Functionalized surfaces and preparation thereof

• US 9,895,673 B2
• Filed: 11/30/2016
• Issued: 02/20/2018
• Est. Priority Date: 12/01/2015
• Status: Active Grant

• Current Assignee: Twist Bioscience Corporation
• Original Assignee: Twist Bioscience Corporation
• Inventors: Peck, Bill James, Indermuhle, Pierre, Marsh, Eugene P., Fernandez, Andres, Stern, David
• Primary Examiner(s): Gross, Christopher M
• Application Number:
  US15/365,826
• Publication Number:
  US 20170151546A1
• Time in Patent Office: 447 Days
• Field of Search: None
• 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 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00441 using lasers
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00619 using hydrophilic or hydrophobic regions
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00693 Means for quality control
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides

Abstract

Compositions, devices, methods and systems are provided for differential functionalization of a surface of a structure to support biopolymer synthesis. Provided herein are processes which include use of lamps, lasers, and/or microcontact printing to add functional groups to surfaces for the efficient and uniform synthesis of oligonucleic acids.

Claims

1. A method for surface patterning, the method comprising:

applying a first set of molecules to a surface of a structure, wherein each of the first set of molecules binds to the surface and lacks a reactive group capable of binding to a nucleo side;

applying electromagnetic radiation (EMR) to predetermined regions of the surface, wherein the EMR comprises a wavelength from about 100 nm to about 300 nm, wherein application of the EMR results in removal of the first set of molecules at the predetermined regions, thereby defining different loci for oligonucleotide extension; and

synthesizing a plurality of oligonucleotides, wherein each oligonucleotide extends from a different locus, and wherein the different loci are at least about 75% uniform when measured by calculating amplitude of signal variation for oligonucleotides extending from each locus divided by total signal intensity following white light illumination using an optical microscope.

2. The method of claim 1, wherein greater than about 90% of the first set of molecules are removed at the predetermined regions of the surface following application of EMR.

3. The method of claim 1, wherein about 100% of the first set of molecules are removed at the predetermined regions of the surface following application of EMR.

4. The method of claim 1, wherein the predetermined regions have a width of about 1 um to about 500 um.

5. The method of claim 1, wherein the first set of molecules comprises a fluorosilane.

6. The method of claim 1, wherein the first set of molecules comprises perfluorooctyltrichlorosilane, (tridecafluoro-1,1,2,2-tetrahydrooctyl)trichlorosilane, or tridecafluoro-1,1,2,2-tetrahydrooctyl)trimethoxysilane.

7. The method of claim 1, further comprising applying a second set of molecules to the surface after application of the EMR, wherein each of the second set of molecules binds to the predetermined regions of the surface and comprises the reactive group capable of binding to a nucleoside.

8. The method of claim 7, wherein the second set of molecules comprises an aminosilane.

9. The method of claim 7, wherein the second set of molecules comprises N-(3-triethoxysilylpropyl)-4-hydroxybutyramide (HAPS), 11-acetoxyundecyltriethoxysilane, n-decyltriethoxysilane, (3-aminopropyl)trimethoxysilane, (3-aminopropyl)triethoxysilane, 3-glycidoxypropyltrimethoxysilane (GOPS), or 3-iodo-propyltrimethoxysilane.

10. The method of claim 1, wherein each of the oligonucleotides comprises about 25 bases to about 2 kb in length.

11. The method of claim 1, wherein the oligonucleotides extending from each locus are about 80% uniform when measured by calculating amplitude of signal variation for oligonucleotides extending from each locus divided by total signal intensity following white light illumination using an optical microscope.

12. The method of claim 1, wherein the EMR comprises a wavelength from about 150 nm to about 200 nm.

13. The method of claim 1, wherein the EMR comprises has a wavelength of about 172 nm.

14. The method of claim 1, wherein the surface is substantially planar.

15. The method of claim 1, wherein the surface comprises microstructures.

16. The method of claim 15, wherein the microstructures comprise channels or wells.

17. The method of claim 1, wherein the EMR is emitted from a lamp or a laser.

18. The method of claim 17, wherein the lamp comprises an emission source in a shape of a cylinder or a flat panel.

19. The method of claim 1, wherein the structure is a plate, tape, or belt.

20. A method for gene synthesis, the method comprising:

providing predetermined sequences for a plurality of oligonucleotides, wherein the plurality of oligonucleotides collectively encode for a plurality of genes;

providing a surface for oligonucleotide synthesis;

synthesizing the plurality of oligonucleotides from the surface, wherein each oligonucleotide extends from a different locus, and wherein the different loci are at least about 75% uniform when measured by calculating amplitude of signal variation for oligonucleotides extending from each locus divided by total signal intensity following white light illumination using an optical microscope; and

assembling the plurality of genes from the plurality of oligonucleotides.

21. The method of claim 20, further comprising, prior to synthesizing:

providing the surface for oligonucleotide synthesis, wherein the surface comprises a first set of molecules, wherein each of the first set of molecules lacks a reactive group capable of binding to a nucleoside;

applying electromagnetic radiation (EMR) to predetermined regions of the surface, wherein the EMR comprises a wavelength from about 100 nm to about 300 nm, wherein application of the EMR results in removal of the first set of molecules at the predetermined regions, thereby defining loci for oligonucleotide extension.