Journal:Acta Cryst D:S2059798318000050
From Proteopedia
A DNA structural alphabet provides new insight into DNA flexibilityBohdan Schneider, Paulina Bozikova, Iva Necasova, Petr Cech, Daniel Svozil and Jiri Cerny [1] Molecular Tour  NtC and CANA assignment, which is accessible at the website https://dnatco.org [2], allows the quantitative assessment and validation of DNA structures and their subsequent analysis by means of pseudo-sequence alignment. We also proposed a projection of the CANA letters onto the graphical representation of the molecular structure that should provide a visual tool to analyze DNA structures. Annotation of the structural properties of a few archetypal types of DNA structures revealed some unexpected features: (i) The Dickerson–Drew dodecamer (for example PDB entry ; 1bna), which is often considered to be a typical B-DNA duplex, is conformationally rich, with a high proportion of features mixing B and A forms. (ii) Our analysis of duplex models based on the fibre-diffraction data discloses the need for their critical evaluation before they are used for computer modeling. (iii) Conformational analysis of guanine quadruplexes (for example PDB entry ; 1jpq) demonstrates the universality of the most frequent B conformer, BB00, which builds the tetrad cores of these folded DNA in combination with more exotic conformers which have a base in syn orientation (NtC BB1S or BBS1). (iv) A Holliday junction (for example PDB entry ) is a DNA intermediate in homologous recombination. It contains four double-stranded DNA arms joined together by short links. The stems of the junctions are usually B-DNA duplexes with very few, if any, B-A and A-B conformers. The NtC class that can be associated with the junction proper is the recurrently occurring unstacked NS04. An analysis of the DNA structures in complexes with transcription factors and with histone proteins by means of the CANA alphabet has been published [3] and is discussed at Proteopedia page Journal:Genes:1. We believe that the NtC and CANA assignment protocol provides impartial characterization of the DNA structures, tools helping to refine and validate DNA crystal and NMR structures, interpret DNA molecular modeling, and facilitate challenging analyses of sequence-dependent features of DNA structures and their interactions with proteins. References
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