The Effects of Flexibility on dsDNA–dsDNA Interactions

Chuanying Chen, B. Montgomery Pettitt

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


A detailed understanding of the physical mechanism of ion-mediated dsDNA interactions is important in biological functions such as DNA packaging and homologous pairing. We report the potential of mean force (PMF) or the effective solvent mediated interactions between two parallel identical dsDNAs as a function of interhelical separation in 0.15 M NaCl solution. Here, we study the influence of flexibility of dsDNAs on the effective interactions by comparing PMFs between rigid models and flexible ones. The role of flexibility of dsDNA pairs in their association is eluci-dated by studying the energetic properties of Na+ ions as well as the fluctuations of ions around dsDNAs. The introduction of flexibility of dsDNAs softens the vdW contact wall and induces more counterion fluctuations around dsDNAs. In addition, flexibility facilitates the Na+ ions dynamics affecting their distribution. The results quantify the extent of attraction influenced by dsDNA flexibility and further emphasize the importance of non-continuum solvation approaches.

Original languageEnglish (US)
Article number699
Issue number5
StatePublished - May 2022
Externally publishedYes


  • dsDNA–dsDNA interactions
  • flexibility
  • molecular dynamics simulation (MD)
  • potential of mean force (PMF)

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • General Biochemistry, Genetics and Molecular Biology
  • Space and Planetary Science
  • Palaeontology


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