title: Structure and properties of DNA in apolar solvents.
abstract: 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.
authors: Institute for Research in Biomedicine (IRB Barcelona) , 08028 Barcelona, Spain.
authors: Annalisa
authors: A
authors: Arcella
authors: Guillem
authors: G
authors: Portella
authors: Rosana
authors: R
authors: Collepardo-Guevara
authors: Debayan
authors: D
authors: Chakraborty
authors: David J
authors: DJ
authors: Wales
authors: Modesto
authors: M
authors: Orozco
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D055029:Inverted Repeat Sequences; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D012997:Solvents; D014867:Water; D004247:DNA