title: Modeling RNA topological structures using small angle X-ray scattering.
abstract: Detailed understanding of the structure and function relationship of RNA requires knowledge about RNA three-dimensional (3D) topological folding. However, there are very few unique RNA entries in structure databases. This is due to challenges in determining 3D structures of RNA using conventional methods, such as X-ray crystallography and NMR spectroscopy, despite significant advances in both of these technologies. Computational methods have come a long way in accurately predicting the 3D structures of small (<50nt) RNAs to within a few angstroms compared to their native folds. However, lack of an apparent correlation between an RNA primary sequence and its 3D fold ultimately limits the success of purely computational approaches. In this context, small angle X-ray scattering (SAXS) serves as a valuable tool by providing global shape information of RNA. In this article, we review the progress in determining RNA 3D topological structures, including a new method that combines secondary structural information and SAXS data to sample conformations generated through hierarchical moves of commonly observed RNA motifs.
authors.affiliation: Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA. Electronic address: bhandariyr@mail.nih.gov.
authors.forename: Yuba R
authors.initials: YR
authors.lastname: Bhandari
authors.affiliation: Argonne National Laboratory, Lemont, IL, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Jiang
authors.affiliation: Data Science and Information Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
authors.forename: Eric A
authors.initials: EA
authors.lastname: Stahlberg
authors.affiliation: Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
authors.forename: Jason R
authors.initials: JR
authors.lastname: Stagno
authors.affiliation: Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
authors.forename: Yun-Xing
authors.initials: YX
authors.lastname: Wang
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
chemical_list: D012313:RNA
keywords: Conformation; Motif; Moves; RNA; SAXS; Topological