Nucleotide sequencing via repetitive single molecule hybridization

• US 7,604,941 B2
• Filed: 09/06/2007
• Issued: 10/20/2009
• Est. Priority Date: 11/17/2003
• Status: Expired due to Fees

• Current Assignee: Joseph M. Jacobson
• Original Assignee: Joseph M. Jacobson
• Inventors: Jacobson, Joseph M.
• Primary Examiner(s): Martinell; James
• Application Number:
  US11/896,897
• Publication Number:
  US 20080070798A1
• Time in Patent Office: 775 Days
• Field of Search: None
• US Class Current: 435/6.14
• CPC Class Codes: B82Y 10/00 Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
• CPC Class Codes: B82Y 5/00 Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

Methods of obtaining sequence information about target oligonucleotides by repetitive single molecule hybridization are disclosed. The methods include exposing a target oligonucleotide to one or more copies of a test oligonucleotide; measuring hybridization; dehybridizing the test oligonucleotide; and repeating until the information content from the hybridization trials equals or exceeds the information content of the target oligonucleotide.

Claims

1. A method of analyzing nucleic acids comprising:

(a) hybridizing one or more copies of a test oligonucleotide comprising at least two informative region sequences to a single molecule of target oligonucleotides under conditions permitting hybridization of the test oligonucleotide to a perfectly complementary sequence;

(b) measuring a signal of said hybridization of the test oligonucleotide to the target oligonucleotide, thereby completing a first hybridization trial;

(c) dehybridizing the test oligonucleotide;

(d) exposing the target oligonucleotide to one or more copies of at least one additional test oligonucleotide, said additional test oligonucleotide comprising at least two informative regions;

(e) measuring a signal from the hybridization of the additional test oligonucleotide to the target oligonucleotide, thereby completing a further hybridization trial;

(f) repeating steps c) to e) until the information content from the hybridization trials exceeds the information content of the target oligonucleotide; and

(g) analyzing said signals.

2. The method of claim 1, wherein said signal of said hybridization comprises a fluorescent tag.

3. The method of claim 1, wherein said signal of said hybridization comprises a quantum dot or nanoparticle tag.

4. The method of claim 1, wherein said measuring is effected mechanically.

5. The method of claim 1, wherein said measuring is effected by sensing a change in charge associated with hybridization.

6. The method of claim 1, wherein said measuring is effected electronically.

7. The method of claim 1, wherein said target oligonucleotide is immobilized on a solid support.

8. The method of claim 1, wherein a plurality of said target oligonucleotides are immobilized on a solid support.

9. The method of claim 8, in which hybridizations to the plurality of target oligonucleotides are measured substantially in parallel.

10. The method of claim 9, in which the substantially parallel detection is carried out using a solid state imaging device.

11. The method of claim 10, in which the solid state imaging device is used without a lens system in close proximity to the target oligonucleotides.

12. The method of claim 8, in which the target oligonucleotides are immobilized on an inverse nucleotide chip.

13. The method of claim 12, in which the inverse nucleotide chip substantially comprises the genetic material of a genome.

14. A method of analyzing nucleic acids comprising:

(a) hybridizing one or more copies of a test oligonucleotide to a single molecule of target oligonucleotides under conditions permitting hybridization of the test oligonucleotide to a perfectly complementary sequence;

(b) measuring a signal of said hybridization of the test oligonucleotide to the target oligonucleotide, thereby completing a first hybridization trial;

(c) dehybridizing the test oligonucleotide;

(d) exposing the target oligonucleotide to one or more copies of at least one additional test oligonucleotide;

(e) measuring a signal from the hybridization of the additional test oligonucleotide to the target oligonucleotide, thereby completing a further hybridization trial;

(f) repeating steps c) to e) until the information content from the hybridization trials exceeds the information content of the target oligonucleotide; and

(g) analyzing said signals; and

(h) analyzing an absence of said signals to eliminate oligonucleotide test members.

15. The method of claim 14, wherein said signal of said hybridization comprises a fluorescent tag.

16. The method of claim 14, wherein said signal of said hybridization comprises a quantum dot or nanoparticle tag.

17. The method of claim 14, wherein said measuring is effected mechanically.

18. The method of claim 14, wherein said measuring is effected by sensing a change in charge associated with hybridization.

19. The method of claim 14, wherein said measuring is effected electronically.

20. The method of claim 14, wherein said target oligonucleotide is immobilized on a solid support.

21. The method of claim 14, wherein a plurality of said target oligonucleotides are immobilized on a solid support.

22. The method of claim 21, in which hybridizations to the plurality of target oligonucleotides are measured substantially in parallel.

23. The method of claim 22, in which the substantially parallel detection is carried out using a solid state imaging device.

24. The method of claim 23, in which said solid state imaging device is used without a lens system in close proximity to the target oligonucleotides.

25. The method of claim 21, in which said target oligonucleotides are immobilized on an inverse nucleotide chip.

26. The method of claim 25, in which the inverse nucleotide chip substantially comprises the genetic material of a genome.