Methods and compositions for capping nucleic acids

A method for sequencing two template regions in a nucleic acid, comprising

• (a) providing a nucleic acid comprising a first primer-template hybrid and a second primer-template hybrid, wherein the first hybrid comprises a first template region hybridized to a first primer, and wherein the second hybrid comprises a second template hybridized to a second primer, the second primer comprising a ternary complex inhibitor moiety at the 3′ end of the second primer;
• (b) performing a sequencing process, comprising:
• (i) binding the first hybrid to a polymerase and nucleotide to form a stabilized ternary complex, wherein the first primer comprises a blocking moiety that precludes enzymatic incorporation of the nucleotide into the first hybrid;
• (ii) detecting the stabilized ternary complex to identify the nucleotide in the stabilized ternary complex;
• (iii) removing the blocking moiety from the primer and extending the first primer to form a modified first hybrid on the nucleic acid;
• and
• (iv) repeating (i), (ii) and (iii) for the modified first hybrid of the nucleic acid, thereby determining a sequence for at least a portion of the first template region;
• (c) capping the extended first primer with a second ternary complex inhibitor moiety, the second ternary complex inhibitor moiety comprising
• (i) a ligand that is exogenous to the first primer, and
• (ii) a receptor bound to the ligand;
• (d) removing the ternary complex inhibitor moiety from the second primer while retaining the second ternary complex inhibitor moiety on the first primer;
• and
• (e) extending the second primer, thereby determining a sequence for at least a portion of the second template region.