Microarray synthesis and assembly of gene-length polynucleotides

• US 9,051,666 B2
• Filed: 09/14/2012
• Issued: 06/09/2015
• Est. Priority Date: 09/12/2002
• Status: Expired due to Term

• Current Assignee: Gen9, Inc. (Ginkgo Bioworks Holdings, Inc.)
• Original Assignee: Gen9, Inc. (Ginkgo Bioworks Holdings, Inc.)
• Inventors: Oleinikov, Andrew V.
• Primary Examiner(s): Kim, Young J
• Application Number:
  US13/617,685
• Publication Number:
  US 20130017977A1
• Time in Patent Office: 998 Days
• US Class Current: 1/1
• 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 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00385 Printing
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00454 by chemical cleavage from the solid support
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00639 the compounds being trapped in or bound to a porous medium
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00713 Electrochemical synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12N 15/1068 : Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/14 : Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: C40B 80/00 : Linkers or spacers specially adapted for combinatorial chemistry or libraries, e.g. traceless linkers or safety-catch linkers

Abstract

There is disclosed a process for in vitro synthesis and assembly of long, gene-length polynucleotides based upon assembly of multiple shorter oligonucleotides synthesized in situ on a microarray platform. Specifically, there is disclosed a process for in situ synthesis of oligonucleotide fragments on a solid phase microarray platform and subsequent, “on device” assembly of larger polynucleotides composed of a plurality of shorter oligonucleotide fragments.

Claims

1. A process for creating a mixture of double-stranded fragments in solution comprising:

(a) synthesizing in situ or spotting a plurality of oligonucleotide sequences on a microarray device or bead device each having a solid or porous surface, wherein the plurality of oligonucleotide sequences are attached to the solid or porous surface and wherein each oligonucleotide sequence comprises a fragment of a target polynucleotide sequence;

(b) amplifying each oligonucleotide sequence to form a plurality of double-stranded oligonucleotide sequences using a primer complementary to a primer region of at least one flanking sequence located at the 3′

end, the 5′

end, or the 3′

end and the 5′

end of each fragment, wherein the at least one flanking sequence is from about 7 to about 50 bases and comprises the primer region and a sequence segment having a restriction enzyme cleavable site; and

(c) cleaving the primer regions from the plurality of double-stranded oligonucleotide sequences at the restriction enzyme cleavable sites, thereby to produce a plurality of double-stranded fragments of the target polynucleotide sequence,

wherein the plurality of double-stranded fragments together comprise the target polynucleotide sequence.

2. The process of claim 1, wherein the at least one flanking sequence is from about 10 to about 20 bases in length.

3. The process of claim 1, wherein the restriction enzyme cleavable site is a class II endonuclease restriction site sequence.

4. The process of claim 3, wherein the restriction endonuclease class II site corresponds to the restriction site for a restriction endonuclease class II enzyme selected from the group consisting of Mly I, BspM I, Bae I, BsaX I, Bsr I, Bmr I, Btr I, Bts I, Fok I, and combinations thereof.

5. The process of claim 1, wherein the at least one flanking sequence further comprises a binding moiety used to purify cleaved oligonucleotides from flanking sequences.

6. The process of claim 1, wherein the process further comprises the step of labeling the at least one flanking sequence during the amplification step (b) using primer sequences labeled with binding moieties.

7. The process of claim 6, wherein the binding moiety is biotin, or fluorescein.

8. The process of claim 1, wherein the at least one flanking sequence for each oligonucleotide is the same.

9. The process of claim 1, wherein the plurality of oligonucleotide sequences has two or more different flanking sequences.

10. The process of claim 1, wherein the at least one flanking sequence is designed to have minimal homology to the oligonucleotide sequences.

11. The process of claim 1, wherein the at least one flanking sequence has a plurality of restriction enzyme cleavable sites.

12. The process of claim 11, wherein at least one restriction enzyme cleavable site is a class II endonuclease restriction sequence.

13. The process of claim 1, further comprising purifying the cleaved double-stranded oligonucleotide sequences by size fractionation.

14. A process for creating a mixture of double-stranded fragments in solution comprising:

(a) providing a plurality of oligonucleotide sequences bound on a solid surface, wherein each oligonucleotide sequence comprises a fragment of a target polynucleotide sequence;

(b) amplifying each oligonucleotide sequence to form a plurality of double-stranded oligonucleotide sequences using a primer complementary to a primer region of at least one flanking sequence located at the 3′

end, the 5′

end, or the 3′

end and the 5′

end of each fragment, wherein the at least one flanking sequence comprises the primer region and a sequence segment having a restriction enzyme cleavable site, and wherein the plurality of oligonucleotides has two or more different flanking sequences; and

(c) cleaving the primer region from the plurality of double-stranded oligonucleotide sequences at the restriction enzyme cleavable sites, thereby to produce a plurality of double-stranded fragments,

wherein the plurality of double-stranded fragments together comprise the target polynucleotide sequence.

15. The process of claim 14, wherein each double-stranded oligonucleotide sequence has an overlapping region corresponding to a next oligonucleotide sequence within the polynucleotide sequence.

16. The process of claim 14, wherein the restriction enzyme cleavable site is a class II endonuclease restriction site sequence.

17. The process of claim 16, wherein the restriction endonuclease class II site corresponds to the restriction site for a restriction endonuclease class II enzyme selected from the group consisting of Mly I, BspM I, Bae I, BsaX I, Bsr I, Bmr I, Btr I, Bts I, Fok I, and combinations thereof.

18. The process of claim 14 wherein the at least one flanking sequence has a plurality of restriction enzyme cleavable sites.

19. The process of claim 18, wherein at least one restriction enzyme cleavable site is a class II endonuclease restriction sequence.

20. A process for creating a mixture of double-stranded fragments in solution comprising:

providing a plurality of oligonucleotides sequences, wherein each oligonucleotide sequence comprises a fragment of a target polynucleotide sequence and further comprises at least one flanking sequence, at the 3′

end, the 5′

end, or the 3′

end and the 5′

end of each fragment, wherein each flanking sequence comprises a primer region and a sequence segment having a restriction enzyme cleavable site;

amplifying each oligonucleotide sequence using a primer complementary to the primer region of the at least one flanking sequence to form a plurality of double-stranded oligonucleotide sequences; and

cleaving the primer region from the plurality of double-stranded oligonucleotide sequences at the restriction enzyme cleavable sites, thereby to produce a plurality of double-stranded fragments,

wherein the plurality of double-stranded fragments together comprise the target polynucleotide sequence.

21. The process of claim 20, wherein the plurality of oligonucleotide sequences has two or more different flanking region sequences.

22. A process for creating a mixture of double-stranded oligonucleotide sequences in solution, the process comprising

providing a plurality of oligonucleotides sequences, wherein each oligonucleotide sequence comprises a fragment of a target polynucleotide sequence and wherein each oligonucleotide further comprises at least one flanking sequence at the 3′

end, the 5′

end, or at the 3′

end and the 5′

end of each fragment, wherein the at least one flanking sequence comprises a primer binding site, each primer binding region being complementary to a primer permitting amplification of the plurality of oligonucleotides; and

subjecting the plurality of oligonucleotides sequences to amplification to form double-stranded oligonucleotides comprising double-stranded fragments, the double-stranded fragments together comprising the target polynucleotide sequence.

23. The process of claim 22, wherein the at least one flanking sequence further comprises a sequence segment permitting removal of the primer binding sites.

24. The process of claim 23, wherein the sequence segment permitting removal of the primer binding site is a class II endonuclease restriction site sequence.

25. The process of claim 22, wherein each oligonucleotide further comprises a cleavable linker moiety.

26. The process of claim 22, wherein the at least one flanking sequence is designed to have minimal homology to the oligonucleotide sequences.

27. The process of claim 22, wherein each oligonucleotide has a sequence region that is the same as or complementary to the sequence region of the next oligonucleotide.

28. The process of claim 22, wherein the plurality of oligonucleotides are provided bound on a solid or porous surface.