Universal template strands for enzymatic polynucleotide synthesis

A method of synthesizing a plurality of polynucleotides having different, predetermined sequences, the method comprising:

• a. contacting primer regions of a plurality of universal template strands with complementary primers, wherein the universal template strands comprise universal regions consisting of a mixture of natural bases and universal base analogs and the universal template strands are bound to a solid substrate;
• b. removing blocking groups from nucleotides hybridized to a subset of the universal template strands;
• c. contacting the plurality of universal template strands with a protected nucleotide selected according to a predetermined polynucleotide sequence and a polymerase so that the protected nucleotide is incorporated into one or more complementary primers or extended versions thereof hybridized to the subset of the universal template strands;
• and
• d. repeating steps b-c with variations in the subset of the universal template strands and in a base of the protected nucleotide to synthesize the plurality of polynucleotides having different, predetermined sequences.

A system for synthesizing a plurality of polynucleotides having different, predetermined sequences, the system comprising:

• a solid substrate coated with a plurality of universal template strands comprising primer regions and universal regions, wherein the universal regions comprise a mixture of natural bases and universal base analogs;
• a reaction chamber containing the solid substrate;
• a plurality of fluid delivery pathways each configured to introduce a single species of protected nucleotide into the reaction chamber;
• and
• control circuitry configured to selectively change local conditions on a portion of the surface of the solid substrate resulting in cleavage of blocking groups attached to the protected nucleotides and to selectively open the plurality of fluid delivery pathways to introduce protected nucleotides into the reaction chamber according to a predetermined polynucleotide sequence.