Power-law solvation dynamics in G-quadruplex DNA: Role of hydration dynamics on ligand solvation inside DNA

Nibedita Pal, Him Shweta, Moirangthem Kiran Singh, Sachin Dev Verma, Sobhan Sen

Research output: Contribution to journalArticlepeer-review

Abstract

G-quadruplex DNA (GqDNA) structures act as promising anticancer targets for small-molecules (ligands). Solvation dynamics of a ligand (DAPI: 4′,6-diamidino-2-phenylindole) inside antiparallel-GqDNA is studied through direct comparison of time-resolved experiments to molecular dynamics (MD) simulation. Dynamic Stokes shifts of DAPI in GqDNA prepared in H2O buffer and D2O are compared to find the effect of water on ligand solvation. Experimental dynamics (in H2O) is then directly compared with the dynamics computed from 65 ns simulation on the same DAPI-GqDNA complex. Ligand solvation follows power-law relaxation (summed with fast exponential relaxation) from ∼100 fs to 10 ns. Simulation results show relaxation below ∼5 ps is dominated by water motion, while both water and DNA contribute comparably to dictate long-time power-law dynamics. Ion contribution is, however, found to be negligible. Simulation results also suggest that anomalous solvation dynamics may have origin in subdiffusive motion of perturbed water near GqDNA.

Original languageEnglish (US)
Pages (from-to)1754-1760
Number of pages7
JournalJournal of Physical Chemistry Letters
Volume6
Issue number9
DOIs
StatePublished - May 7 2015
Externally publishedYes

Keywords

  • DAPI
  • fluorescence stokes shift
  • G-quadruplex DNA
  • hydration dynamics
  • MD simulation
  • power-law relaxation
  • solvation dynamics
  • sublinear water diffusion

ASJC Scopus subject areas

  • Materials Science(all)
  • Physical and Theoretical Chemistry

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