Method for differentiation of polynucleotide strands

A method for selection of a particular strand from a double stranded polynucleotide comprising:

• (a) providing polynucleotide templates, primers, buffer solution, at least one enzyme with polymerase activity, sufficient amounts of the four dNTPs (dATP, dCTP, dGTP and dTTP) or analogues thereof, wherein at least one of the four dNTPs is replaced by a corresponding modified dNTP used for strand-specific selection;
• (b) performing first-strand synthesis on the polynucleotide templates with unmodified dNTPs or corresponding analogues thereof;
• (c) performing second-strand synthesis wherein at least one of the four dNTPs is replaced by a corresponding modified dNTP used for strand-specific selection, so that double-stranded polynucleotides each comprising a second strand and a matching strand are generated, wherein the second strand contains the at least one modified nucleotide;
• (d) optionally performing molecular cloning operations with the double-stranded polynucleotides;
• (e) specific selecting of at least part of the first strand of the double stranded polynucleotides using a differential interaction of the modified and unmodified nucleotides with at least one selection factor;
• and
• (f) producing copies of the first strand sequences selected in step (e).