Methods and device for DNA sequencing using surface enhanced Raman scattering (SERS)

• US 20040110208A1
• Filed: 09/26/2003
• Published: 06/10/2004
• Est. Priority Date: 03/26/2002
• Status: Abandoned Application

• Current Assignee: Intel Corporation
• Original Assignee: Intel Corporation
• Inventors: Su, Xing, Chan, Selena
• Application Number:
  US10/672,149
• Publication Number:
  US 20040110208A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2521/319 Exonuclease
• CPC Class Codes: C12Q 2563/155 Particles of a defined size, e.g. nanoparticles
• CPC Class Codes: C12Q 2565/629 being a microfluidic device
• CPC Class Codes: C12Q 2565/632 being a surface enhanced, e.g. resonance, Raman spectrometer
• CPC Class Codes: G01N 2021/653 Coherent methods [CARS]
• CPC Class Codes: G01N 2021/656 Raman microprobe
• CPC Class Codes: G01N 21/65 Raman scattering
• CPC Class Codes: G01N 21/658 enhancement Raman, e.g. surface plasmons

Abstract

The methods and apparatus disclosed herein concern nucleic acid characterization by enhanced Raman spectroscopy. In certain embodiments of the invention, exonuclease treatment of the nucleic acids results in the release of nucleotides. The nucleotides may pass from a reaction chamber through a microfluidic channel and enter a nanochannel or microchannel. The nanochannel or microchannel may be packed with nanoparticle aggregates containing hot spots for Raman detection. As the nucleotides pass through the nanoparticle hot spots, they may be detected by Raman spectroscopy. Identification of the sequence of nucleotides released from the nucleic acid is used to characterize the nucleic acid, for example by sequencing or identifying the nucleic acid. Other embodiments of the invention concern apparatus for nucleic acid sequencing.

Claims

1. A method comprising:

a) sequentially removing nucleotides from one end of at least one nucleic acid molecule;

b) moving the nucleotides through a channel packed with nanoparticles;

c) identifying one or more nucleotides by Raman spectroscopy; and

d) characterizing the nucleic acid.

2. The method of claim 1, wherein the nucleotides are removed from the nucleic acid by exonuclease activity.

3. The method of claim 1, further comprising identifying single nucleotide molecules.

4. The method of claim 3, wherein the nucleotides are unlabeled.

5. The method of claim 3, wherein the nucleotides are labeled.

6. The method of claim 3, further comprising identifying single adenosine nucleotide molecules

7. The method of claim 1, wherein only adenosine and guanosine nucleotides are identified.

8. The method of claim 1, wherein only cytidine and thymidine nucleotides are identified.

9. The method of claim 1, further comprising separating the purine or pyrimidine bases from the nucleotides.

10. The method of claim 9, wherein the separated purine or pyrimidine bases are identified by Raman spectroscopy.

11. The method of claim 1, wherein a single nucleic acid molecule is sequenced.

12. The method of claim 1, wherein the nucleotides are identified by surface enhanced Raman spectroscopy (SERS), surface enhanced resonance Raman spectroscopy (SERRS) and/or coherent anti-Stokes Raman spectroscopy (CARS).

13. The method of claim 1, wherein the channel is a nanochannel or microchannel.

14. The method of claim 1, further comprising identifying the nucleic acid.

15. The method of claim 1, further comprising sequencing the nucleic acid.

16. The method of claim 1, further comprising identifying a single nucleotide polymorphism in the nucleic acid.

25. The method of claim 12, further comprising recording the time at which each nucleotide passes through said channel.

17. A method comprising:

a) preparing a nucleic acid comprising labeled nucleotides;

b) sequentially removing nucleotides from one end of the nucleic acid;

c) moving the nucleotides through a channel packed with nanoparticles;

d) identifying one or more nucleotides by Raman spectroscopy; and

e) characterizing the nucleic acid.

18. The method of claim 17, wherein each type of nucleotide is labeled with a distinguishable Raman label.

19. The method of claim 18, wherein only pyrimidine nucleotides are labeled.

20. The method of claim 18, wherein only purine nucleotides are labeled.

21. The method of claim 17, wherein single nucleotide molecules are identified.

22. The method of claim 17, further comprising identifying single adenosine nucleotide molecules.

23. The method of claim 17, further comprising separating the nucleotides from the nucleic acid.

24. The method of claim 23, further comprising imposing an electric field to move the nucleotides through the channel.

29. The apparatus of claim 20, wherein the first channel is a microfluidic channel.

30. The apparatus of claim 20, wherein the second channel is a nanochannel or a microchannel.

26. An apparatus comprising:

a) a reaction chamber;

b) a first channel in fluid communication with the reaction chamber;

c) a second channel in fluid communication with the first channel;

d) a multiplicity of nanoparticles packed in the second channel; and

e) a Raman detector operably coupled to the nanoparticle packed channel.

27. The apparatus of claim 26, wherein the apparatus is capable of detecting single nucleotide molecules.

28. The apparatus of claim 26, further comprising a first electrode and a second electrode to move nucleotides from the first channel into the second channel.