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- W2051190318 abstract "The DNA metabolic processes often involve single-stranded DNA (ss-DNA) molecules as important intermediates. In the absence of base complementarity, ss-DNAs are more flexible and interact strongly with water in aqueous media. Ss-DNA–water interactions are expected to control the conformational flexibility of the DNA strand, which in turn should influence the properties of the surrounding water molecules. We have performed room temperature molecular dynamics simulation of an aqueous solution containing the ss-DNA dodecamer, 5′-CGCGAATTCGCG-3′. The conformational flexibility of the DNA strand and the microscopic structure and ordering of water molecules around it have been explored. The simulation reveals transformation of the initial base-stacked form of the ss-DNA to a fluctuating collapsed coil-like conformation with the formation of a few non-sequentially stacked base pairs. A preliminary analysis shows further collapse of the DNA conformation in presence of additional salt (NaCl) due to screening of negative charges along the backbone by excess cations. Additionally, higher packing of water molecules within a short distance from the DNA strand is found to be associated with realignment of water molecules by breaking their regular tetrahedral ordering." @default.
- W2051190318 created "2016-06-24" @default.
- W2051190318 creator A5031144418 @default.
- W2051190318 creator A5051434187 @default.
- W2051190318 creator A5080167244 @default.
- W2051190318 date "2013-08-20" @default.
- W2051190318 modified "2023-10-11" @default.
- W2051190318 title "Molecular dynamics simulation of a single-stranded DNA with heterogeneous distribution of nucleobases in aqueous medium" @default.
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- W2051190318 doi "https://doi.org/10.1063/1.4818537" @default.
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- W2051190318 hasPublicationYear "2013" @default.
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