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

Date Published: July 01, 2017

Publisher: International Union of Crystallography

Author(s): Tomoko Sunami, Toshiyuki Chatake, Hidetoshi Kono.


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.

Partial Text

DNA plasticity plays important roles in various biological processes such as the transcription and packaging of genomic information. A representative example of such plasticity is the sequence-dependent deformability of DNA, which has been shown to be crucial for molecular recognition of DNA-binding proteins (Olson et al., 1998 ▸; Sarai & Kono, 2005 ▸; Rohs et al., 2009 ▸). B-DNA adopts two representative phosphate backbone conformations, BI and BII, which are defined by ∊–ζ values (Supplementary Fig. S1). BI is known to be a major conformer in B-DNA (Schneider et al., 1997 ▸). Several studies have been performed to analyse the DNA deformability from this aspect, as exemplified in the following. NMR data revealed evidence for a BI–BII equilibrium in steps flanking the NF-κB binding site and a curvature of the DNA duplex induced by the equilibrium (Tisné et al., 1998 ▸; Wecker et al., 2002 ▸). A mutation study showed that the distribution of BI–BII conformational equilibria had a critical effect on the binding affinity (Tisné et al., 1999 ▸). Molecular-dynamics (MD) simulations of the binding sites of papillomavirus type 1 E2 protein (Djuranovic & Hartmann, 2005 ▸; Robertson & Cheat­ham, 2015 ▸) demonstrated that a DNA sequence with stronger affinity adopts the BII conformer more frequently, and the BII conformer is also preserved in protein–DNA complexes. In this way, transitions between BI and BII have mainly been studied using MD or NMR spectroscopy.

DNA conformations are important for molecular recognition of DNA-binding proteins. However, multiple conformations have been assigned to only 6.3% of the phosphates in crystal structures solved at a resolution equal to or higher than 1.5 Å. In the present study, a comprehensive analysis demonstrated that conformational variations of DNA are more extensive than recorded in the coordinates of crystal data in the PDB. Based on the unassigned densities of DNA crystal structures obtained by recalculating the m|Fo| − D|Fc| maps, peaks were found in the vicinity of 27% of phosphates. It was also found that the frequency of peak appearance is strongly dependent on the X-ray resolution. Interestingly, more than half of P atoms accompany the m|Fo| − D|Fc| peaks in structures at 1.0 Å resolution. Since the peaks for A/B, ZI and ZII conformers are clearly localized, conformations could be assigned to them. In addition, a relationship between the local environment and transitions of phosphate backbone in Z-DNA structures was found.




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