Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS and NMR experiments

Published

April 28, 2022

Author(s)

Christina Bergonzo, Alexander Grishaev, Sandro Bottaro

Abstract

We describe the conformational ensemble of the single-stranded r(UCAAUC) oligonucleotide obtained using extensive molecular dynamics (MD) simulations. The conformations observed in MD consist of A-form-like structures and variations thereof. By comparing with available NMR measurements, we show that the presence of both A-form-like and other extended conformations is necessary to quantitatively explain experimental data. To further validate our results we measure SAXS data on the RNA hexamer, and and that MD simulations result in more compact structures than observed from these experiments. The integration of simulations with NMR via maximum entropy approach shows that small modifications to the MD ensemble lead to an improved description of the conformational ensemble. Nevertheless, we identify persisting discrepancies with SAXS likely arising from force field inaccuracies.

Citation

RNA: A Publication of the RNA Society

Volume

28

Pub Type

Journals

Download Paper

https://doi.org/10.1261/rna.078888.121

Local Download

Keywords

oligonucleotide, conformational sampling, molecular dynamics, SAXS, NMR

Citation

Bergonzo, C. , Grishaev, A. and Bottaro, S. (2022), Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS and NMR experiments, RNA: A Publication of the RNA Society, [online], https://doi.org/10.1261/rna.078888.121, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=932840 (Accessed October 11, 2025)