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

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 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.
Authors:
 [1] ;  [1] ;  [2] ;  [3] ; ORCiD logo [4] ;  [5] ;  [1]
  1. School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
  2. Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, USA
  3. Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
  4. Pacific Northwest National Laboratory, Richland, Washington 99352, USA
  5. Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, USA; Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, USA
Publication Date:
OSTI Identifier:
1327123
Report Number(s):
PNNL-SA-115068
Journal ID: ISSN 0021-9606; WN0219080
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 144; Journal Issue: 20
Publisher:
American Institute of Physics (AIP)
Research Org:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
electrostatics; solvation; DNA; nucleic acids