Nucleic acid helix structure determination from NMR proton chemical shifts

• Published in: Journal of biomolecular NMR Vol. 56; no. 2; pp. 95 - 112
• Main Authors: van der Werf, Ramon M., Tessari, Marco, Wijmenga, Sybren S.
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.06.2013; Springer Nature B.V
• Subjects: Biochemistry; Biological and Medical Physics; Biophysics; Decomposition; Nuclear Magnetic Resonance, Biomolecular - methods; Nucleic Acid Conformation; Nucleic acids; Nucleic Acids - chemistry; Physics; Physics and Astronomy; Protons; RNA - chemistry; Spectroscopy/Spectrometry; NMR; Proton chemical shift; RNA; Structure; Helix parameters
• ISSN: 0925-2738; 1573-5001; 1573-5001
• DOI: 10.1007/s10858-013-9725-y

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 che mical shift de nov o structure derivation p rotocol employing s ingular 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.