Nucleic acid synthesis techniques

A method for synthesizing nucleic acid fragments, comprising:

• providing a plurality of oligonucleotides immobilized on a substrate via hybridization to a plurality of first immobilized primers complementary to the 5′ ends of the oligonucleotides, wherein each respective oligonucleotide comprises a first adapter sequence at a 5′ end;
• extending the oligonucleotides to generate extended polynucleotides corresponding to a fragment sequence, wherein the extending comprises incorporating a plurality of individual nucleotides or nucleic acids onto a 3′ end of the respective oligonucleotides of the plurality of oligonucleotides to generate the extended polynucleotides having the fragment sequence;
• attaching a second adapter sequence at the 3′ ends of the extended polynucleotides having the fragment sequence;
• annealing the 3′ ends of the extended polynucleotides to the substrate via a plurality of second immobilized primers complementary to the 3′ ends of the extended polynucleotides to form bridges;
• amplifying the bridges to form a plurality of amplified clusters;
• sequencing the plurality of amplified clusters to determine if one or more of the plurality of amplified clusters includes a sequence of the nucleic acid fragment;
• harvesting the one or more of the plurality of amplified clusters if a sequence of the one or more of the plurality of amplified clusters includes the sequence of the nucleic acid fragment or is complementary to the sequence of the nucleic acid fragment to generated harvested amplified clusters having the fragment sequence;
• and
• pooling the harvested amplified clusters having the fragment sequence with a second plurality of amplified clusters, wherein at least a portion of the second plurality of amplified clusters comprises a sequence complementary to only a portion of the fragment sequence.

A method for synthesizing a nucleic acid, comprising:

• providing a plurality of target sequences based on a sequence of the nucleic acid, wherein a combination of the plurality of target sequences form the sequence of the nucleic acid;
• providing a plurality of primer oligonucleotides immobilized on a substrate;
• extending the primer oligonucleotides in a single-stranded manner based on the plurality of target sequences in the presence of a first polymerase to generate a plurality of fragment polynucleotides;
• providing a first sequencing reagent to the plurality of fragment polynucleotides in the presence of a second polymerase, wherein the first sequencing reagent comprises one or more nucleotide monomers, and wherein the one or more nucleotide monomers form a plurality of polynucleotides complementary to at least a portion of the plurality of fragment polynucleotides;
• providing a second sequencing reagent to the plurality of fragment polynucleotides, wherein the second sequencing reagent comprises at least one nucleotide monomer, wherein the at least one nucleotide monomer of the second sequencing reagent comprises a reversibly terminating moiety, and wherein the second sequencing reagent is provided subsequent to providing the first sequencing reagent, whereby a sequence of each of the plurality of fragment polynucleotides is obtained;
• harvesting the plurality of fragment polynucleotides based on comparing the sequence of each of the plurality of fragment polynucleotides with the respective target sequence;
• and
• assembling the plurality of fragment polynucleotides to generate an assembled polynucleotide.

A method for synthesizing a nucleic acid, comprising:

• providing a starting polynucleotide sequence including a target sequence;
• receiving or accessing information representative of sequences of a plurality of overlapping nucleic acid fragments based on the target sequence, wherein the fragments are designed such that the fragments including the target sequence comprise discontinuities in a 5′ to 3′ direction, and wherein the discontinuities between nucleic acid fragments occur when the nucleic acid fragments are hybridized on a complementary strand to the target sequence;
• receiving sequencing information from amplified clusters, wherein the amplified clusters are amplified from bridges generated from synthesized fragments having the sequence of the plurality of nucleic acid fragments;
• and
• determining a quality of one or more of the plurality of amplified clusters based on the sequencing information.