2015
DOI: 10.1021/ct501025q
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Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics

Abstract: Molecular dynamics (MD) simulations for RNA tetramers r(AAAA), r(CAAU), r(GACC), and r(UUUU) are benchmarked against 1H–1H NOESY distances and 3J scalar couplings to test effects of RNA torsion parametrizations. Four different starting structures were used for r(AAAA), r(CAAU), and r(GACC), while five starting structures were used for r(UUUU). On the basis of X-ray structures, criteria are reported for quantifying stacking. The force fields, AMBER ff99, parmbsc0, parm99χ_Yil, ff10, and parmTor, all predict exp… Show more

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Cited by 107 publications
(418 citation statements)
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References 135 publications
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“…18,19 NMR studies showed these tetranucleotides to be mostly in A-form-like conformation in solution. 34,39 At variance with experimental evidence, previous MD simulations showed that compact, interdigitated structures are over-stabilized by the Amberχ OL3 force field. 12,18,40 We thus expect viable force field corrections to improve the agreement with experiments on these systems as well.…”
mentioning
confidence: 91%
“…18,19 NMR studies showed these tetranucleotides to be mostly in A-form-like conformation in solution. 34,39 At variance with experimental evidence, previous MD simulations showed that compact, interdigitated structures are over-stabilized by the Amberχ OL3 force field. 12,18,40 We thus expect viable force field corrections to improve the agreement with experiments on these systems as well.…”
mentioning
confidence: 91%
“…Experimental scalar coupling constants and nuclear Overhauser effects (NOEs) have been reported for a number of different tetranucleotide systems by the Turner group. 1518 Studies carried out by the same group comparing these NMR data with long MD simulations for r(GACC) 15 and r(CCCC) 14 have provided further evidence in favor of the use of reparameterized glycosidic dihedral parameters. 5 In addition, however, they have shown that simulations can predict substantial populations of non-A-form, “intercalated” conformations – in which bases become stacked in an order different from that suggested by the linear sequence – for which no experimental data (NOEs) have been observed.…”
Section: Introductionmentioning
confidence: 96%
“…The use of very long simulation times, 18 or of enhanced sampling methods, 19, 20 has the clear advantage of enabling unambiguous conclusions to be drawn about the simulated behavior of the selected systems. But the exploration of only a few such systems places limits on our ability to determine the extent to which simulation results are sequence or composition dependent.…”
Section: Introductionmentioning
confidence: 99%
“…We used both DC and LC models. DNA and RNA results, including representative snapshots, total hydrogen bonding, WC hydrogen bonding and stacking 39 occupancies, are summarized in supporting information Section S5 ( Figures S14-S24). For RNA, the theoretical CCS distributions, both with the DC and .…”
Section: ) Temperature Replica Exchange MD (T-remd)mentioning
confidence: 99%