A method of preparing immobilized templates for a nucleic acid sequencing reaction comprising: (a) providing a solid support having a forward and reverse amplification primer immobilized thereon; (b) providing a target nucleic acid, wherein the target nucleic acid comprises: (i) a first region of known sequence complementary to the forward amplification primer; (ii) a first template region; (iii) a second region of known sequence substantially identical to the reverse amplification primer, wherein the first template region is between the first region of known sequence and the second region of known sequence; and (iv) a third region of known sequence complementary to the forward amplification primer, wherein the first template region and the second region of known sequence are between the first region of known sequence and the third region of known sequence; (c) applying the target nucleic acid to the solid support under conditions suitable for hybridization whereby the first region of known sequence hybridizes to the forward amplification primer; (d) extending the hybridized forward amplification primer to generate a first immobilized template comprising a complementary copy of the target nucleic acid; (e) denaturing the target nucleic acid from the first immobilized template; (f) hybridizing the first immobilized template to the reverse amplification primer, whereby a complementary copy of the second region of known sequence hybridizes to the reverse amplification primer; and (g) extending the hybridized reverse amplification primer to generate a second immobilized strand comprising the first template region positioned between the first region of known sequence and the second region of known sequence; (h) denaturing the second immobilized strand from the first immobilized template; (i) hybridizing the second immobilized strand to the first immobilized template, whereby the first region of known sequence of the second immobilized strand hybridizes to a complementary copy of the third region of known sequence in the immobilized template; (j) extending a 3' OH of the first region of known sequence to generate a concatemer of the second immobilized strand; and (k) extending a 3' OH of the complementary copy of the third region of known sequence to generate a concatemer of the first immobilized template. (a) providing a solid support having a forward and reverse amplification primer immobilized thereon; (b) providing a target nucleic acid, wherein the target nucleic acid comprises: (i) a first region of known sequence complementary to the forward amplification primer; (ii) a first template region; (iii) a second region of known sequence substantially identical to the reverse amplification primer, wherein the first template region is between the first region of known sequence and the second region of known sequence; and (iv) a third region of known sequence complementary to the forward amplification primer, wherein the first template region and the second region of known sequence are between the first region of known sequence and the third region of known sequence; (i) a first region of known sequence complementary to the forward amplification primer; (ii) a first template region; (iii) a second region of known sequence substantially identical to the reverse amplification primer, wherein the first template region is between the first region of known sequence and the second region of known sequence; and (iv) a third region of known sequence complementary to the forward amplification primer, wherein the first template region and the second region of known sequence are between the first region of known sequence and the third region of known sequence; (c) applying the target nucleic acid to the solid support under conditions suitable for hybridization whereby the first region of known sequence hybridizes to the forward amplification primer; (d) extending the hybridized forward amplification primer to generate a first immobilized template comprising a complementary copy of the target nucleic acid; (e) denaturing the target nucleic acid from the first immobilized template; (f) hybridizing the first immobilized template to the reverse amplification primer, whereby a complementary copy of the second region of known sequence hybridizes to the reverse amplification primer; and (g) extending the hybridized reverse amplification primer to generate a second immobilized strand comprising the first template region positioned between the first region of known sequence and the second region of known sequence; (h) denaturing the second immobilized strand from the first immobilized template; (i) hybridizing the second immobilized strand to the first immobilized template, whereby the first region of known sequence of the second immobilized strand hybridizes to a complementary copy of the third region of known sequence in the immobilized template; (j) extending a 3' OH of the first region of known sequence to generate a concatemer of the second immobilized strand; and (k) extending a 3' OH of the complementary copy of the third region of known sequence to generate a concatemer of the first immobilized template.