DNA polymorphism identity determination using flow cytometry

• US 6,287,766 B1
• Filed: 10/28/1998
• Issued: 09/11/2001
• Est. Priority Date: 10/28/1997
• Status: Expired due to Term

• Current Assignee: TRIAD National Security, LLC
• Original Assignee: Regents of the University of California (University of California)
• Inventors: Cai, Hong, Nolan, John P., White, P. Scott
• Primary Examiner(s): WHISENANT, ETHAN C
• Application Number:
  US09/182,869
• Time in Patent Office: 1,049 Days
• Field of Search: 35/6, 35/76, 35/77, 35/78, 35/912, 36/231, 36/243
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 1/6862 Ligase chain reaction [LCR]
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2533/107 Probe or oligonucleotide ligation
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2563/131 the label being a member of a cognate binding pair, i.e. extends to antibodies, haptens, avidin
• CPC Class Codes: C12Q 2563/155 Particles of a defined size, e.g. nanoparticles
• CPC Class Codes: C12Q 2565/519 characterised by the capture moiety being a single stranded oligonucleotide
• CPC Class Codes: C12Q 2565/626 being a flow cytometer

Abstract

DNA polymorphism identity determination using flow cytometry. Primers designed to be immobilized on microspheres are allowed to anneal to the DNA strand under investigation, and are extended by either DNA polymerase using fluorescent dideoxynucleotides or ligated by DNA ligase to fluorescent reporter oligonucleotides. The fluorescence of either the dideoxynucleotide or the reporter oligonucleotide attached to the immobilized primer is measured by flow cytometry, thereby identifying the nucleotide polymorphism on the DNA strand.

Claims

1. A homogeneous method for determining the identity of a base on a DNA strand, which comprises in order the steps of:

(a) immobilizing an oligonucleotide which is capable of being annealed to the DNA strand immediately adjacent to the base whose identity is to be determined on a microsphere;

(b) annealing the oligonucleotide to the DNA strand;

(c) incubating the microspheres to which the DNA strand has annealed to the immobilized oligonucleotide with four different dideoxynucleotides, one of the dideoxynucleotides having a reporter molecule in the presence of an enzyme, thereby extending the immobilized oligonucleotide by one base unit; and

(d) analyzing the microsphere using flow cytometry whereby the identity of the base is determined.

2. The method as described in claim 1, wherein the reporter is fluorescent and the enzyme is a DNA polymerase.

3. The method as described in claim 1, wherein the oligonucleotide is biotinylated and the microsphere is coated with avidin or streptavidin.

4. The method as described in claim 1, wherein the microsphere is biotinylated and the oligonucleotide is coupled to avidin or streptavidin.

5. The method as described in claim 1, wherein the oligonucleotide is covalently attached to the microsphere.

6. The method as described in claim 1, wherein the oligonucleotide is hybridized to a complementary capture probe immobilized on a microsphere.

7. The method as described in claim 6, wherein the oligonucleotide comprises a sequence tag which is hybridized to the capture probe, and wherein the sequence tag and capture probe comprises a non-natural base selected from the group consisting of iso-C and 5-methyl-iso-G.

8. A homogeneous method for determining the identity of a base on a DNA strand, which comprises in order the steps of:

(a) annealing an oligonucleotide to the DNA strand immediately adjacent to the base whose identity is to be determined;

(b) incubating the annealed DNA strand and oligonucleotide with four different dideoxynucleotides, one of the dideoxynucleotides having a reporter molecule in the presence of an enzyme, thereby extending the oligonucleotide by one base unit;

(c) immobilizing the extended oligonucleotide on a microsphere; and

(d) analyzing the microsphere using flow cytometry whereby the base under investigation is determined.

9. The method of claim 8, wherein the reporter molecule is fluorescent and said fluorescent reporter molecule contains a fluorescent dideoxynucleotide and the enzyme is a DNA polymerase.

10. The method as described in claim 8, wherein the oligonucleotide is biotinylated and the microsphere is coated with avidin or streptavidin.

11. The method as described in claim 8, wherein the microsphere is biotinylated and the oligonucleotide is coupled to avidin or streptavidin.

12. The method as described in claim 8, wherein the oligonucleotide as covalently attached to the microsphere.

13. The method as described in claim 8, wherein the oligonucleotide is hybridized to a complementary capture probe immobilized on a microsphere.

14. The method as described in claim 13, wherein the oligonucleotide comprises a sequence tag which is hybridized to the capture probe, and wherein the sequence tag and capture probe comprises at least one non-natural base selected from the group consisting of iso-,C and 5-methyl-iso-G.

15. A homogeneous method for determining the identity of a base at a site on a DNA strand, which comprises in order the steps of

(a) annealing a first oligonucleotide to the DNA strand immediately adjacent to the base and a second oligonucleotide to the DNA strand adjacent to the first oligonucleotide and in the presence of an enzyme, wherein the second oligonucleotide contains both a reporter molecule and an interrogator base that is complementary to the base whose identity is being determined and wherein the second oligonucleotide attaches to the first oligonucleotide forming a ligated oligonucleotide;

(b) denaturing the DNA strand and immobilizing the ligated oligonucleotide on a microsphere; and

(c) analyzing the microsphere using flow cytometry whereby the identity of the base is determined.

16. The method as described in claim 15 wherein the reporter molecule is fluorescent, and the enzyme is a DNA polymerase.

17. The method as described in claim 15 wherein the first oligonucleotide is biotinylated and the microsphere is coated with avidin or streptavidin.

18. The method as described in claim 15 wherein the microsphere is biotinylated and the first oligonucleotide is coupled to avidin or streptavidin.

19. The method as described in claim 15 wherein the first oligonucleotide is covalently attached to the microsphere.

20. The method as described in claim 15 wherein the first oligonucleotide is hybridized to a complementary capture probe immobilized on a microsphere.

21. The as described in claim 20, wherein a sequence tag is hybridized to capture probe that is complimentary thereto, and wherein the sequence tag and the capture probe comprises a non-natural base selected from the group consisting of iso-C and 5-methyl-iso-G.