The impact of abasic sites on DNA flexibility

J Biomol Struct Dyn. 2000 Feb;17(4):645-53. doi: 10.1080/07391102.2000.10506555.

Abstract

We use internal coordinate molecular mechanics calculations to study the impact of abasic sites on the conformation and the mechanics of the DNA double helix. Abasic sites, which are common mutagenic lesions, are shown to locally modify both the groove geometry and the curvature of DNA in a sequence dependent manner. By controlled twisting and bending, it is also shown that these lesions modify the deformability of the duplex, generally increasing its flexibility, but again to an extent which depends on the nature of the abasic site and on the surrounding base sequence. Both the conformational and mechanical influence of this type of DNA damage may be significant for recognition and repair mechanisms.

MeSH terms

  • Computer Simulation
  • DNA / chemistry*
  • DNA Damage*
  • Deoxyribonucleotides / chemistry
  • Deoxyribonucleotides / genetics
  • Furans / chemistry
  • Mutation
  • Nucleic Acid Conformation*

Substances

  • Deoxyribonucleotides
  • Furans
  • tetrahydrofuran
  • DNA