Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

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Title in English Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by Molecular Dynamics
Authors

FADRNÁ Eva ŠPAČKOVÁ Naděžda JOANNA Sarzynska KOČA Jaroslav OROZCO Modesto CHEATHAM Thomas KULINSKI Tadeusz SPONER Jiri

Year of publication 2009
Type Article in Periodical
Magazine / Source Journal of Chemical Theory and Computation
MU Faculty or unit

Faculty of Science

Citation
Field Biophysics
Keywords DNA quadruplex; MD simulation; force fields
Description We have carried out a set of explicit solvent molecular dynamics (MD) simulations on two DNA quadruplex (G-DNA) molecules. The main purpose of the paper was testing of the capability of the MD simulation technique to describe single-stranded topologies of G-DNA loops, which represent a very challenging task for computational methods.
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