Opposite effect of counterions on the persistence length of nicked and non-nicked DNA

J Mol Biol. 1997 Mar 7;266(4):711-21. doi: 10.1006/jmbi.1996.0825.

Abstract

Using cryo-electron microscopy we reconstructed the three-dimensional trajectories adopted in cryovitrified solutions by double-stranded DNA molecules in which the backbone of one strand lacked a phosphate at regular intervals of 20 nucleotides. The shape of such nicked DNA molecules was compared with that of DNA molecules with exactly the same sequence but without any single-stranded scissions. Upon changing the salt concentration we observed opposite effects of charge neutralization on nicked and non-nicked DNA. In low salt solutions (10 mM Tris-HCl, 10 mM NaCl) the applied dense nicking caused ca 3.5-fold reduction of the DNA persistence length as compared with non-nicked DNA. Upon increasing the salt concentration (to 150 mM NaCl and 10 mM MgCl2) the persistence length of non-nicked DNA appreciably decreased while that of nicked DNA molecules increased by a factor of 2.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemistry*
  • DNA / metabolism
  • DNA Damage*
  • Freezing
  • Image Processing, Computer-Assisted
  • Magnesium Chloride / pharmacology*
  • Microscopy, Electron
  • Models, Molecular
  • Nucleic Acid Conformation*
  • Single-Strand Specific DNA and RNA Endonucleases / metabolism
  • Sodium Chloride / pharmacology*

Substances

  • Magnesium Chloride
  • Sodium Chloride
  • DNA
  • Single-Strand Specific DNA and RNA Endonucleases