Apparatus and methods for synthesizing biopolymers

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.

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.