Abstract: The present invention is directed to methods of isolation of related polynucleotides harboring nucleic acid difference within a polynucleotide sample. The method will be useful in detecting and identifying alternative splicing events and corresponding splicing isoforms and to detect genomic DNA differences between genomes. The method according to the present invention is based on the use of a single-stranded trap. The single-stranded trap preferably involves the use of single-strand binding protein.