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Nucleic Acid Crystallography

Volume 1320 of the series Methods in Molecular Biology pp 259-267

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

  • Alexandre UrzhumtsevAffiliated withCentre for Integrative Biology, Institute of Genetics and of Molecular and Cellular Biology, CNRS UMR 7104/INSERM U964/Université de Strasbourg Email author 
  • , Ludmila UrzhumtsevaAffiliated withInstitut de Biologie Moléculaire et Cellulaire, UPR 9002 CNRS, Université de Strasbourg
  • , Ulrich BaumannAffiliated withInstitute of Biochemistry, University of Cologne

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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