Characterization of individual polymer molecules based on monomer-interface interactions

• US 6,015,714 A
• Filed: 06/16/1998
• Issued: 01/18/2000
• Est. Priority Date: 03/17/1995
• Status: Expired due to Term

• Current Assignee: President and Fellows of Harvard College (Harvard Corporation), The United States of America As Represented By The Secretary of Commerce, Regents of the University of California (University of California)
• Original Assignee: THE GOVERNMENT OF THE UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECRETARY OF COMMERCE, Regents of the University of California (University of California)
• Inventors: Church, George, Baldarelli, Richard, Deamer, David W., Branton, Daniel, Akeson, Mark, Kasianowicz, John
• Primary Examiner(s): Patterson, Jr., Charles L.
• Application Number:
  US09/098,142
• Time in Patent Office: 581 Days
• Field of Search: 436/2, 436/151, 435/4
• US Class Current: 436/2
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07K 14/705 Receptors; Cell surface antigens; Cell surface determinants tumour specific antigens C07K14/4748
• CPC Class Codes: C12N 9/1241 Nucleotidyltransferases (2.7.7)
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2523/307 Denaturation or renaturation by electric current/voltage
• CPC Class Codes: G01N 33/48721 Investigating individual macromolecules, e.g. by translocation through nanopores Coulter counters in general G01N15/12; fabrication methods for nanoscale apertures B81B1/00; sequencing of nucleic acids C12Q1/68
• CPC Class Codes: G01N 33/68 involving proteins, peptides or amino acids involving lipoproteins G01N33/92
• CPC Class Codes: Y10S 977/781 Possessing nonosized surface openings that extend partially into or completely through the host material
• CPC Class Codes: Y10S 977/788 Of specified organic or carbon-based composition
• CPC Class Codes: Y10S 977/84 Manufacture, treatment, or detection of nanostructure
• CPC Class Codes: Y10S 977/88 with arrangement, process, or apparatus for testing
• CPC Class Codes: Y10S 977/924 using nanostructure as support of dna analysis
• CPC Class Codes: Y10S 977/953 Detector using nanostructure

Abstract

A method for sequencing a nucleic acid polymer by (1) providing two separate, adjacent pools of a medium and an interface between the two pools, the interface having a channel so dimensioned as to allow sequential monomer-by-monomer passage from one pool to the other pool of only one nucleic acid polymer at a time; (2) placing the nucleic acid polymer to be sequenced in one of the two pools; and (3) taking measurements as each of the nucleotide monomers of the nucleic acid polymer passes through the channel so as to sequence the nucleic acid polymer.

Claims

1. A method for sequencing a nucleic acid polymer, the method comprising:

providing two separate, adjacent pools of a medium and an interface between the two pools, the interface having a channel so dimensioned as to allow sequential monomer-by-monomer passage from one pool to the other pool of only one nucleic acid polymer at a time;

placing the nucleic acid polymer to be sequenced in one of the two pools; and

taking measurements as each of the nucleotide monomers of the nucleic acid polymer passes through the channel so as to sequence the nucleic acid polymer.

2. The method of claim 1, wherein the medium is electrically conductive.

3. The method of claim 2, wherein the medium is an aqueous solution.

4. The method of claim 3, further comprising applying a voltage across the interface.

5. The method of claim 4, wherein ionic flow between the two pools is measured.

6. The method of claim 5, wherein the duration of ionic flow blockage is measured.

7. The method of claim 5, wherein the amplitude of ionic flow blockage is measured.

8. The method of claim 2, further comprising applying a voltage across the interface.

9. The method of claim 8, wherein ionic flow between the two pools is measured.

10. The method of claim 9, wherein the duration of ionic flow blockage is measured.

11. The method of claim 9, wherein the amplitude of ionic flow blockage is measured.

12. The method of claim 1, wherein the nucleic acid polymer interacts with an inner surface of the channel.

13. The method of claim 12, wherein the medium is electrically conductive.

14. The method of claim 13, wherein the medium is an aqueous solution.

15. The method of claim 14, further comprising applying a voltage across the interface.

16. The method of claim 15, wherein ionic flow between the two pools is measured.

17. The method of claim 16, further comprising applying a voltage across the interface.

18. The method of claim 17, wherein ionic flow between the two pools is measured.

19. The method of claim 18, wherein the duration of ionic flow blockage is measured.

20. The method of claim 18, wherein the amplitude of ionic flow blockage is measured.

21. The method of claim 1, further comprising providing a polymerase or exonuclease in one of the two pools, wherein the polymerase or exonuclease draws the nucleic acid polymer through the channel.

22. The method of claim 21, wherein the medium is an aqueous solution.

23. The method of claim 22, wherein ionic flow between the two pools is measured.

24. The method of claim 21, wherein ionic flow between the two pools is measured.