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Structure solution of DNA-binding proteins and complexes with ARCIM- BOLDO libraries.

Pröpper, K. and Meindl, K. and Sammito, M. and Dittrich, B. and Sheldrick, G.M. and Pohl, E. and Uson, I. (2014) 'Structure solution of DNA-binding proteins and complexes with ARCIM- BOLDO libraries.', Acta crystallographica Section D biological crystallography., 70 (6). pp. 1743-1757.


Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.

Item Type:Article
Additional Information:Published by John Wiley on behalf of the International Union of Crystallography.
Keywords:Protein–DNA complexes and macromolecule structure solutions, Structure-solution pipelines, Molecular replacement, Density modification.
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Publisher statement:This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Date accepted:04 April 2014
Date deposited:04 July 2014
Date of first online publication:30 May 2014
Date first made open access:No date available

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