Nucleic Acid Crystallography pp 259-267

Part of the Methods in Molecular Biology book series (MIMB, volume 1320)

Helical Symmetry of Nucleic Acids: Obstacle or Help in Structure Solution?

  • Alexandre Urzhumtsev
  • Ludmila Urzhumtseva
  • Ulrich Baumann
Protocol

Abstract

Crystallographic molecular replacement method is the key tool to define an atomic structure of nucleic acids. Frequently nucleic acids are packed forming continuous helices in the crystal. This arrangement of individual molecules in “infinite” pseudo helical structures in crystal may be the reason why the molecular replacement fails to find a unique position of the search atomic model as the method requires. The Patterson function, calculated as a Fourier series with diffraction intensities, has auxiliary peaks for such a molecular packing. Those near the origin peak indicate the orientation of the helices. The coordinates of other peaks are related to the molecular position and the rotation angle between two such “infinite” helices. Thus, the peak analysis allows getting molecular position even without a search model. An intelligent selecting and averaging of the phase sets corresponding to multiple probable positions of the search model again result in a unique solution but in the form of a Fourier synthesis and not a model. This synthesis can be used then to build an atomic model as it is the case for usual phasing methods.

Key words

Nucleic acids Atomic structure Molecular replacement Pseudo helical symmetry Patterson analysis Multisolution approach Fourier maps 

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Alexandre Urzhumtsev
    • 1
  • Ludmila Urzhumtseva
    • 2
  • Ulrich Baumann
    • 3
  1. 1.Centre for Integrative Biology, Institute of Genetics and of Molecular and Cellular BiologyCNRS UMR 7104/INSERM U964/Université de StrasbourgIllkirch GraffenstadenFrance
  2. 2.Institut de Biologie Moléculaire et Cellulaire, UPR 9002 CNRSUniversité de StrasbourgStrasbourgFrance
  3. 3.Institute of BiochemistryUniversity of CologneCologneGermany

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