A method for primer extension and paired end sequencing comprising: (a) generating a plurality of template polynucleotides attached to a surface by a method of primer extension comprising (i) a primer hybridization step, (ii) an extension step, and (iii) a template walking step, (b) denaturing the plurality of template polynucleotides using a chemical or heat to produce single stranded template polynucleotides; (c) conducting a forward sequencing reaction on the plurality of single stranded template polynucleotides, wherein the 5' ends of the template polynucleotides are attached to the surface and the plurality of template polynucleotides having at least one cross-linking moiety and at least one cleavable scissile moiety, wherein the cross-linking moiety is positioned 5' of the cleavable scissile moiety and wherein said forward sequencing reaction comprises (i) hybridizing a plurality of first primers to the plurality of template polynucleotides, (ii) extending the plurality of first primers by conducting primer extension reactions by polymerase catalyzed successive nucleotide incorporations and forming a plurality of first extension strands hybridized to the plurality of template polynucleotides, and (iii) identifying the incorporated nucleotides in the first extension strands; (d) inducing cross-linking between the template polynucleotides and the first extension strands with a heat, chemical or photochemical condition, (e) 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 truncated template polynucleotides attached to the surface and cross-linked to the first extension strands, 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 polynucleotides; and (f) conducting a reverse sequencing reaction on the plurality of first extension strands. (a) generating a plurality of template polynucleotides attached to a surface by a method of primer extension comprising (i) a primer hybridization step, (ii) an extension step, and (iii) a template walking step, (b) denaturing the plurality of template polynucleotides using a chemical or heat to produce single stranded template polynucleotides; (c) conducting a forward sequencing reaction on the plurality of single stranded template polynucleotides, wherein the 5' ends of the template polynucleotides are attached to the surface and the plurality of template polynucleotides having at least one cross-linking moiety and at least one cleavable scissile moiety, wherein the cross-linking moiety is positioned 5' of the cleavable scissile moiety and wherein said forward sequencing reaction comprises (i) hybridizing a plurality of first primers to the plurality of template polynucleotides, (ii) extending the plurality of first primers by conducting primer extension reactions by polymerase catalyzed successive nucleotide incorporations and forming a plurality of first extension strands hybridized to the plurality of template polynucleotides, and (iii) identifying the incorporated nucleotides in the first extension strands; (i) hybridizing a plurality of first primers to the plurality of template polynucleotides, (ii) extending the plurality of first primers by conducting primer extension reactions by polymerase catalyzed successive nucleotide incorporations and forming a plurality of first extension strands hybridized to the plurality of template polynucleotides, and (iii) identifying the incorporated nucleotides in the first extension strands; (d) inducing cross-linking between the template polynucleotides and the first extension strands with a heat, chemical or photochemical condition, (e) 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 truncated template polynucleotides attached to the surface and cross-linked to the first extension strands, 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 polynucleotides; and (f) conducting a reverse sequencing reaction on the plurality of first extension strands.