Conformal probes and methods for sequencing nucleic acids

A method of determining nucleotide sequences, comprising

• (a) providing an array of different nucleic acid templates;
• (b) providing a mixture of nucleotide species, the mixture comprising
• (i) at least four different nucleotide species,
• (ii) at least one of the four different nucleotide species comprising a reversible terminator moiety, and
• (iii) at least two of the four different nucleotide species comprising an extendible 3′ hydroxyl moiety;
• (c) contacting the array of nucleic acid templates with conformationally labeled polymerases, wherein the conformationally labeled polymerase comprises a finger domain labeled with a first fluorescent label and a thumb domain labeled with a second label, wherein the first fluorescent label and second label are FRET pairs or wherein the second label is a quencher;
• and the mixture of nucleotide species under conditions wherein the conformationally labeled polymerases catalyze sequential addition of the nucleotide species to form nucleic acid complements of the nucleic acid templates,
• wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase,
• wherein the rate or time duration for the conformational signal change is distinguishable for the at least two nucleotide species comprising the extendible 3′ hydroxyl moiety, and
• wherein a plurality of the nucleic acid complements incorporate the at least one nucleotide species that comprises the reversible terminator moiety;
• (d) removing the reversible terminator moiety;
• (e) detecting a series of changes in the signal from the conformationally labeled polymerase at individual locations of the array;
• and
• (f) determining the sequence of nucleotides for the nucleic acid sample from the series of changes in the signal from the conformationally labeled polymerase.