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• W1865132728 abstract "Nucleic acids, DNA and RNA, together with proteins, belong to the group of biological macromolecules that constitute the central actors in the living world. While nucleic acids, and especially DNA, contain and maintain information, proteins decode and replicate nucleic acids and act upon their environment physically and chemically. Within this universe of proteins, RNAs, which are the only molecules able to code information and promote catalytic processes, act in every single crucial step of the life of a cell. This important role of RNAs reflect the past grandeur of the RNA world in the origins of life. Moreover, the chemistry of life as we know it nowadays could not exist and function without water molecules, ions, lipids, and polysaccharides. The existence of such complex environments around the chemical processes underlying life implies a necessity to unravel, beyond their static structures, the dynamical nature of the biological macromolecules and of their interactions with the surroundings. In thermodynamical terms, we need to understand Gibbs free energies, i.e., enthalpies and entropies of the biological systems under study, including their environment. It is now accepted that water molecules form an integral part of nucleic acids1,2 and it has been established that magnesium ions constitute an absolute necessity for the functional folding of complex RNA molecules, as well as for their catalytic activities (for a review, see Ref. 3). What we can hope to achieve with the help of molecular dynamics (MD) simulations is a more complete understanding of water and ion binding to nucleic acids in structural as well as dynamical terms. Thus, we view MD simulations as an extension of the crystallographic determinations of nucleic acid structures, often plagued by low resolution. In the following, we will detail aspects of MD simulations specific to nucleic acid systems and focus our attention on the advances in the field which contribute to those aims. We will restrict our survey to MD simulations that include an explicit representation of the aqueous and ionic environment." @default.
• W1865132728 created "2016-06-24" @default.
• W1865132728 creator A5018416560 @default.
• W1865132728 creator A5049661679 @default.
• W1865132728 date "1998-09-25" @default.
• W1865132728 modified "2023-10-18" @default.
• W1865132728 title "Molecular Dynamics: Simulations of Nucleic Acids" @default.
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• W1865132728 doi "https://doi.org/10.1002/0470845015.cma022" @default.

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