US5846727A
Expired / Lapsed
US
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Microsystem for rapid DNA sequencing
Assignee: Louisiana State University
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Filing: 1997-05-29
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Granted: 1998-12-08
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Expires: 2017-05-29
Abstract
Abstract A system is disclosed for the rapid and cost-effective sequencing of DNA. There are three principal components of the system: (1) a microreactor, which prepares DNA sequencing "ladders" using solid-phase techniques, preferably in capillary tubes whose volumes are on the order of 10-1000 nanoliters, preferably 10-200 nanoliters; (2) a microfabricated electrophoresis capillary separation unit; and (3) a fluorescence detector with single-mode optical fibers interfaced directly to the electrophoresis capillary. The system is suitable for a highly multiplexed, automated DNA sequencing device Typical. steps in sequencing are as follows: (1) PCR amplification of a DNA template in microtiter dishes using labelled primers, e.g., primers labelled with biotin; (2) immobilizing the labelled PCR products on the walls of one or more capillary tubes having volumes on the order of 10-200 nanoliters; (3) preparing nanoliter quantities of labelled Sanger extension products of the amplified DNA; (4) purifying the oligonucleotide sequencing ladders; (5) high speed electrophoretic separation of the sequencing ladders; and (6) near-infrared, laser-induced fluorescence detection of the oligonucleotides. Base-calling is preferably performed in a single lane format with a single fluorophore, in which the bases are distinguished by different fluorescence lifetimes of dyes that otherwise have similar absorption and fluorescence emission spectra at the wavelengths used. Typical read lengths are on the order of 400-500 bases. Fluorescence is performed on-chip with one single-mode optical fiber carrying the excitation light to the capillary channel, and a second single-mode optical fiber collecting the fluorescent photons. Only sub-microliter volumes of expensive sequencing reagents and dye-labeled ddNTPs are required in this system.
Inventors
- 👤 Steven A. Soper
- 👤 Jack D. Davies
- 👤 Yuli Vladimirsky
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-11-02 02:11
CPC Classifications
B; B01; B01L; B01L7/00; B01L7/52; B01J; B01J19/00; B01J19/0093; C; C07; C07H; C07H21/00; C12; C12Q; C12Q1/00; C12Q1/68; C12Q1/6869; B01L2200/00; B01L2200/10; B01L2300/00; B01L2300/08; B01L2300/0809; B01L2300/0819; B01L2400/00; B01L2400/04; B01L2400/0403; B01L2400/0415; B01L2400/0421; B01L3/00; B01L3/50; B01L3/502; B01L3/5027; B01L3/502753
Claims Analysis
Total Claims: 51
Claim 1
Independent Claim
230 words
A method for sequencing DNA, comprising the sequential steps of: (a) covalently linking the DNA to a first compound; (b) transferring the DNA into a capillary having a volume less than about 1 μL, wherein a second compound is bound to the inner wall of the capillary, wherein the first compound binds to the second compound with high affinity, whereby the DNA becomes immobilized on the inner wall of the capillary; (c) synthesizing oligonucleotides complementary to all or a portion of the immobilized DNA with a DNA polymerase and DNA primers; wherein the oligonucleotides are substantially identical to one another, except that the 3' ends of the oligonucleotides are a variable distance from a common 5' end, so that the oligonucleotides have variable lengths; wherein the terminal nucleotide base on the 3' end of the oligonucleotides is linked to one of four labels that is spectroscopically detectable, and that identifies the nucleotide base to which it is linked; and wherein the oligonucleotides are synthesized within the capillary containing the immobilized DNA; (d) transferring the oligonucleotides to a microfabricated capillary electrophoresis column, and electrophoretically separating the oligonucleotides within the column by size; and (e) spectroscopically detecting and identifying the labels linked to the electrophoretically separated oligonucleotides; whereby the order in which the labels of the electrophoresed oligonucleotides are detected corresponds to the sequence of at least a portion of the DNA.
Claim 2
Independent Claim
230 words
A method for sequencing DNA, comprising the sequential steps of: (a) covalently linking the DNA to a first compound; (b) transferring the DNA into a capillary having a volume less than about 1 μL, wherein a second compound is bound to the inner wall of the capillary, wherein the first compound binds to the second compound with high affinity, whereby the DNA becomes immobilized on the inner wall of the capillary; (c) synthesizing oligonucleotides complementary to all or a portion of the immobilized DNA with a DNA polymerase and DNA primers; wherein the oligonucleotides are substantially identical to one another, except that the 3' ends of the oligonucleotides are a variable distance from a common 5' end, so that the oligonucleotides have variable lengths; wherein the terminal nucleotide base on the 3' end of the oligonucleotides is linked to one of four labels that is spectroscopically detectable, and that identifies the nucleotide base to which it is linked; and wherein the oligonucleotides are synthesized within the capillary containing the immobilized DNA; (d) transferring the oligonucleotides to a microfabricated capillary electrophoresis column, and electrophoretically separating the oligonucleotides within the column by size; and (e) spectroscopically detecting and identifying the labels linked to the electrophoretically separated oligonucleotides; whereby the order in which the labels of the electrophoresed oligonucleotides are detected corresponds to the sequence of at least a portion of the DNA.
Claim 3
Dependent Claim
39 words
A method as recited in claim 1, wherein the first compound comprises biotin, and wherein the second compound comprises biotin that is bound to the inner wall of the capillary and that is also bound to avidin or streptavidin.
Claim 4
Dependent Claim
120 words
A method as recited in claim 2, wherein the method is repeated to sequence new DNA after the original DNA is sequenced; and wherein between the two repetitions of the method the following sequential steps occur: (a) removing the original DNA from the capillary by denaturing the avidin or streptavidin without denaturing the biotin, and then flushing the original DNA and denatured avidin or streptavidin from the capillary; whereby biotin remains bound to the inner wall of the capillary; and (b) transferring new avidin or streptavidin into the capillary, whereby the avidin or streptavidin binds to the biotin on the inner wall of the capillary, whereby the capillary is regenerated to be able to bind new DNA linked to biotin.
Claim 5
Dependent Claim
28 words
A method as recited in claim 1, wherein the first compound comprises an antigen, and wherein the second compound comprises a monoclonal antibody that specifically binds the antigen.
Claim 6
Dependent Claim
24 words
A method as recited in claim 1, wherein the capillary in which the DNA is immobilized has a volume less than about 200 nanoliters.
Claim 7
Dependent Claim
20 words
A method as recited in claim 1, wherein said synthesizing step comprises synthesizing oligonucleotides whose variable end comprises labelled dideoxynucleotides.
Claim 8
Dependent Claim
22 words
A method as recited in claim 1, wherein said spectroscopic detecting and identifying step comprises measuring near-infrared laser-induced fluorescence of the labels.
Claim 9
Dependent Claim
78 words
A method as recited in claim 7, wherein the four labels that identify the nucleotide bases are each near-infrared fluorophores; wherein the near-infrared absorption maxima of each of the four fluorophores are similar; wherein the near-infrared fluorescence maxima of each of the four fluorophores are similar; wherein the fluorescence lifetimes of each of the four fluorophores are different; and wherein the labels linked to the electrophoretically separated oligonucleotides are identified by measuring the fluorescence lifetimes of the labels.
Claim 10
Dependent Claim
85 words
A method as recited in claim 7, wherein said spectroscopic detecting and identifying step comprises transmitting near-infrared laser light through a first single-mode optic fiber to excite the labels of the electrophoretically separated oligonucleotides; and collecting near-infrared fluorescent photons from the labels with a second single-mode optic fibers; wherein the two optic fibers are positioned at approximately 90° relative to one another; and wherein each of the two optic fibers is positioned at approximately 90° relative to the direction of electrophoretic travel of the oligonucleotides.
Claim 11
Dependent Claim
28 words
A method as recited in claim 1, wherein the rate of DNA sequencing of said method is at least about 20 bases per capillary electrophoresis column per minute.
Claim 12
Dependent Claim
28 words
A method as recited in claim 1, wherein the capillary electrophoresis column is fabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge.
Claim 13
Dependent Claim
14 words
A method as recited in claim 11, wherein the x-ray resist comprises a polyacrylate.
Claim 14
Dependent Claim
14 words
A method as recited in claim 12, wherein the x-ray resist comprises poly(methyl methacrylate).
Claim 15
Dependent Claim
15 words
A method as recited in claim 11, wherein the x-ray resist comprises a poly(diene sulfone).
Claim 16
Dependent Claim
14 words
A method as recited in claim 14, wherein the x-ray resist comprises poly(1,3-hexadiene sulfone).
Claim 17
Dependent Claim
15 words
A method as recited in claim 11, wherein the x-ray resist comprises a poly(olefin sulfone).
Claim 18
Dependent Claim
13 words
A method as recited in claim 16, wherein the x-ray resist comprises poly(butene-1-sulfone).
Claim 19
Dependent Claim
15 words
A method as recited in claim 11, wherein the x-ray resist comprises an epoxy resist.
Claim 20
Dependent Claim
20 words
A method as recited in claim 18, wherein the x-ray resist comprises a copolymer of glycidyl methacrylate and ethyl acrylate.
Claim 21
Independent Claim
256 words
An apparatus for sequencing DNA, using first and second compounds that bind to one another with high affinity, said apparatus comprising: (a) a capillary having a volume less than about 200 nanoliters, wherein the inner wall of said capillary binds or is capable of binding the second compound, and wherein said capillary is adapted to immobilize DNA that is linked to the first compound by allowing the first and second compounds to bind to one another, whereby the DNA becomes immobilized on the inner wall of said capillary; wherein said capillary is capable of acting as a reaction vessel for synthesizing, within said capillary, oligonucleotides complementary to all or a portion of the immobilized DNA with a DNA polymerase and DNA primers; wherein the oligonucleotides are substantially identical to one another, except that the 3' ends of the oligonucleotides are a variable distance from a common 5' end, so that the oligonucleotides have variable lengths; and wherein the terminal nucleotide base on the 3' end of the oligonucleotides is linked to a label that is spectroscopically detectable, and that identifies the nucleotide base to which it is linked; (b) a microfabricated capillary electrophoresis column connected to said capillary to receive the synthesized oligonucleotides, and to electrophoretically separate the oligonucleotides within the column by size; and (c) a detector to spectroscopically detect and identify the labels linked to the electrophoretically separated oligonucleotides; whereby the order in which the labels of the electrophoresed oligonucleotides are detected corresponds to the sequence of at least a portion of the DNA.
Claim 22
Independent Claim
256 words
An apparatus for sequencing DNA, using first and second compounds that bind to one another with high affinity, said apparatus comprising: (a) a capillary having a volume less than about 200 nanoliters, wherein the inner wall of said capillary binds or is capable of binding the second compound, and wherein said capillary is adapted to immobilize DNA that is linked to the first compound by allowing the first and second compounds to bind to one another, whereby the DNA becomes immobilized on the inner wall of said capillary; wherein said capillary is capable of acting as a reaction vessel for synthesizing, within said capillary, oligonucleotides complementary to all or a portion of the immobilized DNA with a DNA polymerase and DNA primers; wherein the oligonucleotides are substantially identical to one another, except that the 3' ends of the oligonucleotides are a variable distance from a common 5' end, so that the oligonucleotides have variable lengths; and wherein the terminal nucleotide base on the 3' end of the oligonucleotides is linked to a label that is spectroscopically detectable, and that identifies the nucleotide base to which it is linked; (b) a microfabricated capillary electrophoresis column connected to said capillary to receive the synthesized oligonucleotides, and to electrophoretically separate the oligonucleotides within the column by size; and (c) a detector to spectroscopically detect and identify the labels linked to the electrophoretically separated oligonucleotides; whereby the order in which the labels of the electrophoresed oligonucleotides are detected corresponds to the sequence of at least a portion of the DNA.
Claim 23
Independent Claim
342 words
An apparatus for sequencing DNA, using first and second compounds that bind to one another with high affinity, said apparatus comprising: (a) a capillary having a volume less than about 1 μL, wherein the inner wall of said capillary binds or is capable of binding the second compound, and wherein said capillary is adapted to immobilize DNA that is linked to the first compound by allowing the first and second compounds to bind to one another, whereby the DNA becomes immobilized on the inner wall of said capillary; wherein said capillary is capable of acting as a reaction vessel for synthesizing, within said capillary, oligonucleotides complementary to all or a portion of the immobilized DNA with a DNA polymerase and DNA primers; wherein the oligonucleotides are substantially identical to one another, except that the 3' ends of the oligonucleotides are a variable distance from a common 5' end, so that the oligonucleotides have variable lengths; and wherein the terminal nucleotide base on the 3' end of the oligonucleotides is linked to a label that is spectroscopically detectable, and that identifies the nucleotide base to which it is linked; (b) a microfabricated capillary electrophoresis column connected to said capillary to receive the synthesized oligonucleotides, and to electrophoretically separate the oligonucleotides within the column by size; and (c) a detector to spectroscopically detect and identify the labels linked to the electrophoretically separated oligonucleotides; wherein said detector comprises a first single-mode optic fiber to transmit near-infrared laser light through the electrophoretically separated oligonucleotides to excite the labels of the electrophoretically separated oligonucleotides; and a second single-mode optic fiber to collect near-infrared fluorescent photons from the labels on the electrophoretically separated oligonucleotides; wherein the two said optic fibers are positioned at approximately 90° relative to one another; and wherein each of the two said optic fibers is positioned at approximately 90° relative to the direction of electrophoretic travel of the oligonucleotides; whereby the order in which the labels of the electrophoresed oligonucleotides are detected corresponds to the sequence of at least a portion of the DNA.
Claim 24
Independent Claim
342 words
An apparatus for sequencing DNA, using first and second compounds that bind to one another with high affinity, said apparatus comprising: (a) a capillary having a volume less than about 1 μL, wherein the inner wall of said capillary binds or is capable of binding the second compound, and wherein said capillary is adapted to immobilize DNA that is linked to the first compound by allowing the first and second compounds to bind to one another, whereby the DNA becomes immobilized on the inner wall of said capillary; wherein said capillary is capable of acting as a reaction vessel for synthesizing, within said capillary, oligonucleotides complementary to all or a portion of the immobilized DNA with a DNA polymerase and DNA primers; wherein the oligonucleotides are substantially identical to one another, except that the 3' ends of the oligonucleotides are a variable distance from a common 5' end, so that the oligonucleotides have variable lengths; and wherein the terminal nucleotide base on the 3' end of the oligonucleotides is linked to a label that is spectroscopically detectable, and that identifies the nucleotide base to which it is linked; (b) a microfabricated capillary electrophoresis column connected to said capillary to receive the synthesized oligonucleotides, and to electrophoretically separate the oligonucleotides within the column by size; and (c) a detector to spectroscopically detect and identify the labels linked to the electrophoretically separated oligonucleotides; wherein said detector comprises a first single-mode optic fiber to transmit near-infrared laser light through the electrophoretically separated oligonucleotides to excite the labels of the electrophoretically separated oligonucleotides; and a second single-mode optic fiber to collect near-infrared fluorescent photons from the labels on the electrophoretically separated oligonucleotides; wherein the two said optic fibers are positioned at approximately 90° relative to one another; and wherein each of the two said optic fibers is positioned at approximately 90° relative to the direction of electrophoretic travel of the oligonucleotides; whereby the order in which the labels of the electrophoresed oligonucleotides are detected corresponds to the sequence of at least a portion of the DNA.
Claim 25
Independent Claim
285 words
An apparatus for sequencing DNA, using first and second compounds that bind to one another with high affinity, said apparatus comprising: (a) a capillary having a volume less than about 1 μL, wherein the inner wall of said capillary binds or is capable of binding the second compound, and wherein said capillary is adapted to immobilize DNA that is linked to the first compound by allowing the first and second compounds to bind to one another, whereby the DNA becomes immobilized on the inner wall of said capillary; wherein said capillary is capable of acting as a reaction vessel for synthesizing, within said capillary, oligonucleotides complementary to all or a portion of the immobilized DNA with a DNA polymerase and DNA primers; wherein the oligonucleotides are substantially identical to one another, except that the 3' ends of the oligonucleotides are a variable distance from a common 5' end, so that the oligonucleotides have variable lengths; and wherein the terminal nucleotide base on the 3' end of the oligonucleotides is linked to a label that is spectroscopically detectable, and that identifies the nucleotide base to which it is linked; (b) a microfabricated capillary electrophoresis column connected to said capillary to receive the synthesized oligonucleotides, and to electrophoretically separate the oligonucleotides within the column by size, wherein said capillary electrophoresis column is fabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises a polyacrylate; and (c) a detector to spectroscopically detect and identify the labels linked to the electrophoretically separated oligonucleotides; whereby the order in which the labels of the electrophoresed oligonucleotides are detected corresponds to the sequence of at least a portion of the DNA.
Claim 26
Independent Claim
285 words
An apparatus for sequencing DNA, using first and second compounds that bind to one another with high affinity, said apparatus comprising: (a) a capillary having a volume less than about 1 μL, wherein the inner wall of said capillary binds or is capable of binding the second compound, and wherein said capillary is adapted to immobilize DNA that is linked to the first compound by allowing the first and second compounds to bind to one another, whereby the DNA becomes immobilized on the inner wall of said capillary; wherein said capillary is capable of acting as a reaction vessel for synthesizing, within said capillary, oligonucleotides complementary to all or a portion of the immobilized DNA with a DNA polymerase and DNA primers; wherein the oligonucleotides are substantially identical to one another, except that the 3' ends of the oligonucleotides are a variable distance from a common 5' end, so that the oligonucleotides have variable lengths; and wherein the terminal nucleotide base on the 3' end of the oligonucleotides is linked to a label that is spectroscopically detectable, and that identifies the nucleotide base to which it is linked; (b) a microfabricated capillary electrophoresis column connected to said capillary to receive the synthesized oligonucleotides, and to electrophoretically separate the oligonucleotides within the column by size, wherein said capillary electrophoresis column is fabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises a polyacrylate; and (c) a detector to spectroscopically detect and identify the labels linked to the electrophoretically separated oligonucleotides; whereby the order in which the labels of the electrophoresed oligonucleotides are detected corresponds to the sequence of at least a portion of the DNA.
Claim 27
Dependent Claim
14 words
An apparatus as recited in claim 22, wherein the x-ray resist comprises poly(methyl methacrylate).
Claim 28
Independent Claim
286 words
An apparatus for sequencing DNA, using first and second compounds that bind to one another with high affinity, said apparatus comprising: (a) a capillary having a volume less than about 1 μL, wherein the inner wall of said capillary binds or is capable of binding the second compound, and wherein said capillary is adapted to immobilize DNA that is linked to the first compound by allowing the first and second compounds to bind to one another, whereby the DNA becomes immobilized on the inner wall of said capillary; wherein said capillary is capable of acting as a reaction vessel for synthesizing, within said capillary, oligonucleotides complementary to all or a portion of the immobilized DNA with a DNA polymerase and DNA primers; wherein the oligonucleotides are substantially identical to one another, except that the 3' ends of the oligonucleotides are a variable distance from a common 5' end, so that the oligonucleotides have variable lengths; and wherein the terminal nucleotide base on the 3' end of the oligonucleotides is linked to a label that is spectroscopically detectable, and that identifies the nucleotide base to which it is linked; (b) a microfabricated capillary electrophoresis column connected to said capillary to receive the synthesized oligonucleotides, and to electrophoretically separate the oligonucleotides within the column by size, wherein said capillary electrophoresis column is fabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises a poly(diene sulfone); and (c) a detector to spectroscopically detect and identify the labels linked to the electrophoretically separated oligonucleotides; whereby the order in which the labels of the electrophoresed oligonucleotides are detected corresponds to the sequence of at least a portion of the DNA.
Claim 29
Independent Claim
286 words
An apparatus for sequencing DNA, using first and second compounds that bind to one another with high affinity, said apparatus comprising: (a) a capillary having a volume less than about 1 μL, wherein the inner wall of said capillary binds or is capable of binding the second compound, and wherein said capillary is adapted to immobilize DNA that is linked to the first compound by allowing the first and second compounds to bind to one another, whereby the DNA becomes immobilized on the inner wall of said capillary; wherein said capillary is capable of acting as a reaction vessel for synthesizing, within said capillary, oligonucleotides complementary to all or a portion of the immobilized DNA with a DNA polymerase and DNA primers; wherein the oligonucleotides are substantially identical to one another, except that the 3' ends of the oligonucleotides are a variable distance from a common 5' end, so that the oligonucleotides have variable lengths; and wherein the terminal nucleotide base on the 3' end of the oligonucleotides is linked to a label that is spectroscopically detectable, and that identifies the nucleotide base to which it is linked; (b) a microfabricated capillary electrophoresis column connected to said capillary to receive the synthesized oligonucleotides, and to electrophoretically separate the oligonucleotides within the column by size, wherein said capillary electrophoresis column is fabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises a poly(diene sulfone); and (c) a detector to spectroscopically detect and identify the labels linked to the electrophoretically separated oligonucleotides; whereby the order in which the labels of the electrophoresed oligonucleotides are detected corresponds to the sequence of at least a portion of the DNA.
Claim 30
Dependent Claim
14 words
An apparatus as recited in claim 24, wherein the x-ray resist comprises poly(1,3-hexadiene sulfone).
Claim 31
Independent Claim
284 words
An apparatus for sequencing DNA, using first and second compounds that bind to one another with high affinity, said apparatus comprising: (a) a capillary having a volume less than about 1 μL, wherein the inner wall of said capillary binds or is capable of binding the second compound, and wherein said capillary is adapted to immobilize DNA that is linked to the first compound by allowing the first and second compounds to bind to one another, whereby the DNA becomes immobilized on the inner wall of said capillary; wherein said capillary is capable of acting as a reaction vessel for synthesizing, within said capillary, oligonucleotides complementary to all or a portion of the immobilized DNA with a DNA polymerase and DNA primers; wherein the oligonucleotides are substantially identical to one another, except that the 3' ends of the oligonucleotides are a variable distance from a common 5' end, so that the oligonucleotides have variable lengths; and wherein the terminal nucleotide base on the 3' end of the oligonucleotides is linked to a label that is spectroscopically detectable, and that identifies the nucleotide base to which it is linked; (b) a microfabricated capillary electrophoresis column connected to said capillary to receive the synthesized oligonucleotides, and to electrophoretically separate the oligonucleotides within the column by size, wherein said capillary electrophoresis column is fabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises poly(butene-1-sulfone); and (c) a detector to spectroscopically detect and identify the labels linked to the electrophoretically separated oligonucleotides; whereby the order in which the labels of the electrophoresed oligonucleotides are detected corresponds to the sequence of at least a portion of the DNA.
Claim 32
Independent Claim
284 words
An apparatus for sequencing DNA, using first and second compounds that bind to one another with high affinity, said apparatus comprising: (a) a capillary having a volume less than about 1 μL, wherein the inner wall of said capillary binds or is capable of binding the second compound, and wherein said capillary is adapted to immobilize DNA that is linked to the first compound by allowing the first and second compounds to bind to one another, whereby the DNA becomes immobilized on the inner wall of said capillary; wherein said capillary is capable of acting as a reaction vessel for synthesizing, within said capillary, oligonucleotides complementary to all or a portion of the immobilized DNA with a DNA polymerase and DNA primers; wherein the oligonucleotides are substantially identical to one another, except that the 3' ends of the oligonucleotides are a variable distance from a common 5' end, so that the oligonucleotides have variable lengths; and wherein the terminal nucleotide base on the 3' end of the oligonucleotides is linked to a label that is spectroscopically detectable, and that identifies the nucleotide base to which it is linked; (b) a microfabricated capillary electrophoresis column connected to said capillary to receive the synthesized oligonucleotides, and to electrophoretically separate the oligonucleotides within the column by size, wherein said capillary electrophoresis column is fabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises poly(butene-1-sulfone); and (c) a detector to spectroscopically detect and identify the labels linked to the electrophoretically separated oligonucleotides; whereby the order in which the labels of the electrophoresed oligonucleotides are detected corresponds to the sequence of at least a portion of the DNA.
Claim 33
Independent Claim
286 words
An apparatus for sequencing DNA, using first and second compounds that bind to one another with high affinity, said apparatus comprising: (a) a capillary having a volume less than about 1 μL, wherein the inner wall of said capillary binds or is capable of binding the second compound, and wherein said capillary is adapted to immobilize DNA that is linked to the first compound by allowing the first and second compounds to bind to one another, whereby the DNA becomes immobilized on the inner wall of said capillary; wherein said capillary is capable of acting as a reaction vessel for synthesizing, within said capillary, oligonucleotides complementary to all or a portion of the immobilized DNA with a DNA polymerase and DNA primers; wherein the oligonucleotides are substantially identical to one another, except that the 3' ends of the oligonucleotides are a variable distance from a common 5' end, so that the oligonucleotides have variable lengths; and wherein the terminal nucleotide base on the 3' end of the oligonucleotides is linked to a label that is spectroscopically detectable, and that identifies the nucleotide base to which it is linked; (b) a microfabricated capillary electrophoresis column connected to said capillary to receive the synthesized oligonucleotides, and to electrophoretically separate the oligonucleotides within the column by size, wherein said capillary electrophoresis column is fabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises an epoxy resist; and (c) a detector to spectroscopically detect and identify the labels linked to the electrophoretically separated oligonucleotides; whereby the order in which the labels of the electrophoresed oligonucleotides are detected corresponds to the sequence of at least a portion of the DNA.
Claim 34
Independent Claim
286 words
An apparatus for sequencing DNA, using first and second compounds that bind to one another with high affinity, said apparatus comprising: (a) a capillary having a volume less than about 1 μL, wherein the inner wall of said capillary binds or is capable of binding the second compound, and wherein said capillary is adapted to immobilize DNA that is linked to the first compound by allowing the first and second compounds to bind to one another, whereby the DNA becomes immobilized on the inner wall of said capillary; wherein said capillary is capable of acting as a reaction vessel for synthesizing, within said capillary, oligonucleotides complementary to all or a portion of the immobilized DNA with a DNA polymerase and DNA primers; wherein the oligonucleotides are substantially identical to one another, except that the 3' ends of the oligonucleotides are a variable distance from a common 5' end, so that the oligonucleotides have variable lengths; and wherein the terminal nucleotide base on the 3' end of the oligonucleotides is linked to a label that is spectroscopically detectable, and that identifies the nucleotide base to which it is linked; (b) a microfabricated capillary electrophoresis column connected to said capillary to receive the synthesized oligonucleotides, and to electrophoretically separate the oligonucleotides within the column by size, wherein said capillary electrophoresis column is fabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises an epoxy resist; and (c) a detector to spectroscopically detect and identify the labels linked to the electrophoretically separated oligonucleotides; whereby the order in which the labels of the electrophoresed oligonucleotides are detected corresponds to the sequence of at least a portion of the DNA.
Claim 35
Dependent Claim
20 words
An apparatus as recited in claim 27, wherein the x-ray resist comprises a copolymer of glycidyl methacrylate and ethyl acrylate.
Claim 36
Dependent Claim
27 words
A capillary electrophoresis column microfabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises a polyacrylate.
Claim 37
Dependent Claim
27 words
A capillary electrophoresis column microfabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises a polyacrylate.
Claim 38
Dependent Claim
16 words
A capillary electrophoresis column as recited in claim 29, wherein the x-ray resist comprises poly(methyl methacrylate).
Claim 39
Dependent Claim
28 words
A capillary electrophoresis column microfabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises a poly(diene sulfone).
Claim 40
Dependent Claim
28 words
A capillary electrophoresis column microfabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises a poly(diene sulfone).
Claim 41
Dependent Claim
16 words
A capillary electrophoresis column as recited in claim 31, wherein the x-ray resist comprises poly(1,3-hexadiene sulfone).
Claim 42
Dependent Claim
26 words
A capillary electrophoresis column microfabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises poly(butene-1-sulfone).
Claim 43
Dependent Claim
26 words
A capillary electrophoresis column microfabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises poly(butene-1-sulfone).
Claim 44
Dependent Claim
28 words
A capillary electrophoresis column microfabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises an epoxy resist.
Claim 45
Dependent Claim
28 words
A capillary electrophoresis column microfabricated in an x-ray resist substrate, wherein the x-ray resist has no substantial surface charge, and wherein the x-ray resist comprises an epoxy resist.
Claim 46
Dependent Claim
22 words
A capillary electrophoresis column as recited in claim 34, wherein the x-ray resist comprises a copolymer of glycidyl methacrylate and ethyl acrylate.
Claim 47
Dependent Claim
83 words
A capillary micro-electrophoresis column comprising an integrated optical system for detecting a fluorescent component of a sample in said column, said integrated optical system comprising a first single mode optic fiber for delivering laser excitation light to the sample in said column, and a second single mode optic fiber for collecting fluorescent photons from the sample in said column and delivering the fluorescent photons to a detector, wherein said first and second optic fibers are positioned at approximately 90° relative to one another.
Claim 48
Dependent Claim
83 words
A capillary micro-electrophoresis column comprising an integrated optical system for detecting a fluorescent component of a sample in said column, said integrated optical system comprising a first single mode optic fiber for delivering laser excitation light to the sample in said column, and a second single mode optic fiber for collecting fluorescent photons from the sample in said column and delivering the fluorescent photons to a detector, wherein said first and second optic fibers are positioned at approximately 90° relative to one another.
Claim 49
Dependent Claim
34 words
A capillary electrophoresis column as recited in claim 36, additionally comprising a diode laser integrated into said optical system, wherein said diode laser is positioned to deliver excitation light to said first optic fiber.
Claim 50
Dependent Claim
34 words
A capillary electrophoresis column as recited in claim 36, additionally comprising a detector integrated into said optical system, wherein said detector is positioned to receive and detect fluorescence photons from said second optic fiber.
Claim 51
Dependent Claim
34 words
A capillary electrophoresis column as recited in claim 38, additionally comprising a diode laser integrated into said optical system, wherein said diode laser is positioned to deliver excitation light to said first optic fiber.
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USPTO Annuity & Maintenance Windows
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| 7.5 Years (Year 8) | 2005-12-07 | 2006-06-08 | 2006-12-08 | $3760.00 | Window Closed / Lapsed |
| 11.5 Years (Year 12) | 2009-12-07 | 2010-06-08 | 2010-12-08 | $7700.00 | Window Closed / Lapsed |