Identifying a base in a nucleic acid
AssigneeAffymetrix, Inc.
InventorsStephen P.A. Fodor, Robert J. Lipshutz, Xiaohua Huang
Life of this patent
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Abstract
Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.
Claims24
A method of sequencing a target nucleic acid with a plurality of nucleic acid probes, said probes having fewer bases than said target, comprising the steps of:
- contacting said probes with said target;
- identifying a first probe that specifically hybridizes to said target;
- selecting a first set of extension probes that comprise at least two of A, C, T, U, and G extensions of said first probe;
- and
- identifying one of said first set of extension probes that hybridizes specifically to said target more strongly than others of said first set of extension probes, whereby said one of said extension probes identifies a base in said target nucleic acid.
A method of determining if a nucleotide sequence of a target nucleic acid is the same as a sequence of a first nucleic acid comprising:
- contacting said target nucleic acid to a plurality of nucleic acid probes;
- determining the affinity of said target to probes identical to, but for a single base mismatch, of said subsequence;
- and
- determining that said nucleotide sequence of said target is the same as said first nucleic acid if said affinity of said target to probes identical to but for a single base mismatch follows a predetermined pattern.
A probe array of nucleic acids, said probe array selected from all possible probes to comprise an exact complement to a target nucleic acid, and single base mismatches of said exact complement.
A nucleic acid probe kit comprising a core nucleic acid probe, said core probe exactly complementary to a nucleic acid target, and selected A, C, T, U, and G single base substitutions of said core probe.
Dependencies are inferred from the claim text.