DNA sequence recognition

• US 20060194228A1
• Filed: 01/19/2006
• Published: 08/31/2006
• Est. Priority Date: 01/19/2005
• Status: Abandoned Application

• Current Assignee: Grade Biosense Inc.
• Original Assignee: Grade Biosense Inc.
• Inventors: Dudelzak, Alexander E., Ginovker, Andrey, Rakitin, Andrei
• Application Number:
  US11/334,540
• Publication Number:
  US 20060194228A1
• Time in Patent Office: Days
• US Class Current: 435/6.12
• 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 40/00 Manufacture or treatment of nanostructures
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 2563/161 Vesicles, e.g. liposome
• CPC Class Codes: C12Q 2565/519 characterised by the capture moiety being a single stranded oligonucleotide
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode

Abstract

To detect the presence of a match of a target DNA base sequence with a probe DNA base sequence, a single strand of the probe DNA base sequence is prepared. One end of the single strand probe DNA base sequence is linked to an electrode and the other end to a nano entity capable of exchanging charge with the DNA base sequence. The single strand of the target DNA base sequence is brought into contact with the single strand of the probe DNA base sequence, and the change in the physical properties of the probe DNA base sequence upon hybridization detected.

Claims

18. A DNA detection apparatus, comprising:

a sensor with a surface forming an electrode;

a single strand probe DNA base sequence having one end bonded to an electrode and another end linked to an entity selected from the group consisting of a fullerene molecule, a nanoparticle, and a redox-active molecule; and

a detector for detecting current flowing through the DNA base sequence upon hybridization.

1. A method of detecting the presence of a match of a target DNA base sequence with a probe DNA base sequence, comprising:

preparing a single strand of the probe DNA base sequence;

linking a first end of said single strand probe DNA base sequence to an electrode and a second end to a nano entity capable of exchanging charge with the DNA base sequence;

bringing a single strand of the target DNA base sequence into contact with the single strand of the probe DNA base sequence; and

detecting a change in a physical property of said probe DNA base sequence due to hybridization in the event of a match of and said target DNA base sequence.

2. A method as claimed in claim 1, wherein the transfer of charge between the DNA base sequence and the nano entity is detected upon hybridization.

3. A method as claimed in claim 1 or 2, wherein said nano entity is a fullerene molecule, a nanoparticle or a redox-active molecule.

4. A method as claimed in any one of claims 1 to 3, wherein said entity is optically excited to initiate charge transfer.

5. A method as claimed in any one of claims 1 to 4, further comprising applying an electrical voltage to the electrode and detecting the current generated upon hybridization.

6. A method as claimed in any one of claims 1 to 5, wherein said single strand probe DNA sequence is bonded to said electrode with the aid of a monolayer of said single strand probe sequence deposited on said electrode.

7. A method as claimed in claim 6, wherein said electrode is a gold electrode on an semiconductor substrate.

8. A method as claimed in any one of claims 1 to 7, wherein said entity is linked to the second end of the single strand of probe DNA base sequence with a linker molecule.

9. A method as claimed in any one of claims 1 to 8, further comprising metallizing said single strand DNA probe sequence to enhance conductivity upon hybridization.

10. A method as claimed in claim any one of claims 1 to 8, further comprising adding an intercalator consisting essentially of a solution of divalent metal ions having a d-electron shell to intercalate any double strand DNA formed by hybridization.

11. A method as claimed in claim 10, wherein the single strand probe DNA base sequence is brought into contact with the single strand target DNA base sequence in the presence of said intercalator so that the hybridized DNA is intercalated by said divalent metal ions.

12. A method as claimed in any one of claims 1 to 3, wherein a pair of said single strands of the probe DNA base sequence are interconnected at their respective second ends by said entity and are anchored at their first ends to respective electrodes to create a nanoshuttle.

13. A method as claimed in claim 12, wherein said physical property is an oscillatory property of the nanoshuttle.

14. A method as claimed in claim 13, wherein the resonant frequency of the nanohuttle is detected.

15. A method as claimed in any one of claims 12 to 14, wherein the entity is optically excited to enhance said change.

16. A method as claimed in claim any one of claims 12 to 15, further comprising adding an intercalator consisting essentially of a solution of divalent metal ions having a d-electron shell to intercalate any double strand DNA formed by hybridization.

17. A method as claimed in claim 16, wherein the single strand probe DNA base sequence is brought into contact with the single strand target DNA base sequence in the presence of said intercalator so that the hybridized DNA is intercalated by said divalent metal ions.

19. An apparatus as claimed in claim 18, further comprising a source for optically exciting said entity.

20. An apparatus as claimed in claim 18 or 19, wherein the single strand proble DNA base sequence is attached to said electrode by a monolayer of said DNA probe base sequence.

21. An apparatus as claimed in claim 18, comprising a pair of single strands of said DNA probe base sequence having first ends interconnected through said entity and second ends attached to respective electrodes to form a nanoshuttle.

22. An apparatus as claimed in claim 21, further comprising a detector for detector resonance frequencies of said nanoshuttle.

23. An apparatus as claimed in claim 22, wherein said intercalator comprises a solution of divalent metal ions having d-electron shell.

24. An apparatus as claimed in any one of claims 21 to 23, further comprising a source for optically exciting said entity.

22-1. An apparatus as claimed in any one of claims 18 to 21, further comprising an intercalator for said DNA base sequence.

25. A method of detecting the presence of a match of a target DNA base sequence with a probe DNA base sequence, comprising:

preparing at least first and second single strands of the probe DNA base sequence;

linking one end of each of said first and second single strands of probe DNA base through a nano entity capable of exchanging charge with the DNA base sequence to create a nanoshuttle;

bringing a single strand of the target DNA base sequence into contact with at least one of the single strands of the probe DNA base sequence; and

detecting a change in a physical property of said probe DNA base sequence due to hybridization in the event of a match of and said target DNA base sequence.

26. A method as claimed in claim 25, wherein the detected change is the change in resonant frequency.