De novo synthesized gene libraries

• US 10,384,188 B2
• Filed: 12/13/2016
• Issued: 08/20/2019
• Est. Priority Date: 08/05/2013
• Status: Active Grant

• Current Assignee: Twist Bioscience Corporation
• Original Assignee: Twist Bioscience Corporation
• Inventors: Banyai, William, Peck, Bill James, Fernandez, Andres, Chen, Siyuan, Indermuhle, Pierre
• Primary Examiner(s): Levkovich, Natalia
• Application Number:
  US15/377,547
• Publication Number:
  US 20170095785A1
• Time in Patent Office: 980 Days
• Field of Search: 422552, 422551
• 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 2219/00313 the reactor vessels being formed by arrays of wells in blocks
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00587 High throughput processes
• CPC Class Codes: B01J 2219/0059 Sequential 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 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00619 using hydrophilic or hydrophobic regions
• CPC Class Codes: B01J 2219/00623 Immobilisation or binding
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00709 Type of synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12N 15/09 Recombinant DNA-technology
• CPC Class Codes: C12N 15/1093 General methods of preparing gene libraries, not provided for in other subgroups
• CPC Class Codes: C12N 15/1096 cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
• 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: C12N 15/74 : Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora
• CPC Class Codes: C12Q 1/6806 : Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 2525/117 : incorporating modified base
• CPC Class Codes: C12Q 2525/186 : incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2565/513 : characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/00 : Methods of creating libraries, e.g. combinatorial synthesis
• 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 50/18 : using a particular method of attachment to the solid support

Abstract

De novo synthesized large libraries of nucleic acids are provided herein with low error rates. Further, devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Longer nucleic acids can be synthesized in parallel using microfluidic assemblies. Further, methods herein allow for the fast construction of large libraries of long, high-quality genes. Devices for the manufacturing of large libraries of long and high-quality nucleic acids are further described herein.

Claims

1. A device for nucleic acid collection, comprising:

a) a plate, the plate comprising;

a base layer of the plate; and

one or more wells, wherein each well of the one or more wells comprises;

a side wall that extends vertically from the base layer;

an interior region of the well; and

an exterior region of the well,

wherein the exterior region of the well has a lower surface energy than the interior region of the well; and

b) a solid support structure, wherein the solid support structure comprises a plurality of clusters, wherein each cluster comprises a plurality of loci, wherein each locus comprises a substantially planar region having a single fluidic opening, wherein each cluster is vertically aligned to a respective well of the plate, wherein the solid support structure comprises nylon, nitrocellulose, polypropylene, silicon, silica, polystyrene, agarose, dextran, cellulosic polymer, polyacrylamide, or polydimethylsiloxane (PDMS), and wherein each cluster of the plurality of clusters has a lower surface energy than the interior region of each well of the plurality of wells of the plate.

2. The device of claim 1, wherein the solid support structure is in the form of a sheet.

3. The device of claim 1, wherein the plate is silicon or plastic.

4. The device of claim 1, wherein the interior region of the well has a width from 0.8 to 2.0 mm.

5. The device of claim 4, wherein the interior region of the well has a width of 1.15 mm.

6. The device of claim 1, wherein the side wall has a length from 0.1 to 0.6 mm.

7. The device of claim 6, wherein the side wall has a length of 0.45 mm.

8. The device of claim 1, wherein each well of the one or more wells comprises an aqueous liquid.

9. The device of claim 1, wherein the device further comprises an enclosure, and wherein the plate and the solid support structure are both within the enclosure.

10. The device of claim 1, wherein each well of the one or more wells comprises a sealing means located at a distal end of the side wall of said well.

11. The device of claim 1, wherein the interior region of each well of the one or more wells comprises a silane.

12. The device of claim 11, wherein the silane is methoxyethoxyundecyltrichlorosilane, methacryloxypropyltrimethoxysilane, ethyltrimethoxysilane, propyltrimethoxysilane, trifluoropropyltrimethoxysilane, 3-(2-aminoethyl)aminopropyltrimethoxysilane, p-tolyltrimethoxysilane, cyanoethyltrimethoxysilane, aminopropyltriethoxysilane, acetoxypropyltrimethoxysilane, phenyltrimethoxysilane, chloropropyltrimethoxysilane, mercaptopropyltrimethoxysilane, trichloro-octodecyl-silane, methyltrimethoxysilane, butyl-aldehyde-trimethoxysilane, heptadecafluorodecyltrimethoxysilane, or glycidoxypropyltrimethoxysilane.

13. The device of claim 1, wherein the exterior region of each well of the one or more wells comprises a fluorosilane.

14. The device of claim 13, wherein the fluorosilane is (tridecafluorotetrahydrooctyl)-triethoxysilane.

15. A device for nucleic acid collection, comprising:

a) a plate, the plate comprising;

a base layer of the plate; and

one or more wells, wherein each well of the one or more wells comprises;

a side wall that extends vertically from the base layer;

an interior region of the well; and

an exterior region of the well,

wherein the exterior region of the well has a lower surface energy than the interior region of the well; and

b) a solid support structure, wherein the solid support structure comprises a plurality of clusters, wherein each cluster comprises a plurality of loci, wherein each locus comprises a substantially planar region having a single fluidic opening, wherein each cluster is vertically aligned to a respective well of the plate, and wherein each cluster of the plurality of clusters has a lower surface energy than the interior region of each well of the plurality of wells of the plate.