Structure and Properties of DNA in Apolar Solvents

The study of nucleic acids in low-polarity environments paves the way for novel biotechnological applications of DNA. Here, we use a repertoire of atomistic molecular simulation tools to study the nature of DNA when placed in a highly apolar environment and when transferred from aqueous to apolar so...

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Bibliographic Details
Published in:The journal of physical chemistry. B 2014-07, Vol.118 (29), p.8540-8548
Main Authors: Arcella, Annalisa, Portella, Guillem, Collepardo-Guevara, Rosana, Chakraborty, Debayan, Wales, David J, Orozco, Modesto
Format: Article
Language:English
Subjects:
Base Sequence
DNA - chemistry
DNA - genetics
Inverted Repeat Sequences
Molecular Dynamics Simulation
Nucleic Acid Conformation
Solvents - chemistry
Water - chemistry
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Summary:The study of nucleic acids in low-polarity environments paves the way for novel biotechnological applications of DNA. Here, we use a repertoire of atomistic molecular simulation tools to study the nature of DNA when placed in a highly apolar environment and when transferred from aqueous to apolar solvent. Our results show that DNA becomes stiffer in apolar solvents and suggest that highly negatively charged states, which are the most prevalent in water, are strongly disfavored in apolar solvents and neutral states with conformations not far from the aqueous ones are the dominant forms. Transfer from water to an apolar solvent such as CCl4 is unlikely to occur, but our results suggest that if forced, the DNA would migrate surrounded by a small shell of water (the higher the DNA charge, the larger the number of water molecules in this shell). Even the neutral form (predicted to be the dominant one in apolar solvents) would surround itself by a small number of highly stable water molecules when moved from water to a highly apolar environment. Neutralization of DNA charges seems a crucial requirement for transfer of DNA to apolar media, and the most likely mechanism to achieve good transfer properties.
ISSN:1520-6106
1520-5207
DOI:10.1021/jp503816r