Bimodal 1/f noise and anticorrelation between DNA-Water and DNA-Ion energy fluctuations

Abstract

Coupling between the fluctuations of DNA and its surroundings consisting of water and ions in solution remains poorly understood and relatively less investigated as compared to proteins. Here, with the help of molecular dynamics simulations and statistical mechanical analyses, we explore the dynamical coupling between DNA, water, and counterions through correlations among respective energy fluctuations in both double (ds-) and single-stranded (ss-) DNA solutions. Fluctuations in the collective DNA-Water and DNA-Ion interaction energies are found to be strongly anti-correlated across all the systems. The fluctuations of DNA self-energy, however, are weakly coupled to DNA-water and DNA-ion interactions in ds-DNA. An enhancement of the DNA-water coupling is observed in ss-DNA, where the system is less rigid. All the interaction energies exhibit 1/f noise in their energy power spectra with surprisingly prominent bimodality in the DNA-water and DNA-ion fluctuations. The nature of the energy spectra appears to be indifferent to the relative rigidity of the DNA. We discuss the role of the observed correlations in ion-water motions on a DNA duplex in the experimentally observed anomalous slow dielectric relaxation and solvation dynamics, and in furthering our understanding of the DNA energy landscape. TOC GRAPHIC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/520228v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@806797org.highwire.dtl.DTLVardef@110c9corg.highwire.dtl.DTLVardef@1531566org.highwire.dtl.DTLVardef@1a1fe12_HPS_FORMAT_FIGEXP M_FIG C_FIG