Patent ID: 6872521

Claim:
A method for analyzing the sequence of a template comprising: a) capturing the template with a sequencing reagent to form a captured template, said sequencing reagent being immobilized to a solid surface and comprising: (i) a capture moiety capable of forming a stable duplex with a region of the template nucleic acid molecule; (ii) a primer region comprising from 3 to 7 bases; and between said capture moiety and said primer region (iii) a spacer region that minimizes template independent noise; and b) scanning the captured template using a primer-polymerase complex for regions of complementarity to the primer region and forming a duplex; c) extending the primer region by at least one nucleotide moiety by means of a template-homology dependent extension reaction to form an extended primer; and d) detecting the extended primer, wherein said detecting of the extended primer indicates the presence of one or more regions of complementarity to the primer region in the captured template; wherein the steps of the method are repeated for sequencing reagents that are bound in an array pattern onto to said solid surface so that a pattern of signals is generated for the template.