Compositions and techniques for nucleic acid primer extension

A method of characterizing a template nucleic acid, wherein the template comprises a linker region that is adjacent to and between first and second regions of the template nucleic acid, comprising steps of

• (a) obtaining a single base resolution sequence of the first region by extending a primer along the first region of the template nucleic acid, thereby producing an extended primer-template hybrid;
• (b) obtaining a signature for the linker region by
• (i) further extending the extended primer of the extended primer-template hybrid using a mixture of nucleotides, wherein the mixture of nucleotides comprises nucleotide cognates of first, second, third and fourth different base types, wherein the nucleotide cognate of the first base type comprises a reversible terminator, and wherein at least one of the nucleotide cognates of the second, third or fourth base types is extendable, and
• (ii) detecting a stabilized ternary complex, the stabilized ternary complex comprising the further extended primer-template hybrid, a polymerase and a nucleotide cognate of the next base in the template, wherein the signature comprises a base multiplet comprising the first base type followed by the next base;
• and
• (c) obtaining a single base resolution sequence of the second region by extending the further extended primer of the further extended primer-template hybrid.