A method for paired end sequencing comprising: (a) conducting a forward sequencing reaction on a plurality of single stranded template polynucleotides attached to a surface and having at least one photo inducible cross linking moiety and at least one cleavable scissile moiety, wherein said forward sequencing reaction comprises (i) hybridizing a first primer to the template polynucleotide, (ii) extending the first primer by conducting primer extension reactions 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 the plurality of template polynucleotides and a plurality of first extension strands, wherein the crosslinking is induced by treating a template polynucleotide hybridized to a first extension strand with irradiation to induce direct cross-linking of a nucleoside on the template polynucleotide with a nucleoside on the first extension strand, (c) cleaving the plurality of template polynucleotides by reacting the scissile moiety with heat, irradiation, at least one chemical, or at least one enzyme, to form a truncated template polynucleotide that is attached to the surface and cross-linked to the first extension strand, optionally forming a terminal 3' phosphate group, and optionally 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 plurality of first extension strands wherein said reverse sequencing reaction comprises (i) hybridizing a second primer to the first extension strand and (ii) extending the second primer by conducting a primer extension reaction and forming a second extension strand; and (iii) identifying the incorporated nucleotides in the second extension strand. (a) conducting a forward sequencing reaction on a plurality of single stranded template polynucleotides attached to a surface and having at least one photo inducible cross linking moiety and at least one cleavable scissile moiety, wherein said forward sequencing reaction comprises (i) hybridizing a first primer to the template polynucleotide, (ii) extending the first primer by conducting primer extension reactions 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 the plurality of template polynucleotides and a plurality of first extension strands, wherein the crosslinking is induced by treating a template polynucleotide hybridized to a first extension strand with irradiation to induce direct cross-linking of a nucleoside on the template polynucleotide with a nucleoside on the first extension strand, (c) cleaving the plurality of template polynucleotides by reacting the scissile moiety with heat, irradiation, at least one chemical, or at least one enzyme, to form a truncated template polynucleotide that is attached to the surface and cross-linked to the first extension strand, optionally forming a terminal 3' phosphate group, and optionally 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 plurality of first extension strands wherein said reverse sequencing reaction comprises (i) hybridizing a second primer to the first extension strand and (ii) extending the second primer by conducting a primer extension reaction and forming a second extension strand; and (iii) identifying the incorporated nucleotides in the second extension strand.