Methods and devices for de novo oligonucleic acid assembly

Patent metadata

Field	Value
Publication number	US-2023331765-A1
Application number	US-202318319405-A
Country	US
Kind code	A1
Filing date	May 17, 2023
Priority date	Feb 4, 2015
Publication date	Oct 19, 2023
Grant date	—

Abstract

Methods and devices are provided herein for surfaces for de novo nucleic acid synthesis which provide for low error rates. In addition, methods and devices are provided herein for increased nucleic acid mass yield resulting from de novo nucleic acid synthesis.

First claim

What is claimed is:

1 . A method for preparing a surface for oligonucleic acid synthesis, the method comprising:
(a) providing a structure comprising a surface, wherein the structure comprises silicon dioxide; (b) depositing a first molecule on the surface at a first region, wherein the first molecule binds to the surface and lacks a reactive group that binds to a nucleoside phosphoramidite; (c) depositing a second molecule on the surface at a second region, wherein the second region comprises a plurality of loci surrounded by the first region, wherein the second molecule binds to the surface and lacks a reactive group that binds to the nucleoside phosphoramidite; and (d) depositing a mixture on the surface at the second region, wherein the mixture comprises the second molecule and a third molecule, wherein the third molecule binds to the surface and nucleoside phosphoramidite, and wherein the mixture comprises a greater amount of the second molecule than the third molecule.

2 . The method of claim 1 , wherein the second molecule and the third molecule both have a higher surface energy than a surface energy of the first molecule, and wherein surface energy is a measurement of water contact angle on a smooth planar surface.

3 . The method of claim 2 , wherein a difference in water contact angle between the first region and the second region is at least 10, 20, 50, or 75 degrees.

4 . The method of any one of claims 1 to 3 , wherein the third molecule is a silane.

5 . The method of any one of claims 1 to 4 , wherein the third molecule is N-(3-triethoxysilylpropyl)-4-hydroxybutyramide (HAPS), 11-acetoxyundecyltriethoxysilane, n-decyltriethoxysilane, (3-aminopropyl)trimethoxysilane, (3-aminopropyl)triethoxysilane, 3-glycidoxypropyltrimethoxysilane, 3-iodo-propyltrimethoxysilane, or octylchlorosilane.

6 . The method of any one of claims 1 to 5 , wherein the third molecule is 3-glycidoxypropyltrimethoxysilane.

7 . The method of claim 4 , wherein the silane is an aminosilane.

8 . The method of any one of claims 1 to 7 , wherein the second molecule is propyltrimethoxysilane.

9 . The method of any one of claims 1 to 8 , wherein the first molecule is a fluorosilane.

10 . The method of claim 9 , wherein the fluorosilane is (tridecafluoro-1,1,2,2-tetrahydrooctyl)trichlorosilane.

11 . The method of any one of claims 1 to 10 , wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of about 100:1 to about 2500:1.

12 . The method of claim 11 , wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of about 2000:1.

13 . The method of claim 12 , wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of 2000:1.

14 . The method of any one of claims 1 to 13 , wherein the first molecule lacks a free hydroxyl, amino, or carboxyl group.

15 . The method of any one of claims 1 to 14 , wherein the second molecule lacks a free hydroxyl, amino, or carboxyl group.

16 . The method of any one of claims 1 to 15 , wherein the mixture or the first molecule is in a gaseous state when deposited on the surface.

17 . The method of any one of claims 1 to 16 , wherein the surface comprises a layer of silicon oxide.

18 . A method for preparing a surface for oligonucleic acid synthesis, the method comprising:
(a) providing a structure comprising a surface, wherein the structure comprises silicon dioxide; wherein the surface comprises a layer of silicon oxide; (b) coating the surface with a light-sensitive material that binds silicon oxide; (c) exposing predetermined regions of the surface to a light source to remove a portion of the light-sensitive material coated on the surface; (d) depositing a first molecule on the surface, wherein the first molecule binds the surface at the predetermined regions and lacks a reactive group that binds to a nucleoside phosphoramidite; (e) removing a remaining portion of the light-sensitive material coated on the surface to expose loci, wherein each of the loci are surrounded by the predetermined regions comprising the first molecule; (f) depositing a second molecule on the surface at the loci, wherein the second molecule binds to the loci and lacks a reactive group that binds to the nucleoside phosphoramidite; and (g) depositing a mixture on the surface at the loci, the mixture comprises the second molecule and a third molecule, wherein the third molecule binds to the surface and nucleoside phosphoramidite.

19 . The method of claim 18 , wherein the second molecule and the third molecule both have a higher surface energy than a surface energy of the first molecule, and wherein surface energy is a measurement of water contact angle on a smooth planar surface.

20 . The method of claim 19 , wherein a difference in water contact angle between the first region and the second region is at least 10, 20, 50, or 75 degrees.

21 . The method of any one of claims 18 to 20 , wherein the third molecule is a silane.

22 . The method of any one of claims 18 to 21 , wherein the third molecule is N-(3-triethoxysilylpropyl)-4-hydroxybutyramide (HAPS), 11-acetoxyundecyltriethoxysilane, n-decyltriethoxysilane, (3-aminopropyl)trimethoxysilane, (3-aminopropyl)triethoxysilane, 3-glycidoxypropyltrimethoxysilane, 3-iodo-propyltrimethoxysilane, or octylchlorosilane.

23 . The method of any one of claims 18 to 22 , wherein the third molecule is 3-glycidoxypropyltrimethoxysilane.

24 . The method of claim 21 , wherein the silane is an aminosilane.

25 . The method of any one of claims 18 to 24 , wherein the second molecule is propyltrimethoxysilane.

26 . The method of any one of claims 18 to 25 , wherein the first molecule is a fluorosilane.

27 . The method of claim 26 , wherein the fluorosilane is (tridecafluoro-1,1,2,2-tetrahydrooctyl)trichlorosilane.

28 . The method of any one of claims 18 to 27 , wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of about 100:1 to about 2500:1.

29 . The method of claim 28 , wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of about 2000:1.

30 . The method of claim 29 , wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of 2000:1.

31 . The method of any one of claims 18 to 30 , wherein the first molecule lacks a free hydroxyl, amino, or carboxyl group.

32 . The method of any one of claims 18 to 31 , wherein the second molecule lacks a free hydroxyl, amino, or carboxyl group.

33 . The method of any one of claims 18 to 32 , wherein the first molecule is in a gaseous state when deposited on the surface.

34 . The method of any one of claims 18 to 33 , wherein the mixture is in a gaseous state when deposited on the surface.

35 . The method of any one of claims 18 to 34 , further comprising applying oxygen plasma to the surface prior to coating the surface with the light-sensitive material that binds silicon oxide.

36 . The method of any one of claims 18 to 35 , further comprising applying oxygen plasma to the surface after

Assignees

• Twist Bioscience Corp

Inventors

• Indermuhle Pierre F
• Marsh Eugene P
• Fernandez Andres
• Banyai William
• Peck Bill J

Classifications

• C07H21/04 Primary

  with deoxyribosyl as saccharide radical · CPC title

• B01J19/0046

  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 title

• C07H1/00

  Processes for the preparation of sugar derivatives · CPC title

• C12P19/34

  Polynucleotides, e.g. nucleic acids, oligoribonucleotides · CPC title

• C23C16/455

  characterised by the method used for introducing gases into reaction chamber or for modifying gas flows in reaction chamber · CPC title