Sequence-specific targeting of duplex DNA by peptide nucleic acids via triplex strand invasion

Because of a set of exceptional chemical, physical, and biological proper t ies, polyamide or peptide nucleic acids (PNAs) hold a distinctive position among various synthetic ligands designed for DNA-targeting purposes. Cation ic pyrimidine PNAs (cpyPNAs) represent a special group of PNAs, which effec tively form strand invasion triplexes with double-stranded DNA (dsDNA) also known as P-loops. Extraordinary stability of the invasion triplexes and hi gh sequence specificity of their formation combined with local opening of t he DNA double helix within the P-loops make these complexes very attractive for sequence-specific manipulation with dsDNA. important for applications is the fact that the discrimination between correct and mismatched binding sites in dsDNA by cpyPNAs is a nonequilibrium, kinetically controlled proce ss. Therefore, a careful choice of experimental conditions that are optimal for the kinetic discrimination of correct versus mismatched cpyPNA binding is crucial for sequence-specific recognition of dsDNA by cpyPNAs. The expe rimental and theoretical data presented make it possible to select those so lution parameters and cpyPNA constructions that are most favorable for sequ ence specificity without compromising the affinity of dsDNA targeting. (C) 2001 Academic Press.