Stopped-flow kinetics of Peptide Nucleic Acid (PNA)-oligonucleotide duplex formation: studies of PNA-DNA interactions

Stopped-flow technique is useful for studying fast reactions that have half-lives as short as a few milliseconds.(a) This technique has never been used to study the interaction between Peptide nucleic acids (PNA) and DNA strands in the formation of hybrids. Oligonucleotides that contain PNA monomers are considered most promising candidates for the efficient recognition with its complementary sequence in nucleic acid duplex. PNA are DNA analogues in which the sugarphosphate backbone is replaced by a peptide amide bond backbone. PNAs show unique properties that set them apart from other traditional DNA analogues.(b) Normally the affinity of PNA for DNA is detected by using melting temperature but sometimes this technique is not appropriate especially, if PNA contain some thermal sensitive functional groups. So, we have started an innovative study of PNA-DNA interaction by using stopped-flow technique for this we have synthesised the PNA sequences. (a) R. A. Harvey and W. O. Borcherdt, Anal. Chem. 44 (1972) 1926-1928. (b) B. Hyrup and P. E. Nielsen, Bioorg. Med. Chem. Lett. 4 (1996) 5-13.