Functionalized surfaces and preparation thereof

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.

What is claimed is: 
     
         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 comprises a reactive group capable of binding to a nucleoside;   synthesizing a first layer of oligonucleotides, wherein each oligonucleotide in the first layer of oligonucleotides comprises about 10 to about 100 bases in length and extends from the surface;   applying electromagnetic radiation (EMR) to a predetermined region of the surface to selectively remove a portion of the layer of oligonucleotides, wherein the EMR comprises a wavelength from about 100 nm to about 300 nm; and   synthesizing a second layer of oligonucleotides, wherein each oligonucleotide in the second layer of oligonucleotides extends oligonucleotides from the remaining portion of the first layer of oligonucleotides.   
     
     
         2 . The method of  claim 1 , wherein the surface comprises a plurality of loci for oligonucleotides extension, and wherein the 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. 
     
     
         3 . The method of  claim 1 , wherein the first set of molecules comprises an aminosilane. 
     
     
         4 . The method of  claim 1 , wherein the first 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. 
     
     
         5 . The method of  claim 1 , wherein the second layer of oligonucleotides comprises about 25 bases to about 2 kb in length. 
     
     
         6 . The method of  claim 1 , wherein the structure is a plate, tape, or belt. 
     
     
         7 . The method of  claim 1 , further comprising releasing the second layer of oligonucleotides and assembling a plurality of genes. 
     
     
         8 . The method of  claim 1 , wherein the predetermined region has a width of about 1 um to about 500 um. 
     
     
         9 . The method of  claim 1 , wherein the predetermined regions has a width of at least 3 um. 
     
     
         10 . The method of  claim 1 , wherein the predetermined region has a perimeter that is a circle or a rectangle in shape. 
     
     
         11 . The method of  claim 1 , wherein greater than about 90% of the first layer of oligonucleotides are removed at the predetermined region of the surface following application of EMR. 
     
     
         12 . The method of  claim 1 , wherein about 100% of the first layer of oligonucleotides are removed at the predetermined region of the surface following application of EMR. 
     
     
         13 . The method of  claim 1 , wherein the EMR comprises a wavelength from about 150 nm to about 200 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 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 lacks the reactive group capable of binding to the nucleoside. 
     
     
         19 . The method of  claim 18 , wherein the second set of molecules comprises a fluorosilane. 
     
     
         20 . The method of  claim 18 , wherein the second set of molecules comprises perfluorooctyltrichlorosilane, octylchlorosilane, octadecyltrichlorosilane, (tridecafluoro-1,1,2,2-tetrahydrooctyl)trichlorosilane, or tridecafluoro-1,1,2,2-tetrahydrooctyl)trimethoxysilane. 
     
     
         21 . A library of synthesized oligonucleic acids, comprising a plurality of different oligonucleic acids, each different oligonucleic acid extending from a structure at a different loci, wherein the different loci are at least about 75% uniform when measured by calculating amplitude of signal variation for oligonucleic acids extending from each locus divided by total signal intensity following white light illumination using an optical microscope. 
     
     
         22 . The library of  claim 21 , wherein the plurality of different oligonucleic acids comprises at least 20,000 different oligonucleic acids. 
     
     
         23 . The library of  claim 21 , wherein the oligonucleic acids extending from each locus are about 80% uniform when measured by calculating amplitude of signal variation for oligonucleic acids extending from each locus divided by total signal intensity following white light illumination using an optical microscope. 
     
     
         24 . A method for gene synthesis, the method comprising:
 providing predetermined sequences for a plurality of oligonucleic acids, wherein the plurality of oligonucleic acids collectively encode for a plurality of genes;   providing a surface for oligonucleic acid synthesis;   synthesizing the plurality of oligonucleic acids from the surface, wherein each oligonucleic acid 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 oligonucleic acids 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 oligonucleic acids.   
     
     
         25 . The method of  claim 24 , further comprising, prior to synthesizing:
 providing the surface for oligonucleic acid 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 oligonucleic acid extension.   
     
     
         26 . The method of  claim 25 , wherein greater than about 90% of the first set of molecules are removed at the predetermined regions of the surface following application of EMR. 
     
     
         27 . The method of  claim 25 , wherein about 100% of the first set of molecules are removed at the predetermined regions of the surface following application of EMR. 
     
     
         28 . The method of  claim 25 , wherein the predetermined regions have a width of about 1 to about 500 um. 
     
     
         29 . The method of  claim 25 , wherein the predetermined regions have a width of about 3 um to about 60 um. 
     
     
         30 . The method of  claim 25 , wherein the predetermined regions have a width of at least 3 um. 
     
     
         31 . The method of any one of  claim 25 , wherein the predetermined regions have a perimeter that is a circle or a rectangle in shape. 
     
     
         32 . The method of  claim 25 , wherein the first set of molecules comprises a fluorosilane. 
     
     
         33 . The method of  claim 25 , wherein the first set of molecules comprises perfluorooctyltrichlorosilane, octylchlorosilane, octadecyltrichlorosilane, (tridecafluoro-1,1,2,2-tetrahydrooctyl)trichlorosilane, or tridecafluoro-1,1,2,2-tetrahydrooctyl)trimethoxysilane. 
     
     
         34 . The method of  claim 25 , 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 a reactive group capable of binding to a nucleoside. 
     
     
         35 . The method of  claim 34 , wherein the second set of molecules comprises an aminosilane. 
     
     
         36 . The method of  claim 34 , 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 (GOP S), or 3-iodo-propyltrimethoxysilane. 
     
     
         37 . The method of  claim 24 , wherein each of the oligonucleic acids comprises about 25 bases to about 2 kb in length. 
     
     
         38 . The method of  claim 24 , wherein each locus comprises a population of oligonucleic acids about 80% uniform when measured by calculating amplitude of signal variation for oligonucleic acids extending from each locus divided by total signal intensity following white light illumination using an optical microscope. 
     
     
         39 . The method of  claim 25 , wherein the EMR comprises a wavelength from about 150 nm to about 200 nm. 
     
     
         40 . The method of  claim 25 , wherein the EMR has a wavelength of about 172 nm. 
     
     
         41 . The method of  claim 24 , wherein the surface is substantially planar. 
     
     
         42 . The method of  claim 24 , wherein the surface comprises microstructures. 
     
     
         43 . The method of  claim 42 , wherein the microstructures comprise channels or wells. 
     
     
         44 . The method of  claim 25 , wherein the EMR is emitted from a lamp or a laser.