Methods and devices for high fidelity polynucleotide synthesis

• US 8,808,986 B2
• Filed: 08/27/2009
• Issued: 08/19/2014
• Est. Priority Date: 08/27/2008
• Status: Active Grant

• Current Assignee: Gen9, Inc. (Ginkgo Bioworks Holdings, Inc.)
• Original Assignee: Gen9, Inc. (Ginkgo Bioworks Holdings, Inc.)
• Inventors: Jacobson, Joseph, Church, George, Chu, Larry Li-Yang
• Primary Examiner(s): Whisenant, Ethan C
• Application Number:
  US13/060,178
• Publication Number:
  US 20110172127A1
• Time in Patent Office: 1,818 Days
• Field of Search: 435/6.1, 536/22.1, 536/23.1, 536/24.3, 536/25.3
• US Class Current: 435/6.1
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00389 Feeding through valves
• CPC Class Codes: B01J 2219/0052 in the shape of elongated tubes
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00599 Solution-phase processes
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00693 Means for quality control
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 2400/0436 acoustic forces, e.g. surface acoustic waves [SAW]
• CPC Class Codes: B01L 2400/0439 ultrasonic vibrations, vibrating piezo elements
• CPC Class Codes: B01L 3/0268 using pulse dispensing or spraying, eg. inkjet type, piezo actuated ejection of droplets from capillaries
• CPC Class Codes: B01L 3/502792 for moving individual droplets on a plate, e.g. by locally altering surface tension
• CPC Class Codes: C12N 15/10 Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12N 15/1093 General methods of preparing gene libraries, not provided for in other subgroups
• CPC Class Codes: C12N 15/66 General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligation; Use of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6844 : Nucleic acid amplification reactions
• CPC Class Codes: C12Q 2521/514 : Mismatch repair protein
• CPC Class Codes: C12Q 2525/131 : incorporating a restriction site
• CPC Class Codes: C12Q 2565/501 : being an array of oligonucleotides

Abstract

Disclosed are methods for synthesizing and/or assembling at least one polynucleotide product having a predefined sequence from a plurality of different oligonucleotides. In exemplary embodiments, the methods involve synthesis and/or amplification of different oligonucleotides immobilized on a solid support, release of synthesized/amplified oligonucleotides in solution to form droplets, recognition and removal of error-containing oligonucleotides, moving or combining two droplets to allow hybridization and/or ligation between two different oligonucleotides, and further chain extension reaction following hybridization and/or ligation to hierarchically generate desired length of polynucleotide products.

Claims

1. A method for assembling a polynucleotide having a predefined sequence from a plurality of different oligonucleotides, the method comprising:

a) providing a plurality of single-stranded template oligonucleotides at different features on a solid support, wherein each of the plurality of template oligonucleotides comprises a predefined sequence, a primer binding site and a sequence region that is the same or complementary to a sequence region of a single-stranded oligonucleotide present at a different feature of the solid support;

b) generating a complementary oligonucleotide for each of the plurality of template oligonucleotides by enzyme-catalyzed synthesis within a primary droplet, thereby producing a plurality of double-stranded oligonucleotides;

c) releasing the complementary oligonucleotides from the double-stranded oligonucleotides into the primary droplet;

d) combining at least a first and second primary droplets on the support, thereby forming a secondary droplet, wherein the first primary droplet includes a released oligonucleotide that comprises a sequence region that is complementary to a sequence region of a released or template oligonucleotide from the second primary droplet; and

e) exposing the secondary droplet to conditions suitable for hybridization and ligation, polymerase extension, or polymerase extension and ligation to assemble a double-stranded polynucleotide having a predefined sequence.

2. The method of claim 1 wherein the plurality of single-stranded template oligonucleotides are synthesized onto the solid support.

3. The method of claim 1 wherein the plurality of template oligonucleotides are immobilized onto the solid support.

4. The method of claim 1 wherein the plurality of template oligonucleotides are spotted onto the solid support.

5. The method of claim 1 wherein each of the plurality of template oligonucleotides includes a universal primer binding site.

6. The method of claim 1 wherein at least one of the plurality of template oligonucleotides includes a primer binding site that is different than at least one other template oligonucleotides.

7. The method of claim 1 wherein each of the plurality of single-stranded oligonucleotides is provided on a different feature of the solid support.

8. The method of claim 1 wherein the complementary oligonucleotides are released in a plurality of primary droplets and wherein the plurality of primary droplets is separately defined by surface tension.

9. The method of claim 1 wherein at least one feature is spotted with a solution suitable for primer extension.

10. The method of claim 9 wherein the solution comprises a polymerase, a primer and dNTPs.

11. The method of claim 9 wherein the at least one feature is subjected to thermocycling promoting primer extension.

12. The method of claim 11 wherein the thermocycling is performed using a scanning laser.

13. The method of claim 11 wherein the thermocycling is modulated at individual features.

14. The method of claim 9 wherein spotting is performed using a mechanical wave liquid handler.

15. The method of claim 1 wherein the step of combining is performed by spotting a solution in between two first or two primary droplets.

16. The method of claim 1 wherein primary or secondary droplets are combined in parallel sets or two or more.

17. The method of claim 1 further comprising confirming the sequence of assembled polynucleotide.

18. The method of claim 1 further comprising for each assembled polynucleotide, consecutively interrogating the identity of each of a plurality of contiguous nucleotides of the polynucleotide thereby determining a sequence for each polynucleotide.

19. The method of claim 18 further comprising selectively isolating a polynucleotide determined to have a desired sequence from one or more polynucleotides determined not to have the desired sequence.

20. The method of claim 19 wherein the step of isolating comprises selectively inactivating one or more polynucleotides determined not to have the desired sequence.

21. The method of claim 19 wherein the step of isolating comprises selectively irradiating one or more polynucleotides determined not to have the desired sequence.

22. The method of claim 19 wherein the polynucleotides determined to have the correct sequence are selectively captured using a laser tweezer.

23. The method of claim 1 wherein the secondary droplet comprises at least two different oligonucleotides, wherein the oligonucleotides are at least about 20, at least about 50, at least about 100, at least about 200, at least about 300 nucleotides in length.

24. The method of claim 1 wherein the assembled polynucleotide is at least about 1,000, at least about 1,500, at least about 2,000, at least about 5,000, at least about 10,000, at least about 50,000 nucleotides in length.

51. The method of claim 1 or 25 further comprising the step of removing an error-containing oligonucleotide from a first plurality of oligonucleotides, comprising the steps of:

a) contacting the first plurality of oligonucleotides with a second plurality of oligonucleotides immobilized on a solid support under hybridization conditions to form duplexes, wherein the first plurality of oligonucleotides comprises sequences that are complementary to at least portions of the second plurality of oligonucleotides, wherein a first duplex comprising said error-containing oligonucleotide comprises a mismatch in a complementary region, and wherein a second duplex does not comprise a mismatch in the complementary region;

b) denaturing said first duplex comprising said error-containing oligonucleotide under stringent melt conditions without denaturing said second duplex;

c) removing said error-containing oligonucleotide from the solid support; and

d) denaturing said second duplex, thereby forming a purified plurality of oligonucleotides.

52. The method of claim 51, wherein the solid support is a microarray.

53. The method of claim 51, wherein each of the first plurality of oligonucleotides comprises a detectable tag at one terminus.

54. The method of claim 51, wherein each of the second plurality of oligonucleotides comprises a detectable tag at one terminus.

55. The method of claim 53 or 54, wherein the detectable tag comprises a fluorescence tag.

56. The method of claim 51, further comprising prior to step a):

synthesizing the first plurality of oligonucleotides in a chain extension reaction, wherein the second plurality of oligonucleotides serves as templates in the chain extension reaction; and

denaturing products of the chain extension reaction.

57. The method of claim 56, wherein said denaturing step comprises melting said products by raising temperature, using a helicase, or both.

58. The method of claim 51, further comprising reusing the solid support in synthesizing oligonucleotides, hybridizing oligonucleotides, or both.

59. The method of claim 51, further comprising using a digital mirror device to selectively heat different spots on the solid support.

60. The method of claim 51, further comprising repeating a)-c) at least one time prior to forming the purified plurality of oligonucleotides.

25. A method for assembling at least one polynucleotide having a predefined sequence, the method comprising:

a) providing a plurality of different oligonucleotides segregated in separate primary droplets, wherein each of the plurality of oligonucleotides is provided on a different feature of a solid support, wherein the plurality of oligonucleotides together comprise the polynucleotide sequence, and wherein each of said primary droplets comprises multiple copies of at least one of said plurality of different oligonucleotides;

b) combining at least two primary droplets, thereby forming a secondary droplet;

c) exposing the secondary droplet to hybridization conditions and ligation, chain extension, or chain extension and ligation to generate a polynucleotide having a predefined sequence;

d) combining at least two secondary droplets, each droplet comprising a different polynucleotide thereby generating a third stage droplet; and

e) exposing the third stage droplet to hybridization conditions and ligation, chain extension, or chain extension and ligation to generate a longer polynucleotide having a predefined sequence.

26. The method of claim 25 wherein the oligonucleotides are at least about 20, at least about 50, at least about 100, at least about 200, at least about 300nucleotides in length.

27. The method of claim 25 wherein the polynucleotides are at least about 1 kb, at least about 5 kb, at least about 10 kb, at least about 50 kb in length.

28. The method of claim 25 wherein the oligonucleotides comprise at least one primer binding site.

29. The method of claim 28 further comprising a pair of primers wherein the pair of primers are universal primers.

30. The method of claim 28 further comprising a pair of primers wherein the pair of primers are unique primers.

31. The method of claim 25 further comprising amplifying the oligonucleotides before combining the two primary droplets.

32. The method of claim 25 wherein the oligonucleotides are spotted onto the solid support.

33. The method of claim 25 wherein the oligonucleotides are immobilized onto the solid support.

34. The method of claim 25 wherein the oligonucleotides are synthesized onto the solid support.

35. The method of claim 25 wherein the droplets are separated to each others by surface tension.

36. The method of claim 32 wherein at least a portion of the features are spotted with a solution promoting amplification.

37. The method of claim 36 wherein the solution comprises a polymerase, a primer pair and dNTPs.

38. The method of claim 25 wherein at least one primary droplet is subjected to thermocycling promoting amplification.

39. The method of claim 25 wherein hybridization conditions comprise controlling the temperature of at least one droplet.

40. The method of claim 38 or 39 wherein the temperature control or the thermocycling is performed using a scanning laser.

41. The method of claim 40 wherein the thermocycling is modulated at individual features.

42. The method of claim 32 or 36 wherein spotting is performed using an acoustic liquid handler.

43. The method of claim 25 wherein the step of combining is performed by spotting a solution in between two first or two secondary droplets.

44. The method of claim 25 wherein a plurality of two primary or secondary droplets are combined in parallel.

45. The method of claim 25 further comprising determining the sequence of the assembled polynucleotides.

46. The method of claim 25 further comprising for each assembled polynucleotide, consecutively interrogating the identity of each of a plurality of contiguous nucleobases of the polynucleotide thereby determining a sequence for each polynucleotide.

47. The method of claim 46 further comprising selectively isolating the polynucleotides determined to have a desired sequence from one or more polynucleotide determined not to have the desired sequence.

48. The method of claim 46 wherein the step of isolating comprises selectively inactivating one or more polynucleotides determined not to have the desired sequence.

49. The method of claim 47 wherein the step of isolating comprises selectively irradiating one or more polynucleotides determined not to have the desired sequence.

50. The method of claim 47 wherein the polynucleotides determined to have the correct sequence are selectively captured using a laser tweezer.

61. A method of assembling a polynucleotide product on a solid support comprising:

a) moving a first droplet comprising a first plurality of oligonucleotides from a first spot on said solid support to a second spot on said solid support, wherein said second spot comprises a second plurality of oligonucleotides, wherein a terminal region of said second plurality of oligonucleotides comprises complementary sequences with a terminal region of said first plurality of oligonucleotides; and

b) contacting said first and second plurality of oligonucleotides under conditions that allow one or more of;

annealing, chain extension, and denaturing.

62. The method of claim 61, further comprising moving a second droplet from a third spot to a fourth spot substantially in parallel to step a), wherein the second droplet comprising a third plurality of oligonucleotides, wherein said fourth spot comprises a fourth plurality of oligonucleotides, and wherein a terminal region of said third or fourth plurality of oligonucleotides comprises complementary sequences with a terminal region of said first or second plurality of oligonucleotides.

63. The method of claim 62, further comprising hierarchically assembling said polynucleotide product that comprises sequence of said first, second, third, and fourth plurality of oligonucleotides.

64. The method of claim 61, wherein said first droplet is moved by a surface acoustic wave device.