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

Journal Article · Sat May 28 00:00:00 EDT 2016 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.4950814· OSTI ID:22657834

Pabit, Suzette A.; Katz, Andrea M.; Pollack, Lois ^[1]; Tolokh, Igor S. ^[2]; Drozdetski, Aleksander ^[3]; Baker, Nathan ^[4]; Onufriev, Alexey V. ^[2]

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1. School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853 (United States)
2. Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061 (United States)
3. Department of Physics, Virginia Tech, Blacksburg, Virginia 24061 (United States)
4. Pacific Northwest National Laboratory, Richland, Washington 99352 (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, we show how WAXS can qualitatively characterize 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 into 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.

• OSTI ID: 22657834
• Journal Information: Journal of Chemical Physics, Vol. 144, Issue 20; Other Information: (c) 2016 Author(s); Country of input: International Atomic Energy Agency (IAEA); ISSN 0021-9606
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC
ORGANIC
PHYSICAL AND ANALYTICAL CHEMISTRY
COMPUTERIZED SIMULATION
IONS
MOLECULAR DYNAMICS METHOD
SMALL ANGLE SCATTERING
WAXES
X-RAY DIFFRACTION