Methods and apparatus for analyzing polynucleotide sequences by asynchronous base extension
First Claim
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1. A method of analyzing sequence of a target polynucleotide, comprising:
- (a) providing a primed target polynucleotide comprising a substantially complementary fluorescently labeled primer and a target polynucleotide, the primed target polynucleotide being immobilized to a substrate comprising a polyelectrolyte coated multilayer surface, wherein the target polynucleotide is randomly attached to the polyelectrolyte multilayer coated surface with single molecule resolution;
(b) adding a first fluorescently labeled nucleotide to the surface of the substrate under conditions whereby the first nucleotide is added to the primer;
(c) determining whether a fluorescence signal from the fluorescently labeled nucleotide is present in at least one molecule of the primed target polynucleotide on the surface of the substrate, wherein the presence of the signal from the fluorescently labeled nucleotide indicates that the fluorescent nucleotide is added to the primer;
(d) removing the fluorescent signal from the fluorescently labeled nucleotide; and
(e) repeating steps (b)-(d) with a further fluorescently labeled nucleotide, thereby analyzing the sequence of the target polynucleotide, wherein if the primer label and the nucleotide label are the same, detecting and then bleaching the fluorescent signal from the primer label prior to adding the first fluorescently labeled nucleotide.
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Abstract
The invention provides methods and apparatus for analyzing polynucleotide sequences by asynchronous base extension. Some applications of the invention utilize total internal reflection fluorescence microscopy to image polynucleotide molecules at single molecule resolution.
701 Citations
24 Claims
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1. A method of analyzing sequence of a target polynucleotide, comprising:
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(a) providing a primed target polynucleotide comprising a substantially complementary fluorescently labeled primer and a target polynucleotide, the primed target polynucleotide being immobilized to a substrate comprising a polyelectrolyte coated multilayer surface, wherein the target polynucleotide is randomly attached to the polyelectrolyte multilayer coated surface with single molecule resolution; (b) adding a first fluorescently labeled nucleotide to the surface of the substrate under conditions whereby the first nucleotide is added to the primer; (c) determining whether a fluorescence signal from the fluorescently labeled nucleotide is present in at least one molecule of the primed target polynucleotide on the surface of the substrate, wherein the presence of the signal from the fluorescently labeled nucleotide indicates that the fluorescent nucleotide is added to the primer; (d) removing the fluorescent signal from the fluorescently labeled nucleotide; and (e) repeating steps (b)-(d) with a further fluorescently labeled nucleotide, thereby analyzing the sequence of the target polynucleotide, wherein if the primer label and the nucleotide label are the same, detecting and then bleaching the fluorescent signal from the primer label prior to adding the first fluorescently labeled nucleotide. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
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18. A method of analyzing sequence of a target polynucleotide, comprising:
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(a) providing a primed target polynucleotide comprising a substantially complementary fluorescently labeled primer and a target polynucleotide, the primed target polynucleotide being immobilized to a substrate comprising a coated surface, wherein the target polynucleotide is randomly attached to the surface with single molecule resolution; (b) adding four types of nucleotides to the surface of the substrate under conditions whereby nucleotides are added to the primer dynamically, at least one type of nucleotide being fluorescently labeled; and (c) monitoring a time course of fluorescent signal from addition of at least one fluorescent nucleotide to the primer, thereby analyzing the sequence of the target polynucleotide, wherein if the primer label and the nucleotide label are the same, detecting and then bleaching the signal from the primer label prior to adding the four types of nucleotides. - View Dependent Claims (19, 20, 21, 22, 23, 24)
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Specification