Enhanced peptide nucleic acid binding to supercoiled DNA: Possible implications for DNA ''breathing'' dynamics

The influence of DNA topology on peptide nucleic acid (PNA) binding was studied. Formation of sequence-specific PNA(2)/dsDNA (double-stranded DNA) complexes was monitored by a potassium permanganate probing/primer extension assay. At low ionic strengths, the binding of PNA was 2-3 times more efficient with supercoiled than with linear DNA. In the presence of 140 mM KCI, the PNA binding rate was reduced but, notably, highly dependent on template topology. Negative supercoiling (mean superhelix density, sigma approximate to -0.051) increased the rate of binding by 2 orders of magnitude compared to that of relaxed DNA. The pseudo-first-order rate constant [k(psi)(sigma)] obeys an exponential function, k(psi)(sigma) = k(psi lin)e(-sigma delta), where delta is a constant of 105 and k(psi lin) is the rate of PNA binding to linear DNA (sigma = 0). The activation energy [Ea(sigma)] was determined as approximate to 93 and approximate to 48 kJ mol(-1) for PNA binding to linear and supercoiled DNA, respectively. The results are discussed in relation to the possible future use of PNA as an antigene agent and in the framework of DNA ''breathing'' dynamics.