Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

Journal Article · Tue May 24 00:00:00 EDT 2016 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.4950814· OSTI ID:1327123

Pabit, Suzette A. ^[1]; Katz, Andrea M. ^[1]; Tolokh, Igor S. ^[2]; Drozdetski, Aleksander ^[2]; Baker, Nathan  ^[3]; Onufriev, Alexey V. ^[2]; Pollack, Lois ^[1]

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1. Cornell Univ., Ithaca, NY (United States)
2. Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets higher scattering angles and can enhance structural studies of molecules by accessing finer details of solution structures. Although the extension from SAXS to WAXS is easy to implement experimentally, the computational tools required to fully harness the power of WAXS are still under development. Currently, WAXS is employed to study structural changes and ligand binding in proteins; however the methods are not as fully developed for nucleic acids. Here, in this work, we show how WAXS can qualitatively char- acterize nucleic acid structures as well as the small but significant structural changes driven by the addition of multivalent ions. We show the potential of WAXS to test all-atom molecular dynamics (MD) simulations and to provide insight in understanding how the trivalent ion cobalt(III) hexammine (CoHex) affects the structure of RNA and DNA helices. We find that MD simulations capture the RNA structural change that occurs due to addition of CoHex.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
• Sponsoring Organization: USDOE; National Institutes of Health (NIH); National Science Foundation (NSF)
• Grant/Contract Number: AC05-76RL01830; R01 GM-099450; CNS-0960081; DGE-1144153; DMR-1332208; GM-103485
• OSTI ID: 1327123
• Report Number(s): PNNL-SA-115068; WN0219080
• Journal Information: Journal of Chemical Physics, Vol. 144, Issue 20; ISSN 0021-9606
• Publisher: American Institute of Physics (AIP)
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
electrostatics
solvation
DNA
nucleic acids