Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Double-duplex Invasion of Pseudocomplementary Peptide Nucleic Acids into Duplex DNA at Elevated Salt Concentration

Synthetic reagents, which are capable of sequence-specific targeting of double-stranded DNA (dsDNA), are of significant interest in various fields of molecular biotechnology as they may provide tools for highly selective, nondenaturing manipulation with designated DNA sequences. In this connection, peptide nucleic acids (PNA) represent one of the most promising oligonucleotide mimics with unique physicochemical and biochemical characteristics. When adenines and thymines in two mutually complementary mixed-base PNA oligomers are substituted with diaminopurines and thiouracils, respectively, so-called pseudo-complementary PNAs (pcPNAs) are created. Pairs of pcPNAs efficiently target essentially any designated site on dsDNA by forming very stable PNA?DNA strand-displacement complexes via double-duplex invasion. One of the characteristic features of interaction between PNAs and dsDNA consists in strong inhibition of double helix invasion at high ionic strength (e.g. physiological conditions). To overcome this limitation we introduced a nick (single-stranded break) in dsDNA near the pcPNA target site. The results will be presented concerning the effect of salt concentration on the kinetics of pcPNA binding to dsDNA depending on the distance between the nick and the pcPNA binding site.

Peter Yakovchuk1,*
Ekaterina Protozanova2
Vadim Demidov3
Maxim Frank-Kamenetskii4

Center for Advanced Biotechnology
36 Cummington St.
Boston, MA 02215
Boston University
College of Engineering
Department of Biomedical Engineering
44 Cummington St.
Boston, MA 02215