Direct DNA sequencing with a transcription protein and a nanometer scale electrometer

• US 6,770,472 B2
• Filed: 11/13/2001
• Issued: 08/03/2004
• Est. Priority Date: 11/17/2000
• Status: Expired due to Fees

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Inventors: Quate, Calvin F., Manalis, Scott R., Minne, Stephen C.
• Primary Examiner(s): Redding, David A.
• Application Number:
  US09/993,338
• Publication Number:
  US 20020086318A1
• Time in Patent Office: 994 Days
• Field of Search: 204/403.01, 204/403.03, 204/403.13, 435/6, 435/7.1, 435/23, 435/287.2, 435/288.3, 257/14, 257/24, 257/30
• US Class Current: 435/287.2
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2521/119 RNA polymerase
• CPC Class Codes: C12Q 2521/543 Immobilised enzyme(s)
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode

Abstract

The present invention provides an apparatus and method for nucleotide or DNA sequencing by monitoring the molecular charge configuration as the DNA moves through a protein that is capable of transcribing the DNA. The apparatus and method provides a nanoscale electrometer that immobilizes the protein. The protein receives the DNA and transcribes the DNA. The nanoscale electrometer is a sensitive device that is capable of sensing and measuring the electronic charge that is released during the transcription process. The apparatus and method of the present invention further provides monitoring means that are attached to the nanoscale electrometer to monitor the electronic charge configuration as the DNA moves through the protein. Once the electronic charge configuration is established, a correlation is computed, using computing means, between the electronic charge configuration and a nucleotide signature of the DNA.

Claims

1. An apparatus for sequencing DNA, comprising:

(a) a nanoparticle device comprising;

(i) two electrodes; and

(ii) a nanoparticle positioned in between said two electrodes; and

(b) a protein that is capable of transcribing said DNA, wherein said protein is immobilized on said nanoparticle device to receive and transcribe said DNA.

2. The apparatus as set forth in claim 1, wherein said protein is immobilized on said nanoparticle to receive said DNA.

3. The apparatus as set forth in claim 1, wherein said nanoparticle is a gold nanoparticle.

4. The apparatus as set forth in claim 1, wherein said nanoparticle is less than 2 nm in diameter.

5. The apparatus as set forth in claim 1, wherein said nanoparticle device has a sensitivity on the order of a hundredth of an electron with a 100 μ

s response time.

6. The apparatus as set forth in claim 1, wherein said nanoparticle is a room temperature nanoparticle.

7. The apparatus as set forth in claim 1, wherein said protein is a RNA polymerase.

8. The apparatus as set forth in claim 1, further comprising monitoring means attached to said nanoparticle device to monitor an electronic charge configuration as said DNA moves through said protein.

9. The apparatus as set forth in claim 8, further comprising computing means to compute a correlation between said electronic charge configuration and a nucleotide signature of said DNA.

10. An integrated circuit chip for sequencing one or more DNA samples, comprising:

(a) a plurality of interconnected nanoparticle devices, each comprising;

(i) two electrodes; and

(ii) a nanoparticle positioned in between said two electrodes; and

(b) a plurality of proteins that are capable of transcribing said one or more DNA samples, wherein said proteins are immobilized on said plurality of interconnected nanoparticle devices to receive and transcribe said one or more DNA samples.

11. The integrated circuit chip as set forth in claim 10, wherein for each of said nanoparticles one of said proteins is immobilized.

12. The integrated circuit chip as set forth in claim 10, wherein said nanoparticle is a gold nanoparticle.

13. The integrated circuit chip as set forth in claim 10, wherein said nanoparticle is less than 2 nm in diameter.

14. The integrated circuit chip as set forth in claim 10, wherein said nanoparticle device has a sensitivity on the order of a hundredth of an electron with a 100 μ

s response time.

15. The integrated circuit chip as set forth in claim 10, wherein said nanoparticle is a room temperature nanoparticle.

16. The integrated circuit chip as set forth in claim 10, wherein said proteins are RNA polymerases.

17. The integrated circuit chip as set forth in claim 10, further comprising monitoring means attached to said nanoparticle devices to monitor electronic charge configurations as said one or more DNA samples move through said proteins.

18. The integrated circuit chip as set forth in claim 17, further comprising computing means to compute one or more correlations between said electronic charge configurations and nucleotide signatures of said one or more DNA samples.