Method for sequencing nucleic acids by observing the uptake of nucleotides modified with bulky groups

• US 20040209280A1
• Filed: 10/15/2003
• Published: 10/21/2004
• Est. Priority Date: 05/20/2002
• Status: Abandoned Application

• Current Assignee: Andrew A. Berlin, Mineo Yamakawa, Narayan Sundararajan, Selena Chan, Su Xing, Tae-Woong Koo
• Original Assignee: Andrew A. Berlin, Mineo Yamakawa, Narayan Sundararajan, Selena Chan, Su Xing, Tae-Woong Koo
• Inventors: Koo, Tae-Woong, Yamakawa, Mineo, Su, Xing, Berlin, Andrew A., Sundararajan, Narayan, Chan, Selena
• Application Number:
  US10/686,083
• Publication Number:
  US 20040209280A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B82Y 15/00 Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: B82Y 5/00 Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2563/155 Particles of a defined size, e.g. nanoparticles
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode

Abstract

The present methods and apparatus 100 concern nucleic acid 214 sequencing by incorporation of nucleotides 218 into nucleic acid strands 220. The incorporation of nucleotides 218 is detected by changes in the mass and/or surface stress of the structure 116, 212. In some embodiments of the invention, the structure 116, 212 comprises one or more nanoscale or microscale cantilevers. In certain embodiments of the invention, each different type of nucleotide 218 is distinguishably labeled with a bulky group and each incorporated nucleotide 218 is identified by the changes in mass and/or surface stress of the structure 116, 212 upon incorporation of the nucleotide 218. In alternative embodiments of the invention only one type of nucleotide 218 is exposed at a time to the nucleic acids 214, 220. Changes in the properties of the structure 116, 212 may be detected by a variety of methods, such as piezoelectric detection, shifts in resonant frequency of the structure 116, 212, and/or position sensitive photodetection.

Claims

1. An apparatus comprising:

a. an analysis chamber containing one or more structures;

b. one or more reagent reservoirs in fluid communication with the analysis chamber;

c. a detection unit operably coupled to the structures; and

d. a data processing and control unit.

2. The apparatus of claim 1, further comprising one or more nucleic acids attached to the structures.

3. The apparatus of claim 2, further comprising one or more polymerases in the analysis chamber.

4. The apparatus of claim 1, wherein the structures are cantilevers.

5. The apparatus of claim 1, wherein the detection unit comprises a position sensitive photodetector, a piezoelectric detector or a piezoresistor.

6. The apparatus of claim 1, wherein the detection unit comprises a laser.

7. The apparatus of claim 2, said detection unit to detect changes in mass of nucleic acids attached to said structures and/or the surface stress of said structures.

8. An apparatus comprising:

a) an analysis chamber containing at least one cantilever;

b) one or more nucleic acids molecules attached to the at least one cantilever;

c) a detection unit to detect, deflection of the at least one cantilever; and

d.) a data processing and control unit.

9. The apparatus of claim 8, further comprising an information processing and control system.

10. The apparatus of claim 9, wherein the information processing and control system is a computer.

11. The apparatus of claim 8, wherein the detection unit comprises a laser and a position sensitive photodetector.

12. The apparatus of claim 8, wherein the detection unit comprises a piezoelectric detector, a piezoresistive detector or a piezomagnetic detector.

13. The apparatus of claim 8, wherein the nucleic acids molecules comprise a template from about 10 to approximately 100,000 nucleotides in length.

14. The apparatus of claim 8, further comprising an array of cantilevers, each associated with the same molecule.

15. The apparatus of claim 8, further comprising an array of cantilevers, each associated with a different molecule.

16. An apparatus comprising:

a) an analysis chamber containing at least one cantilever;

b) one or more nucleic acids molecules attached to the at least one cantilever;

c) a piezoresistive resistor embedded at the fixed end of at least one cantilever;

d) a detection unit to detect deflection of the at least one cantilever; and

e) a data processing and control unit.

17. The apparatus of claim 16, further comprising a resistance measuring device.

18. The apparatus of claim 16, wherein the nucleic acids molecules comprise a template from about 10 to approximately 100,000 nucleotides in length.

22. The apparatus of claim 18, wherein the nucleic acids molecules are anchored to the cantilever through a thiol group.

19. An apparatus comprising:

a) an analysis chamber containing at least one cantilever;

b) the at least one cantilever coated with a substance;

c) one or more nucleic acids molecules associated with the at least one cantilever;

d) one or more polymerases in the analysis chamber;

d) a detection unit to detect deflection of the at least one cantilever; and

e) a data processing and control unit.

20. The apparatus of claim 19, wherein the substance comprises an alloy.

21. The apparatus of claim 20, wherein the alloy is gold.