PMID: 9421519Feb 28, 1998Paper

Kinetic sequence discrimination of cationic bis-PNAs upon targeting of double-stranded DNA

Nucleic Acids Research
H KuhnP Nielsen

Abstract

Strand displacement binding kinetics of cationic pseudoisocytosine-containing linked homopyrimidine peptide nucleic acids (bis-PNAs) to fully matched and singly mismatched decapurine targets in double-stranded DNA (dsDNA) are reported. PNA-dsDNA complex formation was monitored by gel mobility shift assay and pseudo-first order kinetics of binding was obeyed in all cases studied. The kinetic specificity of PNA binding to dsDNA, defined as the ratio of the initial rates of binding to matched and mismatched targets, increases with increasing ionic strength, whereas the apparent rate constant for bis-PNA-dsDNA complex formation decreases exponentially. Surprisingly, at very low ionic strength two equally charged bis-PNAs which have the same sequence of nucleobases but different linkers and consequently different locations of three positive charges differ in their specificity of binding by one order of magnitude. Under appropriate experimental conditions the kinetic specificity for bis-PNA targeting of dsDNA is as high as 300. Thus multiply charged cationic bis-PNAs containing pseudoisocytosines (J bases) in the Hoogsteen strand combined with enhanced binding affinity also exhibit very high sequence specificity, thereby making such ...Continue Reading

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Citations

Dec 14, 2004·Chembiochem : a European Journal of Chemical Biology·Peter E NielsenCarsten Behrens
Mar 20, 2010·Molecular Biotechnology·Iulian I OpreaC I Edvard Smith
Apr 29, 2004·Biomolecular Engineering·Karin E LundinC I Edvard Smith
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