Methods and devices for de novo oligonucleic acid assembly

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.

A method for oligonucleic acid synthesis, the method comprising:

• (a) providing predetermined sequences for at least 30,000 non-identical oligonucleic acids;
• (b) providing a structure comprising a patterned surface, wherein the structure comprises silicon dioxide;
• wherein the patterned surface is generated by:
• (i) 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;
• and
• (ii) 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
• (iii) 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, wherein the mixture comprises a greater amount of the second molecule than the third molecule;
• and
• (c) synthesizing the at least 30,000 non-identical oligonucleic acids each at least 10 bases in length, wherein the at least 30,000 non-identical oligonucleic acids encode sequences with an aggregate deletion error rate of less than 1 in 1500 bases compared to the predetermined sequences, and wherein each of the at least 30,000 non-identical oligonucleic acids extends from a different locus.

A method for nucleic acid synthesis, the method comprising

• (a) providing predetermined sequences for at least 200 preselected nucleic acids;
• (b) providing a structure comprising a patterned surface, wherein the structure comprises silicon dioxide;
• wherein the patterned surface is generated by:
• (i) 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;
• and
• (ii) 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
• (iii) 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, wherein the mixture comprises a greater amount of the second molecule than the third molecule;
• (c) synthesizing at least 20,000 non-identical oligonucleic acids each at least 50 bases in length, wherein each of the at least 20,000 non-identical oligonucleic acids extends from a different locus of the patterned surface;
• (d) releasing the at least 20,000 non-identical oligonucleic acids from the patterned surface;
• (e) suspending the at least 20,000 non-identical oligonucleic acids in a solution;
• and
• (f) subjecting the solution comprising at least 20,000 non-identical oligonucleic acids to a polymerase chain assembly reaction to assemble at least 200 genes, wherein the assembled at least 200 preselected nucleic acids encode sequences with an aggregate deletion error rate of less than 1 in 1500 bases compared to the predetermined sequences.

A device for oligonucleic acid synthesis, the device comprising:

• (a) a structure having a surface, wherein the structure comprises silicon dioxide;
• (b) a plurality of recesses or posts on the surface, wherein each recess or post comprises:
• (i) a width length that is 6.8 nm to 500 nm,
• (ii) a pitch length that is about twice the width length, and
• (iii) a depth length that is about 60% to about 125% of the pitch length;
• (c) a plurality of loci on the surface, wherein each locus has a diameter of 0.5 to 100 μm, wherein each locus comprises at least two of the plurality of recesses or posts;
• and
• (d) a plurality of clusters on the surface, wherein each of the clusters comprise 50 to 500 loci and has a cross-section of 0.5 to 2 mm.