Methods for high fidelity production of long nucleic acid molecules

• US 8,507,226 B2
• Filed: 06/26/2012
• Issued: 08/13/2013
• Est. Priority Date: 12/10/2002
• Status: Active Grant

• Current Assignee: Massachusetts Institute of Technology
• Original Assignee: Massachusetts Institute of Technology
• Inventors: Carr, Peter A., Chow, Brian Y., Jacobson, Joseph M., Mosley, David W., Emig, Christopher
• Primary Examiner(s): Lu, Frank
• Application Number:
  US13/533,948
• Publication Number:
  US 20120264653A1
• Time in Patent Office: 413 Days
• Field of Search: 435/6.1, 435/6.11, 435/6.12, 435/91.1, 435/91.2, 435/91.51, 435/283.1, 435/287.1, 435/287.2, 436/94, 436/501, 536/23.1, 536/24.3, 536/24.33, 536/25.3, 422/50, 422/68.1
• US Class Current: 435/91.2
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6848 characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
• CPC Class Codes: C12Q 2521/514 Mismatch repair protein
• CPC Class Codes: C12Q 2565/513 characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target

Abstract

In a method for synthesizing a pool of nucleic acid molecules, a first nucleic acid has a first 5′ region and a first 3′ region and a second nucleic acid has a second 5′ region and a second 3′ region. The second 3′ region and the first 5′ region have identical nucleic acid sequences. The first 3′ region is hybridized with an oligonucleotide, extending the hybridized oligonucleotide and producing a first extension product having a 3′ region complementary to the first 5′ region. The second nucleic acid is hybridized with the first extension product to hybridize the 3′ region of the first extension product to the second 3′ region, extending the 3′ region of the first extension product and producing a second extension product having a 3′ region complementary to the second 5′ region. Error-containing molecules are separated from error-free molecules by a component that selects for a sequence error.

Claims

1. A method for removing or controlling errors in a plurality or pool of nucleic acid molecules, the method comprising the steps of:

a) synthesizing said plurality or pool of nucleic acid molecules by the steps of;

providing a first immobilized nucleic acid comprising a first 5′

region and a first 3′

region;

providing a second immobilized nucleic acid comprising a second 5′

region and a second 3′

region, wherein said second 3′

region and said first 5′

region comprise identical nucleic acid sequences;

hybridizing said first immobilized nucleic acid with an oligonucleotide under conditions promoting hybridization of said oligonucleotide to said first 3′

region,

extending the hybridized oligonucleotide, and producing a first extension product comprising a 3′

region that is complementary to said first 5′

region; and

hybridizing said second immobilized nucleic acid with said first extension product under conditions promoting hybridization of said 3′

region of said first extension product to said second 3′

region, extending the 3′

region of said first extension product, and producing a second extension product comprising a 3′

region that is complementary to said second 5′

region, wherein said second extension product comprises a sequence complementary to said first 3′ and

5′

regions and said second 3′ and

5′

regions, and the individual nucleic acid molecules of said second extension product comprise said plurality or pool of nucleic acid molecules;

b) separating error-containing nucleic acid molecules of said plurality or pool of nucleic acid molecules from error-free nucleic acid molecules of said plurality or pool of nucleic acid molecules by contacting said plurality or pool of nucleic acid molecules with a component that actively selects for a sequence error under conditions permitting said error-containing nucleic acid molecules to bind with the component that actively selects for a sequence error, wherein the component that actively selects for a sequence error only specifically binds to said error-containing nucleic acid molecules; and

c) removing or controlling errors in the plurality or pool of nucleic acid molecules by removing nucleic acid molecules that bind with the component that actively selects for a sequence error from the plurality or pool of nucleic acid molecules such that said error-containing nucleic acid molecules from said plurality or pool of nucleic acid molecules are separated from said error-free nucleic acid molecules.

2. The method of claim 1, wherein the errors in said error-containing nucleic acid molecules are mismatches and the component that actively selects for a sequence error is a mismatch recognition protein.

3. The method of claim 2, wherein the mismatch recognition protein is MutS or a functional homolog of MutS.

4. The method of claim 1, wherein the component that actively selects for a sequence error comprises more than one molecule.

5. The method of claim 1, further comprising a step of monitoring the synthesis of said plurality or pool of nucleic acid molecules by the steps of:

attaching a fluorescent group to the 5′

terminus of the oligonucleotide; and

detecting said plurality or pool of nucleic acid molecules using fluorescence microscopy.

6. The method of claim 1, wherein said first and second immobilized nucleic acids comprise at least a part of an oligonucleotide microarray.

7. The method of claim 6, wherein the oligonucleotide microarray comprises a plurality of regions, each of the regions containing only nucleic acids comprising a single, distinct sequence.

8. The method of claim 6, wherein the oligonucleotide has a 5′

region having a fluorescent group at 5′

terminus of the oligonucleotide.

9. The method of claim 8, further comprising a step of monitoring said plurality or pool of nucleic acid molecules by monitoring regional concentration of the fluorescent group at 5′

terminus of the oligonucleotide on the microarray, such that the presence of high concentration of the fluorescent group on a region of the microarray indicates that said plurality or pool of nucleic acid molecules are produced at said region of the microarray.