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Bimodal 1/f Noise and Anticorrelation between DNA-Water and DNA-Ion Energy Fluctuations

Mukherjee, S and Mondal, S and Bagchi, B (2022) Bimodal 1/f Noise and Anticorrelation between DNA-Water and DNA-Ion Energy Fluctuations. In: Journal of Physical Chemistry B .

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Official URL: https://doi.org/10.1021/acs.jpcb.2c08402


The coupling between the conformational fluctuations of DNA and its surrounding environment, 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 among 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 anticorrelated 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. © 2023 American Chemical Society.

Item Type: Journal Article
Publication: Journal of Physical Chemistry B
Publisher: American Chemical Society
Additional Information: The copyright for this article belongs to the Authors.
Keywords: Bioinformatics; Dielectric relaxation; Ions; Molecular dynamics, 1/F noise; 1/f-noise; Anticorrelation; Conformational fluctuations; Dynamics simulation; Energy fluctuation; Interaction energies; Ion energies; Ion interactions; Surrounding environment, DNA
Department/Centre: Division of Chemical Sciences > Solid State & Structural Chemistry Unit
Date Deposited: 17 Mar 2023 09:59
Last Modified: 17 Mar 2023 09:59
URI: https://eprints.iisc.ac.in/id/eprint/81038

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