Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations

RNA and DNA are rapidly emerging
as targets for therapeutics and
as potential frameworks for nanotechnology. Accurate methods for predicting
and designing structures and dynamics of nucleic acids would accelerate
progress in these and other applications. Suitable approximations
for modeling nucleic acids are being developed but require validation
against disparate experimental observations. Here, nuclear magnetic
resonance spectra for RNA and DNA single strands, CAAU and UCAAUC,
are used as benchmarks to test molecular dynamics simulations with
AMBER force fields OL3 and ROC-RNA for RNA and BSC1 for DNA. A detailed
scheme for making comparisons is also presented. The results reflect
recent progress in approximations and reveal remaining challenges.