Apparatus and methods for synthesizing biopolymers

1 . An apparatus for synthesizing a biopolymer, the apparatus comprising:

(a) a substrate comprising a passivized top surface and a plurality of wells, wherein each of the plurality of wells comprises a first electrode disposed on the bottom of the well and a linker attached to the sides of the well; and

(b) a fluidic chamber system disposed on the top surface of the substrate, wherein the diameter of a first well of the plurality of wells is about 1 μm to about 200 μm.

2 . The apparatus according to claim 1 , wherein the substrate is selected from glass, sputtered SiO 2 , and SiO 2 .

3 . The apparatus according to claim 1 , wherein the depth of the first well is from about 500 nm to about 500 μm.

4 . The apparatus according to claim 1 , wherein the depth of the first well is from about 1 μm to 10 μm.

5 . The apparatus according to claim 1 , further comprising a system for introducing and removing liquids from the first well.

6 . A method for preparing an apparatus, comprising

a. forming a plurality of wells on a substrate;

b. applying a first electrode to the bottom of a first well of the plurality of wells;

c. passivating a connection of the first electrode;

d. attaching a linker to the sides of the first well; and

e. affixing a fluidic chamber onto the substrate.

7 . The method of claim 6 , wherein step (a) comprises:

i. applying a photo resist onto the surface of the substrate to define the plurality of wells; and

ii. etching the substrate to create the plurality of wells.

8 . The method of claim 7 , wherein the substrate is selected from glass, sputtered SiO 2 , and SiO 2 .

9 . The method of claim 7 , wherein the first electrode is a material selected from gold, iridium, palladium, platinum or carbon.

10 . The method of claim 7 , wherein step (b) comprises physical vapor deposition of material selected from gold, iridium, palladium, platinum or carbon.

11 . The method of claim 8 , wherein step (b) further comprises removing the photo resist.

12 . The method of claim 7 , wherein step (c) comprises immersing the substrate from step (b) into a linker solution for a period of time; and removing the linker solution.

13 . The method of claim 7 , wherein the apparatus further comprises a system for introducing and removing liquids from the first well.

14 . A method of synthesizing an oligonucleotide, the method comprising

(a) providing an apparatus, the apparatus comprising:

i. a substrate comprising a passivized top surface and a plurality of wells, wherein each of the plurality of wells comprises a first electrode disposed on the bottom of the well and a linker attached to the sides of the well; and

ii. a fluidic chamber system disposed on the top surface of the substrate;

(b) introducing a solution comprising a first nucleoside phosphoramidite monomer and an activator into a first well of the plurality of wells, wherein the first nucleoside phosphoramidite monomer comprises a 5′-protecting group, an acid sensitive protecting group and optionally a base sensitive protecting group, and wherein the first nucleoside phosphoramidite monomer reacts with the linker attached to the side walls of the first well to form a linked nucleoside through a phosphite triester;

(c) removing the solution from step (b) from the first well;

(d) introducing a solution comprising a capping reagent into the well, wherein the capping reagent reacts with any unreacted linker from step (b) to form a capped linker;

(e) removing the solution from step (d) from the first well;

(f) introducing a solution comprising an oxidant into the first well, wherein the oxidant converts the phosphite triester of the linked nucleoside to a phosphate triester;

(g) removing the solution from step (f) from the first well;

(h) introducing a solution comprising a first deprotecting reagent into the first well, wherein an electrochemically generated proton in the first deprotecting reagent removes the 5′-protecting group;

(i) removing the solution from step (h) from the first well;

(j) repeating steps (b) through (i) to synthesize a protected oligonucleotide; and

(k) introducing a solution comprising a second deprotecting reagent into the first well, wherein the second deprotecting agent removes the protecting groups on the oligonucleotide.

15 . The method of claim 14 , wherein the capping reagent is acetic anhydride.

16 . The method of claim 14 , wherein the capped linker comprises an acetate group.

17 . The method of claim 14 , wherein the oxidant is (1S)-(+)-(10-camphorsulfonyl)-oxaziridine (CSO).

18 . The method of claim 14 , wherein the first deprotecting reagent removes a 5′-dimethyltrityl group.

19 . The method of claim 18 , wherein the first deprotecting reagent is hydroquinone.

20 . The method of claim 14 , wherein the second deprotecting reagent removes a phosphate protecting group.

21 . The method of claim 14 , wherein the second deprotecting reagent removes the base protecting groups.

22 . The method of claim 20 , wherein the second deprotecting reagent is ethylenediamine.