 3, as (204), in order to retain the clarity of the drawing.) When twist clamps (204) are in the horizontal orientation, they service to secure the glass plates in the holder, and, when twist clamps (204) are in a vertical orientation, they allow the glass plates to be conveniently inserted or removed from the plate holder. The rectangular frame includes two locational registration notices (208) to insure the proper positioning of the plate holder in the analyzer. Beam stop (212) is -7a-positioned so as to protect the user from direct W'O 95121377 - - PCT/US95/01353 exposure to the excitation laser light. The frame also includes two handles (202) to facilitate transportation of the plate holder assembly. The plate holder provides a means for detachably mounting upper buffer reservoir (216). A protrusion (228) on each side of upper buffer reservoir (216) is positioned such that when the uppermost twist clamps are in the horizontal position, the upper buffer reservoir (216) is forced against the front glass plate, thereby creating a liquid-tight seal between the upper buffer chamber and the front glass plate. Upper buffer reservoir (216) contains electrode (220) and electrical cable (224) for connecting electrode (220) to an electrophoresis power supply. The plate holder is designed to secure glass plates of varying lengths. For applications requiring less separation and/or a shorter atlalysis time, a shorter length would be used, and for applications requiring more separation and for which longer analysis times can be tolerated, a longer length would be used.
A fiuther important aspect of the present invention is the plate locating mechanism. In order to efficiently collect the fluorescence emission light, the detection region of the electrophoresis chamber must be properly positioned with respect to the collection optics. Specifically, the detection region must be aligned such that the focal point of the collection optics is Located within the separation medium, and not in the wall of the electrophoresis chamber. The plate locating mechanism insures that this positioning is reproducibly achieved. The mechanism will be described with reference to Figure 4.
When a thin electrophoresis chamber is being used, i.e. less than 0.2 mm, preadjusted locating pins (300) fit through notches (304) in back glass plate (308) and push front glass plate (312) against front tip (324) oflocating pins (300). When a thick electrophoresis cfiamber is being used, i.e. greater than 0.2 mm, step-portion (320) of locating pins (300) is forced against back glass plate (312). Locating pins (300) are preadjusted such that the interior of the electrophoresis chamber is at the focal point ofthe collection optics. Glass plates (308 and 312) are forced against locating pins (300) by twist clamps (330).
While increasing the electric freId across the electrophoresis chamber increases the speed of the electrophoretic separation, it also leads to increased Joule heat generated within the electrophoresis medium, which in turn can lead to destruction of the electrophoresis medium. To remove the heat generated by running "fast"
electrophoresis, a temperature control mechanism (Figure 5 ) has been developed. The temperature control mechanism includes a back heat transfer plate (400) against which back glass plate (404) is mounted to the instrument. Preferably, heat transfer plate (400) is made from coated aluminum. The coating acts as an electrical insulator to inhibit arcing _g_ WO 95/213TT 21 l 9 710 PCT~2'S951DI353 between back glass plate (404) and the rest of the instrument. Within back cooling plate (400) are channels through which a flowable heat transfer medium can be circulated.
Front heat transfer plate (408), also containing channels capable of being &lled with a flowable heat transfer medium, is contacted with front glass plate (412). Pump (416) circulates the flowable heat transfer medium from reservoir (420) through front and back heat transfer plates (400 and 408). Heat is removed from the circulating flowable heat transfer medium by passing it through heat exchanger (424), thereby cooling the flowable heat transfer medium to ambient temperature. If superambient heating or subambient cooling of the gels is desired for a specific application, the ffowable heat transfer medium passes through a heater or cooler (not shown) before flowing through the heat transfer plates. Active temperature control of the gel is effected by means of temperature sensors (430) mounted to the heat transfer plates in combination with computer (434) which regulates the temperature of the plates by controlling the flow rate of the flowable heat transfer medium through the heat transfer plates.
Although the invention has been illustrated by the foregoing description it is not to be construed as being limited to the materials employed therein but rather the invention is directed to the generic area as hereinbefore disclosed. Various modifications and embodiments thereof can be made without departing from the spirit or scope thereof.
Claims (14)
- We claim:
I . An improved real-time scanning fluorescence electrophoresis apparatus for the electrophoretic analysis of fluorescently-labeled polynucleotide fragments of the type having an electrophoresis chamber containing an electrophoretic separation medium capable of accommodating multiple electrophoresis lanes arranged in a planar array, a fluorescence detector mounted on a translatable stage, a light source for exciting fluorescent molecules, and a computer for collecting data consisting of time, location, fluorescent wavelength and fluorescent intensity information wherein the improvement comprises:
(a) a spectral-array detector for detecting emission light from said fluorescently-labeled polynucleotide fragments including the simultaneous detection of multiple fluorescent labels, (b) a temperature control means to control the temperature of the electrophoretic separation medium during electrophoresis. - 2. The apparatus of claim 1 wherein the output of the spectral-array detector isprocessed so as to effect a virtual filter.
- 3. The apparatus of claim 2 wherein the wavelengths of said virtual filter are 540, 560, 580, and 610 nm, each 10 nm wide.
- 4. The apparatus of claim 2 wherein the wavelengths of said virtual filter are 530, 545, 560, 580 nm, each 10 nm wide.
- 5. The apparatus of claim 1 wherein the spectral-array detector comprises:
(a) a diffraction grating to separate the emission light, (b) a CCD array to detect the location and intensity of the separated emission light, (c) a laser excitation light source, (d) an optical arrangement to direct and condition the excitation and emission light in order to minimize the amount of scattered excitation light reaching the detector. - 6. The spectral-array detector of claim 5 having an optical arrangement comprising:
(a) turning mirrors which direct the laser light to a desired location, (b) telescopic lenses which focus the laser light to a position within the electophoresis chamber, (c) a bending mirror that directs the laser light at a right angles to the electrophoresis chamber, (d) an aspheric collection lens that collimates the fluorescence emission light in the direction of the detector, (e) a set of laser rejection filters that reduce the level of extraneous laser light entering the detector, and, (f) a plano-convex lens which focuses the emission light at a desired location - 7. The apparatus of claim 1 wherein the temperature control means comprises thermally controlled front and back heat transfer plates which are in contact with a front and back face of the electrophoresis chamber.
- 8. The apparatus of claim 7 wherein the front and back heat transfer plates are made from coated aluminum wherein the coating acts to electrically insulate the heat transfer plates from the electrophoresis voltage.
- 9. The apparatus of claim 7 wherein the temperature control means comprises:
(a) a front heat transfer plate placed in contact with a front face of the electrophoresis chamber, wherein flow channels are formed within the front heat transfer plate including inlet and outlet ports, (b) a back heat transfer plate placed in contact with a back face of the electrophoresis chamber, wherein flow channels are formed within the front heat transfer plate including inlet and outlet ports, (c) a flowable heat transfer medium which is circulated through the flow channels in the front and back heat transfer plates, (d) a pump to circulate the flowable heat transfer medium, (e) a heat exchanger in which the flowable heat transfer medium can exchange heat with the ambient atmosphere, (f) a computer for controlling the temperature of the heat transfer plates by controlling the flow of the circulating heat transfer medium, (g) a temperature sensor in contact with the front and back heat transfer plates and electrically connected to the computer to relay temperature information to the computer. - 10. The apparatus of claim 9 wherein said heat exchanger is replaced by a coolerwherein the cooler cools the flowable heat transfer medium below the temperature of the ambient atmosphere
- 11. The apparatus of claim 9 wherein said heat exchanger is replaced by a heaterwhere n the heater heats the flowable heat transfer medium above the temperature of the ambient atmosphere.
- 12. The apparatus of claim 1 wherein the electrophoresis chamber comprises:
(a) front and a back glass plates, where the back plate is defined as the plate through which the excitation laser light enters the electrophoresis chamber, (b) two spacers which serve to maintain a uniform separation between the glass plates, spaced so as to provide a chamber thickness of from about 0.1 to about 1.0 mm, (c) a plate holder which can accommodate glass plates of varying lengths and which acts to support and secure said electrophoresis medium and wherein said plates are held firmly in place within the plate holder by clamps which keep the edges of tile plates sealed to prevent separation medium from leaking - 13. The apparatus of claim 12 having a plate locating mechanism which optimally positions the detection region of the electrophoresis chamber with respect to the detection optics.
- 14. The apparatus of claim 12 having a mirror coating applied to the inside-facing surface of the front plate so that the excitation laser light, after passing through the back plate and the electrophoresis chamber, strikes the mirror surface and is reflected back through the electrophoresis chamber, thereby exciting additional fluorophores whose light is then collected, resulting in an increased emitted light signal.
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US08/192,485 US5543026A (en) | 1994-02-07 | 1994-02-07 | Real-time scanning fluorescence electrophoresis apparatus for the analysis of polynucleotide fragments |
| US08/192,485 | 1994-02-07 | ||
| PCT/US1995/001353 WO1995021377A1 (en) | 1994-02-07 | 1995-01-31 | Improved real-time scanning fluorescence electrophoresis apparatus for the analysis of polynucleotide fragments |
Publications (2)
| Publication Number | Publication Date |
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| CA2179710A1 CA2179710A1 (en) | 1995-08-10 |
| CA2179710C true CA2179710C (en) | 2000-01-18 |
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| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA002179710A Expired - Fee Related CA2179710C (en) | 1994-02-07 | 1995-01-31 | Improved real-time scanning fluorescence electrophoresis apparatus for the analysis of polynucleotide fragments |
Country Status (8)
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| US (1) | US5543026A (en) |
| EP (1) | EP0744023B1 (en) |
| JP (2) | JP3003104B2 (en) |
| AT (1) | ATE157168T1 (en) |
| AU (1) | AU676964B2 (en) |
| CA (1) | CA2179710C (en) |
| DE (1) | DE69500580T2 (en) |
| WO (1) | WO1995021377A1 (en) |
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| US5936087A (en) | 1997-11-25 | 1999-08-10 | The Perkin-Elmer Corporation | Dibenzorhodamine dyes |
| US6583168B1 (en) | 1997-11-25 | 2003-06-24 | Applera Corporation | Sulfonated diarylrhodamine dyes |
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| US6413780B1 (en) | 1998-10-14 | 2002-07-02 | Abbott Laboratories | Structure and method for performing a determination of an item of interest in a sample |
| SE9804606D0 (en) * | 1998-12-30 | 1998-12-30 | Amersham Pharm Biotech Ab | Method and device for measuring labels in a carrier |
| US6558945B1 (en) | 1999-03-08 | 2003-05-06 | Aclara Biosciences, Inc. | Method and device for rapid color detection |
| AU1312502A (en) * | 2000-10-11 | 2002-04-22 | Pe Corp Ny | Fluorescent nucleobase conjugates having anionic linkers |
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| US20030136921A1 (en) * | 2002-01-23 | 2003-07-24 | Reel Richard T | Methods for fluorescence detection that minimizes undesirable background fluorescence |
| US20040091850A1 (en) * | 2002-11-08 | 2004-05-13 | Travis Boone | Single cell analysis of membrane molecules |
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| JP2550106B2 (en) * | 1987-10-30 | 1996-11-06 | 株式会社日立製作所 | Optical dispersion detection type electrophoretic device |
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| JP2901004B2 (en) * | 1989-04-12 | 1999-06-02 | 株式会社日立製作所 | DNA sequencing |
| US4975170A (en) * | 1990-03-29 | 1990-12-04 | Eastman Kodak Company | Back support for an electrophoresis gel plate assembly |
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1994
- 1994-02-07 US US08/192,485 patent/US5543026A/en not_active Expired - Lifetime
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1995
- 1995-01-31 DE DE69500580T patent/DE69500580T2/en not_active Expired - Lifetime
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- 1995-01-31 WO PCT/US1995/001353 patent/WO1995021377A1/en active IP Right Grant
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- 1995-01-31 EP EP95908153A patent/EP0744023B1/en not_active Expired - Lifetime
- 1995-01-31 AU AU16099/95A patent/AU676964B2/en not_active Ceased
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1999
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| DE69500580D1 (en) | 1997-09-25 |
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| JPH09505669A (en) | 1997-06-03 |
| AU1609995A (en) | 1995-08-21 |
| JP2000137022A (en) | 2000-05-16 |
| JP3111064B2 (en) | 2000-11-20 |
| WO1995021377A1 (en) | 1995-08-10 |
| US5543026A (en) | 1996-08-06 |
| ATE157168T1 (en) | 1997-09-15 |
| CA2179710A1 (en) | 1995-08-10 |
| AU676964B2 (en) | 1997-03-27 |
| EP0744023A1 (en) | 1996-11-27 |
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