Sequencing a polynucleotide on a generic chip

• US 6,692,915 B1
• Filed: 07/20/2000
• Issued: 02/17/2004
• Est. Priority Date: 07/22/1999
• Status: Expired due to Fees

• Current Assignee: Girish N. Nallur
• Original Assignee: Girish N. Nallur
• Inventors: Nallur, Girish N.
• Primary Examiner(s): Brusca, John S.
• Assistant Examiner(s): ZHOU, SHUBO
• Application Number:
  US09/619,812
• Time in Patent Office: 1,307 Days
• Field of Search: 435/6, 435/91, 435/172.3, 435/320.1, 435/805, 702/19, 702/20, 436/501, 436/508, 436/538
• US Class Current: 435/6.15
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2525/301 Hairpin oligonucleotides
• CPC Class Codes: C12Q 2565/519 characterised by the capture moiety being a single stranded oligonucleotide
• CPC Class Codes: Y10S 436/815 Test for named compound or class of compounds

Abstract

The present invention describes methods and devices for sequencing a polynucleotide by determining subsets of composite subsequences present in nucleic acid subsamples generated from the sample polynucleotide. A hairpin primer interrogates the composite subsequences in a two-step process resulting first in a polymerase extended product whose synthesis identifies the first subsequence of the composite subsequence. The second subsequences are identified by hybridizing the polymerase extended products or amplified products therefrom to an array of capture probes wherein each capture probe is positionally distinguishable from other capture probes. The invention is applicable to the quantitative determination of the presence of nucleic acids in a sample, for identifying differences in the relative abundance of nucleic acids in a mixture of nucleic acids, and generally, to diagnostic aids for the identification of nucleic acids.

Claims

1. A method for identifying and quantifying a nucleic acid in a sample of nucleic acids, the method comprising:

(a) providing at least one of a plurality of subsequence sets present in the sample of nucleic acids, wherein each subsequence set comprises;

a first recognizable sequence;

a composite subsequence of nucleotides comprising a first subsequence and a second subsequence; and

a second recognizable sequence, such that;

the composite subsequence is adjacent to the first recognizable sequence and non adjacent to the second recognizable sequence;

the second recognizable sequence comprises a recognition site of a restriction endonuclease that cuts nucleic acids within the recognition site; and

the subsequence set is observed to be present in the sample of nucleic acids;

(b) digesting nucleic acids from the sample so as to provide at least one subsample of partially single-stranded nucleic acid fragments;

(c) determining the sequences of composite sequences located in the single-stranded portion of said partially single-stranded nucleic acid fragments in each subsample, by;

annealing the nucleic acid fragments with at least one species of a polynucleotide primer having a hairpin structure, wherein the hairpin primer comprises, from 5′

- to 3′

-direction;

a nucleic acid contacting region hybridizable to a first subsequence from at least one nucleic acid fragment from the subsample;

a first stem region;

a loop region;

a second stem region that is complementary to the first stem region; and

a second nucleic acid contacting region hybridizable to a second subsequence of the nucleic acid fragment from the subsample, to obtain a plurality of primed nucleic acid fragments wherein the first and second stem regions remain double-stranded after hybridization;

incubating the primed nucleic acid fragments with a DNA polymerase and at least two deoxyribonucleotide triphosphates under conditions promoting polymerization of nucleotides at the 3′

-terminus of the hairpin primer, so as to produce polymerase extended products and to determine the nucleotide sequence of the extended products;

(d) detecting the polymerase extended products;

(e) quantifying the polymerase extended products using any standard quantification method including fluorescent labeling, hapten labeling, and hybridization to similarly labeled complementary oligonucleotides; and

(f) searching a database of nucleic acid sequences in order to locate database sequences having the observed subsequence sets, the database nucleic acid sequences comprising nucleic acid sequences that might be present in the sample, and identifying the located database sequences as sequences of the subsequence sets nucleic acids present in the sample.

2. The method of claim 1, wherein the composite subsequence comprises a first subsequence adjacent to a second subsequence, such that:

the first subsequence may be contiguous to or is spaced apart from the second subsequence by at least one nucleotide having the same sequence and length in all subsets;

the second subsequence is spaced apart from the first recognizable sequence by a length of nucleotides at least equal to the number of nucleotides in the first subsequence; and

the second recognizable sequence is spaced apart from the composite subsequence by a variable number of nucleotides.

3. The method of claim 1, further comprising:

hybridizing the digested nucleic acids with adapter nucleic acids, the adapter nucleic acids being partially double stranded, each adapter nucleic acid being complementary to an end of the resulting restriction enzyme digested nucleic acid;

ligating the hybridized nucleic acids and adapter nucleic acids;

denaturing the nucleic acid fragments to produce single stranded fragments; and

incubating the single stranded fragments with at least one species of anchoring oligonucleotide under conditions that promote hybridization of the anchoring oligonucleotide with the single stranded fragments, wherein the anchoring oligonucleotide is a hybridizing primer that hybridizes adjacent to the composite subsequence.

4. A method of identifying a nucleic acid in a sample of nucleic acids, the method comprising:

(a) providing at least one of a plurality of subsequence sets present in the sample of nucleic acids, wherein each subsequence set comprises;

first and second recognizable sequences wherein the second recognizable sequence comprises a recognition site of a restriction endonuclease;

at least one composite subsequence adjacent to the first recognizable sequence and non-adjacent to the second recognizable sequence;

(b) digesting nucleic acids derived from the sample with an exonuclease so as to provide at least one subsample of partially single-stranded nucleic acid fragments derived from the nucleic acids in the sample;

(c) determining the sequences of composite subsequences located in the single-stranded portion of the partially single-stranded fragments in each subsample by;

annealing the nucleic acid fragments with at least one species of polynucleotide primer having a hairpin structure, wherein the hairpin primer comprises, from 5′

-to 3′

-direction;

a first nucleic acid contacting region hybridizable to a first subsequence from at least one nucleic acid fragment from the subsample;

a first stem region;

a loop region;

a second stem region that is complementary to the first stem region; and

a second nucleic acid contacting region hybridizable to a second subsequence of the at least one nucleic acid fragment from the subsample, to obtain a plurality of primed nucleic acid fragments wherein the first and second

stem regions remain double-stranded after hybridization; and

incubating the primed nucleic acid fragments with a DNA polymerase and at least two deoxyribonucleotide triphosphates under conditions promoting polymerization of nucleotides at the 3′

-terminus of the hairpin primer; and

(d) identifying polymerase extended products.

5. The method of claim 4, wherein digesting further comprises:

digesting the sample with at least one endonuclease whose recognition site has the second recognizable sequence; and

hybridizing the digested nucleic acids with adapter nucleic acids, the adapter nucleic acids being partially double stranded, each adapter nucleic acid being complementary to an end of the digested nucleic acid;

ligating the hybridized nucleic acids and adapter nucleic acids.

6. The method of claim 4, further comprising:

amplifying the polymerase extended products; and

detecting the polymerase extended products present in the subsample.

7. The method of claim 6, wherein the amplifying is selected from the group consisting of:

polymerase chain reaction, ligase chain reaction, rolling circle amplification, nucleic acid sequence based amplification, and strand displacement amplification.

8. The method of claim 6, wherein detecting further comprises sequencing at least a portion of the amplified products.

9. The method of claim 4, wherein the detecting further comprises the steps of:

hybridizing a plurality of species of a probe with the polymerase extended products, each of the species of probe capable of hybridizing with the polymerase extended products that have a particular sequence for at least a portion of the composite subsequence; and

analyzing which of the species of probe has hybridized with the polymerase extended products, thereby determining the composite subsequence.

10. The method of claim 9, wherein the plurality of species of probes are fixed on a surface such that each of the species of probe is positionally distinguishable from other of the plurality of probes fixed on the surface, to form a plurality of addressable capture molecules.

11. The method of claim 10, wherein the plurality of species of probes comprise a plurality of probe nucleotide sequences, each probe nucleotide sequence having a terminal nucleotide subsequence and a core nucleotide subsequence, wherein the step of hybridizing further comprises:

annealing the plurality of species of probes with the polymerase extended products and with a detector oligomer to form a hybridization structure, wherein the detector oligomer has a sequence that is complementary to a hybridizable portion of at least one of the polymerase extended products to form a plurality of annealed capture molecules; and

detecting the annealed capture molecules.

12. The method of claim 11, further comprising, after hybridizing and prior to detecting, ligating nicks in the hybridization structure.

13. The method of claim 10, wherein each of the species of the probes comprises a nucleotide sequence having a terminal nucleotide subsequence and a core nucleotide subsequence, wherein the hybridizing comprises:

annealing a plurality of species of probe with the products to form a hybridization structure;

incubating the hybridization structure with a polymerase and at least one deoxynucleotide triphosphate; and

detecting which of the probes is extended.

14. The method of claim 10, wherein each of the species of probe comprises a nucleotide sequence, wherein the nucleotide sequence is a sequence of interest, and wherein the hybridizing comprises:

annealing a plurality of species of probes with the polymerase extended products;

incubating with a polymerase and at least one species of deoxynucleotide triphosphates; and

detecting which of the plurality of species of probe is extended.

15. The method of claim 9, wherein the analyzing further comprises:

generating a detectable signal for each of the species of probes hybridized; and

quantifying the signal, thereby quantifying the nucleic acids present in the sample.

16. The method of claim 15, wherein the detectable signal generated at each of the species of probes is positionally distinguishable from other of the plurality of probes fixed on the surface.