A predetermined fragment in the human genome was successfully isolated by affinity separation using biotin-streptavidin interaction. The whole genome from human cells was first digested by restriction enzymes and then treated with a pair of pseudo-complementary peptide nucleic acids (pcPNAs). A biotin was covalently bound to either of the pcPNAs. With the use of streptavidin-coupled resin, the targeted fragment involving the invasion site of the pcPNAs was selectively picked up from the genomic digests in high yields.