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 wa s studied. Formation of sequence-specific PNA(2)/dsDNA (double-strande d DNA) complexes was monitored by a potassium permanganate probing/pri mer extension assay. At low ionic strengths, the binding of PNA was 2- 3 times more efficient with supercoiled than with linear DNA. In the p resence of 140 mM KCI, the PNA binding rate was reduced but, notably, highly dependent on template topology. Negative supercoiling (mean sup erhelix density, sigma approximate to -0.051) increased the rate of bi nding by 2 orders of magnitude compared to that of relaxed DNA. The ps eudo-first-order rate constant [k(psi)(sigma)] obeys an exponential fu nction, k(psi)(sigma) = k(psi lin)e(-sigma delta), where delta is a co nstant 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 appro ximate to 93 and approximate to 48 kJ mol(-1) for PNA binding to linea r and supercoiled DNA, respectively. The results are discussed in rela tion to the possible future use of PNA as an antigene agent and in the framework of DNA ''breathing'' dynamics.