Molecular dynamics investigation of the double stranded oligonucleotide d(AT)6d(AT)6

Nucleic Acids Res Suppl. 2002:(2):175-6. doi: 10.1093/nass/2.1.175.

Abstract

Molecular dynamics simulation of double stranded 12-meric oligonucleotide carrying an A and T alternating sequence, d(AT)6d(AT)6, over 1 ns was carried out under low NaCl conditions by using AMBER 6. It was found that the d(AT)6d(AT)6 was stabilized in the D-type structure which is an intermediate structure between A- and B-type ones and this result was in agreement with the previous report.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Nucleic Acid Conformation
  • Oligonucleotides / chemistry*

Substances

  • Oligonucleotides