Enhanced peptide nucleic acid binding to supercoiled DNA: possible implications for DNA "breathing" dynamics

Biochemistry. 1996 Jul 9;35(27):8863-9. doi: 10.1021/bi960436k.


The influence of DNA topology on peptide nucleic acid (PNA) binding was studied. Formation of sequence-specific PNA2/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 approximately -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 approximately 93 and approximately 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA, Superhelical / metabolism*
  • Deoxyribonucleases, Type II Site-Specific
  • Dose-Response Relationship, Drug
  • Kinetics
  • Manganese Compounds
  • Models, Chemical
  • Molecular Probes
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Oligodeoxyribonucleotides / metabolism*
  • Oxides
  • Potassium Chloride / pharmacology
  • Thermodynamics


  • DNA, Superhelical
  • Manganese Compounds
  • Molecular Probes
  • Oligodeoxyribonucleotides
  • Oxides
  • permanganic acid
  • Potassium Chloride
  • CTGCAG-specific type II deoxyribonucleases
  • Deoxyribonucleases, Type II Site-Specific