Methods, compositions, systems, apparatuses and kits for nucleic acid amplification

A method for paired end sequencing comprising:

• (a) conducting a forward sequencing reaction on a template polynucleotide attached to a surface and having at least one cross linking moiety and at least one cleavable scissile moiety by (i) hybridizing a first primer to the template polynucleotide, (ii) extending the first primer by conducting primer extension reactions by polymerase-catalyzed successive nucleotide incorporations and forming a first extension strand hybridized to the template polynucleotide, and (iii) identifying the incorporated nucleotides in the first extension strand;
• (b) inducing cross linking between a nucleoside of the template polynucleotide and a nucleoside of the first extension strand with a heat, chemical or photochemical condition;
• (c) cleaving the template polynucleotide by reacting the scissile moiety with heat, irradiation, at least one chemical, or at least one enzyme, to form a truncated template polynucleotide and forming a terminal 3′ phosphate group, converting the terminal 3′ phosphate group to an —OH group, and removing a portion of the cleaved template polynucleotide;
• and
• (d) conducting a reverse sequencing reaction on the first extension strand by extending the terminal 3′ OH group on the truncated template polynucleotide with primer extension reactions by polymerase-catalyzed successive nucleotide incorporations and forming a second extension strand, and (iii) identifying the incorporated nucleotides in the second extension strand.