National Institute of Standards and Technology (NIST)

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Hosts:  Vincenzo Venditti and Adam Barb

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“Structure, Conformational Dynamics and Hydration of RNA and DNA from Wide-angle X-ray Scattering, NMR, and Computation”

Determination of accurate structural models of RNA and DNA at native conditions remains incredibly challenging for both the experimental biophysical techniques such as X-ray crystallography, NMR, or cryo-EM, and the molecular simulation-based approaches. Small- and wide-angle x-ray scattering offers a very attractive way to characterize these systems but the majority of such studies concentrate on the lower-angle scattering and low-resolution reconstructions, leaving out feature-rich wide angle scattering due to known difficulties in modeling these data from the atomic coordinates of oligonucleotides.

In this study we investigate the reason for this structure/data discrepancy concentrating on a carefully selected set of RNA and DNA model systems characterized by NMR that represent state-of-the art of the technique’s applications. We find that even with the highest density of the experimental restraints and the best available force fields, leading to the most accurate NMR-determined RNA and DNA structures up to date, the resulting atomic coordinates nearly universally fail to quantitatively match the experimental wide-angle solution X-ray scattering data.

We show that the effect most strongly contributing to this discrepancy is the single-conformation representation of these models. We thus propose a new methodology for simultaneously determining the average structure, conformational fluctuations, and the structure of the hydration layer of RNA and DNA from the joint analysis of NMR and wide angle solution scattering data, aiming to minimize data over-fitting and incorporating structural information from both high-level MD simulations in explicit solvent, and the conformational preferences extracted from the high-resolution subset of oligonucleotide structures in the PDB.