3 years ago

DNA conformational transitions inferred from re-evaluation of m|Fo| − D|Fc| electron-density maps

DNA conformational transitions inferred from re-evaluation of m|Fo| − D|Fc| electron-density maps
Toshiyuki Chatake, Tomoko Sunami, Hidetoshi Kono
Conformational flexibility of DNA plays important roles in biological processes such as transcriptional regulation and DNA packaging etc. To understand the mechanisms of these processes, it is important to analyse when, where and how DNA shows conformational variations. Recent analyses have indicated that conventional refinement methods do not always provide accurate models of crystallographic heterogeneities and that some information on polymorphism has been overlooked in previous crystallographic studies. In the present study, the m|Fo| − D|Fc| electron-density maps of double-helical DNA crystal structures were calculated at a resolution equal to or better than 1.5 Å and potential conformational transitions were found in 27% of DNA phosphates. Detailed analyses of the m|Fo| − D|Fc| peaks indicated that some of these unassigned densities correspond to ZI ZII or A/B BI conformational transitions. A relationship was also found between ZI/ZII transitions and metal coordination in Z-DNA from the detected peaks. The present study highlights that frequent transitions of phosphate backbones occur even in crystals and that some of these transitions are affected by the local molecular environment.A re-evaluation of m|Fo| − D|Fc| electron-density maps revealed that potential conformational transitions of 27% of DNA phosphates are found in previous crystallographic data. The analysis suggests that some of these unassigned densities correspond to ZI ZII or A/B BI transitions.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1107/S2059798317007707

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