Methods and apparatuses for chip-based DNA error reduction

• US 9,422,600 B2
• Filed: 06/20/2011
• Issued: 08/23/2016
• Est. Priority Date: 11/25/2009
• Status: Active Grant

• Current Assignee: Gen9, Inc. (Ginkgo Bioworks Holdings, Inc.)
• Original Assignee: Gen9, Inc. (Ginkgo Bioworks Holdings, Inc.)
• Inventors: Ramu, Senthil, Jacobson, Joseph
• Primary Examiner(s): Lu, Frank
• Application Number:
  US13/164,045
• Publication Number:
  US 20120028843A1
• Time in Patent Office: 1,891 Days
• Field of Search: 435/6.1, 435/6.11, 435/91.1, 435/183, 435/283.1, 435/287.1, 435/287.2, 435/6.12, 435/91.2, 436/94, 436/501, 536/23.1, 536/24.3, 536/24.33, 536/25.3
• US Class Current: 1/1
• CPC Class Codes: C12N 15/1058 Directional evolution of libraries, e.g. evolution of libraries is achieved by mutagenesis and screening or selection of mixed population of organisms
• 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 2565/537 characterised by the capture oligonucleotide acting as a primer

Abstract

Methods and apparatus relate to reduction of sequence errors generated during synthesis of nucleic acids on a microarray chip. The error reduction can include synthesis of complementary stands (to template strands), using a short universal primer complementary to the template strands and polymerase. Heteroduplex can be formed be melting and re-annealing complementary stands and template strands. The heteroduplexes containing a mismatch can be recognized and cleaved by a mismatch endonuclease. The mismatch-containing cleaved heteroduplexes can be removed from the microarray chip using a global buffer exchange. The error free synthetic nucleic acids generated therefrom can be used for a variety of applications, including synthesis of biofuels and value-added pharmaceutical products.

Claims

1. A method for producing a population of double-stranded oligonucleotides having improved fidelity on a solid support, the method comprising:

(a) contacting, on a solid support, a plurality of support-bound single-stranded oligonucleotides with a solution comprising a primer and a polymerase enzyme under conditions suitable for a template-dependent synthesis reaction, thereby producing a plurality of double-stranded oligonucleotides comprising synthesized complementary oligonucleotides base paired with the support-bound single-stranded oligonucleotides, wherein the support-bound single-stranded oligonucleotides are bound on the solid support at their 3′

ends and comprise error-free oligonucleotides and error-containing oligonucleotides;

(b) denaturing the plurality of double-stranded oligonucleotides such that the synthesized complementary oligonucleotides are released in one or more droplets;

(c) reannealing the synthesized complementary oligonucleotides in the one or more droplets to the support-bound single-stranded oligonucleotides, thereby producing reannealed double-stranded oligonucleotides comprising homoduplexes and heteroduplexes, wherein each of the heteroduplexes comprises a mismatch;

(d) exposing the reannealed double-stranded oligonucleotides to a mismatch recognizing and cleaving component under conditions suitable for cleavage of the heteroduplexes, thereby cleaving at least a portion of the heteroduplexes; and

(e) removing at least a portion of the cleaved heteroduplexes, thereby producing the population of double-stranded oligonucleotides having improved fidelity on the solid support.

3. The method of claim 1 or 2 further comprising selectively denaturing the population of double-stranded oligonucleotides having improved fidelity.

4. A method of assembling nucleic acid polymers comprising the steps of:

(a) producing two or more populations of double-stranded oligonucleotides having improved fidelity according to the method of claim 1 or 2;

(b) denaturing selected populations of the double-stranded oligonucleotides from the two or more populations of double-stranded oligonucleotides having improved fidelity, thereby releasing at least a first desirable pool and a second desirable pool of single-stranded oligonucleotides having improved fidelity in a solution;

(c) combining the at least a first desirable pool and a second desirable pool of single-stranded oligonucleotides into a droplet;

(d) subjecting the single-stranded oligonucleotides in the droplet to conditions suitable for hybridization, and

(e) assembling the nucleic acid polymers by ligation, or by chain extension, or by chain extension and ligation of the single-stranded oligonucleotides.

8. The method of claim 1 or 2 wherein the mismatch recognizing and cleaving component comprises a mismatch endonuclease.

9. The method of claim 1 or 2 wherein the mismatch recognizing and cleaving component performs a chemical cleavage.

10. The method of claim 1 or 2 wherein the removing step comprises buffer exchange.

11. The method of claim 1 or 2 wherein the solid support is a microarray.

12. The method of claim 1 wherein the removing step reduces the number of error-containing oligonucleotides on the solid support.

13. The method of claim 1 further comprising denaturing the population of double-stranded oligonucleotides having improved fidelity obtained in the removing step.

2. A method for producing a population of double-stranded oligonucleotides having improved fidelity on a solid support, the method comprising:

(a) synthesizing a first plurality of oligonucleotides in a chain extension reaction using a second plurality of support-bound oligonucleotides as templates in the presence of a solution comprising a primer, wherein the second plurality of oligonucleotides is bound on a solid support at their 3′

ends and comprise an error-containing oligonucleotide having a sequence error at an error-containing position, thereby producing a first plurality of duplexes, wherein the first plurality of duplexes comprises homoduplexes;

(b) denaturing the first plurality of duplexes, thereby releasing the first plurality of oligonucleotides in one or more droplets, wherein the first plurality of oligonucleotides comprise error-free oligonucleotides that are free of error at a position corresponding to the error-containing position of the error-containing oligonucleotide in the second plurality of oligonucleotides;

(c) contacting the first plurality of oligonucleotides in the one or more droplets with the second plurality of oligonucleotides under hybridization conditions such that a second plurality of duplexes is formed, wherein the second plurality of duplexes comprise a mismatch-containing heteroduplex formed between the error-containing oligonucleotide and one of the error-free oligonucleotides;

(d) cleaving the mismatch-containing heteroduplex by a mismatch recognizing and cleaving component; and

(e) removing the mismatch-containing heteroduplex, thereby producing the population of double-stranded oligonucleotides having improved fidelity on the solid support.

5. The method of claim 2 wherein the second plurality of oligonucleotides are chemically synthesized on the solid support and immobilized within one or more features on the solid support.

6. The method of claim 2 wherein the first plurality of oligonucleotides are enzymatically synthesized on the solid support.

7. The method of claim 2 wherein the second plurality of oligonucleotides are attached to two or more features on the solid support and wherein after step (b), one or more of the first plurality of oligonucleotides diffuse away from the two or more features.

14. A method for producing at least one support-bound error-free oligonucleotide having a predefined sequence on a solid support, the method comprising:

(a) synthesizing a first plurality of oligonucleotides on a solid support using a second plurality of support-bound oligonucleotides as templates in the presence of at least one primer, wherein the second plurality of support-bound oligonucleotides is bound on the solid support at their 3′

ends,

wherein the at least one primer is complementary to a primer binding site on the second plurality of oligonucleotides,

wherein each of the second plurality of oligonucleotides has a predefined sequence, and wherein at least one of the second plurality of support-bound oligonucleotides comprises a sequence error;

(b) releasing the first plurality of oligonucleotides in one or more droplets;

(c) contacting the second plurality of support-bound oligonucleotides with the first plurality of oligonucleotides in the one or more droplets under hybridization conditions such that a plurality of double-stranded oligonucleotides is formed, wherein the plurality of double-stranded oligonucleotides comprises a double-stranded oligonucleotide having a mismatch with the sequence error;

(d) contacting and cleaving the second plurality of double-stranded oligonucleotides with a mismatch binding agent, wherein the mismatch binding agent selectively binds and cleaves the double-stranded oligonucleotide having the mismatch; and

(e) removing the double-stranded oligonucleotide having the mismatch, thereby producing the at least one support-bound error-free oligonucleotide having the predefined sequence on the solid support.

15. The method of claim 14 wherein the mismatch binding agent is a mismatch specific endonuclease.

16. The method of claim 15 wherein the mismatch specific endonuclease cleaves the nucleotide at the region of the mismatch.

17. The method of claim 15 wherein the mismatch specific endonuclease is a CEL enzyme.

18. The method of claim 14 wherein the first plurality of oligonucleotides in the releasing step is released under denaturing conditions.

19. The method of claim 14 wherein the second plurality of oligonucleotides is bound to one or more discrete features of the solid support and wherein the one or more features are selectively hydrated such that the second plurality of oligonucleotides are present within the one or more droplets.

20. The method of claim 19 wherein the synthesizing step further comprises selectively hydrating the one or more features by spotting a solution comprising the at least one primer, a polymerase, dNTPs, and a buffer capable of promoting primer extension.

21. The method of claim 14 further comprising releasing at least one error-free single-stranded oligonucleotide in solution.