Methods and arrays for producing and sequencing monoclonal clusters of nucleic acid

A method for modifying one or more immobilized capture primers comprising:

• a) contacting a substrate comprising a plurality of immobilized capture primers with a plurality of template nucleic acids under conditions sufficient for hybridization to produce one or more immobilized template nucleic acids,
• wherein the plurality of immobilized capture primers comprises a first plurality of primers comprising a 5′-terminal universal capture region Y and a second plurality of primers comprising a 3′-terminal universal capture region Z, and
• wherein each template nucleic acid is flanked by a 5′-terminal and a 3′-terminal complementary universal capture regions Y or Z, and wherein each template nucleic acid further comprises one or more restriction sites and a target-specific capture region, wherein the target-specific capture region is between the 5′-terminal universal capture region and the one or more restriction sites or the target-specific capture region is between the 3′-terminal universal capture region and the one or more restriction sites, and
• b) extending one or more immobilized capture primers to produce one or more immobilized extension products complementary to the one or more immobilized template nucleic acids.