A study of the hydrogen-bonded network around the left-handed and right-handed DNA in an ionic solution

Nam Sook Kang, Kyung Tai No, Shik Jhon Mu

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Molecular dynamics simulations were carried out for a right-handed and left-handed DNA heteropolymeric fragment, in which four different types of nucleotides constituted the sequence. The average structures obtained from the simulation converged to within ∼ 1.4 Å rms fluctuation for the left-handed and for the right-handed DNA. The distribution of hydration sites and the hydrogen-bonded circular network of water molecules around guanine and cytosine bases were distinctively different in two DNA conformations. The hydrogen-bonded circular network, ring structure, of water molecules within 4.0 A around two DNA molecules was better formed in the right-handed DNA than in the left-handed DNA, showing a higher ratio of hexameric ring to pentameric ring (R6/R5).

Original languageEnglish
Pages (from-to)83-89
Number of pages7
JournalMolecular Simulation
Volume29
Issue number2
DOIs
Publication statusPublished - 2003 Jan 1

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Information Systems
  • Modelling and Simulation
  • Chemical Engineering(all)
  • Materials Science(all)
  • Condensed Matter Physics

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