title: Nucleic acid helix structure determination from NMR proton chemical shifts.
abstract: We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.
authors.affiliation: Department of Biophysical Chemistry, Institute of Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
authors.forename: Ramon M
authors.initials: RM
authors.lastname: van der Werf
authors.forename: Marco
authors.initials: M
authors.lastname: Tessari
authors.forename: Sybren S
authors.initials: SS
authors.lastname: Wijmenga
mesh_terms: D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D011522:Protons; D012313:RNA / Q000737:chemistry
chemical_list: D009696:Nucleic Acids; D011522:Protons; D012313:RNA
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