title: Kinetic analysis of specificity of duplex DNA targeting by homopyrimidine peptide nucleic acids.
abstract: A simple theoretical analysis shows that specificity of double-stranded DNA (dsDNA) targeting by homopyrimidine peptide nucleic acids (hpyPNAs) is a kinetically controlled phenomenon. Our computations give the optimum conditions for sequence-specific targeting of dsDNA by hpyPNAs. The analysis shows that, in agreement with the available experimental data, kinetic factors play a crucial role in the selective targeting of dsDNA by hpyPNAs. The selectivity may be completely lost if PNA concentration is too high and/or during prolonged incubation of dsDNA with PNA. However, quantitative estimations show that the experimentally observed differences in the kinetic constants for hpyPNA binding with the correct and mismatched DNA sites are sufficient for sequence-specific targeting of long genomic DNA by hpyPNAs with a high yield under appropriate experimental conditions. Differential dissociation of hpyPNA/dsDNA complexes is shown to enhance the selectivity of DNA targeting by PNA.
authors.affiliation: Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, Massachusetts 02215, USA. vvd@enga.bu.edu
authors.forename: V V
authors.initials: VV
authors.lastname: Demidov
authors.forename: M V
authors.initials: MV
authors.lastname: Yavnilovich
authors.forename: M D
authors.initials: MD
authors.lastname: Frank-Kamenetskii
mesh_terms: D001665:Binding Sites; D055592:Biophysical Phenomena; D001703:Biophysics; D004247:DNA / Q000737:chemistry*; D007700:Kinetics; D008956:Models, Chemical; D009696:Nucleic Acids / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry
chemical_list: D009696:Nucleic Acids; D010455:Peptides; D011743:Pyrimidines; D004247:DNA