Electrochemical arrays

• US 20060094024A1
• Filed: 11/01/2004
• Published: 05/04/2006
• Est. Priority Date: 11/01/2004
• Status: Abandoned Application

• Current Assignee: Duke University, University of North Carolina At Chapel Hill (University of North Carolina System)
• Original Assignee: Duke University
• Inventors: Thorp, H. Holden, Pirrung, Michael C.
• Application Number:
  US10/978,789
• Publication Number:
  US 20060094024A1
• Time in Patent Office: Days
• US Class Current: 435/6.19
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00653 the compounds being bound to electrodes embedded in or on the solid supports
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites

Abstract

The present invention relates to methods for synthesizing nucleic acids. The invention also relates to the production of an array of nucleic acids as well as methods for making such an array. Electrochemical methods may be used to both fabricate and interrogate the nucleic acid arrays.

Claims

1. A method for synthesizing a nucleic acid comprising:

(a) providing a first nucleic acid having a 3′

-terminal and a 5′

-protecting group;

(b) covalently coupling said 3′

-terminal of the first nucleic acid to an electrode; and

(c) cleaving said 5′

-protecting group from said first nucleic acid by passing a current therethrough under reaction conditions in which said first nucleic acid remains covalently coupled to said electrode to provide a nucleic acid having a deprotected 5′

terminal.

2. The method according to claim 1, further comprising:

(d) providing a subsequent nucleic acid having a 3′

-terminal and a 5′

-protecting group;

(e) covalently coupling said 3′

-terminal of the subsequent nucleic acid to said deprotected 5′

terminal of said first nucleic acid; and

(f) cleaving said 5′

-protecting group from said subsequent nucleic acid by passing a current therethrough under reaction conditions in which said subsequent nucleic acid remains covalently coupled to said deprotected nucleic acid and in which said deprotected nucleic acid remains covalently coupled to said electrode.

3. The method according to claim 2, comprising:

(g) cyclically repeating steps (d) through (f) at least one additional time to produce a further elongated nucleic acid.

4. The method of claim 3, wherein at least one of said first nucleic acid and said subsequent nucleic acid further comprises at least one N-protecting group, said method further comprising the step of:

(h) cleaving the at least one N-protecting group.

5. The method according to claim 1, wherein said covalently coupling is a thiol coupling.

6. The method according to claim 1, wherein said electrode comprises a metal.

7. The method according to claim 6, wherein said metal comprises gold.

8. The method according to claim 1, wherein said electrode comprises carbon.

9. The method according to claim 1, wherein said electrode comprises a metal oxide.

10. An array of nucleic acids comprising:

a microelectronic substrate having at least a first surface;

a plurality of different nucleic acids attached to the first surface of the substrate at a density exceeding at least 1000 different nucleic acids/cm², wherein each of the different nucleic acids is attached to the surface of the microelectronic substrate in a different known location, and has a different determinable sequence;

a plurality of different binding detection electrodes on said first surface; and

wherein each different nucleic acid has a different binding detection electrode operatively associated therewith.

11. The array of claim 10, wherein the plurality of different nucleic acids is attached to the first surface of the substrate by the 3′

-terminal of a first nucleic acid.

12. The array of claim 10, further comprising a contact electrically connected to each of said electrodes.

13. The array of claim 10, wherein each nucleic acid is at least two nucleotides in length.

14. The array of claim 10, wherein said electrode comprises a metal.

15. The array of claim 10, wherein said electrode comprises a metal oxide.

16. The array of claim 10, wherein said electrode comprises carbon.

17. The array of claim 10, wherein a second plurality of nucleic acids is covalently coupled to the first plurality of nucleic acids.

18. A method of making an array of nucleic acids comprising:

(a) providing a plurality of nucleotides with a 3′

-terminal and a 5′

-protecting group;

(b) covalently coupling the 3′

-terminal of one of the nucleotides to a first surface of a microelectronic substrate, the nucleotides having different predetermined sequences and being attached at different localized areas having a width of less than 100 microns on the first surface of a microelectronic substrate;

(c) cleaving said 5′

-protecting group from the first nucleotide attached to the microelectronic substrate by passing a current therethrough under reaction conditions in which said first nucleotide remains covalently coupled to said electrode to provide elongated oligonucleotides; and

(d) covalently coupling a 3′

-terminal of a subsequent nucleotide having a 3′

-terminal and a 5′

-protecting group to the first nucleotide to produce further elongated oligonucleotides; and

wherein each of said first nucleotide coupled to the microelectronic substrate has a different binding detection electrode operatively associated therewith.

19. The method according to claim 18, further comprising cyclically repeating steps (c) through (d) at least one additional time to produce further elongated oligonucleotides.

20. The method according to claim 18, further comprising deprotecting the 5′

-terminal of the terminal nucleotide.

21. The method according to claim 18, further comprising oxidizing the H-phosphonate.

22. The method according to claim 18, wherein said cleaving said 5′

-protecting group from said first nucleic acid comprises;

passing a current therethrough under reaction conditions in which said first nucleic acid remains covalently coupled to said microelectronic substrate to provide a deprotected nucleic acid.

23. The method according to claim 18, wherein said electrode comprises a metal.

24. The method according to claim 18, wherein said electrode comprises a metal oxide.

25. The method according to claim 18, wherein said electrode comprises carbon.

26. The method according to claim 18, wherein said covalently coupling is a thiol coupling.