Structural alphabet for structural analysis of nucleic acids

Bohdan Schneider and Jiří Černý

Institute of Biotechnology of the Czech Academy of Sciences,
Prumyslova 595, Vestec, 252 50, Czech Republic

A newly developed structural alphabet [1] is the first alphabet universally applicable to both types of nucleic acids, RNA and DNA. In the talk, I will demonstrate some of the applications of the alphabet. It can be used to statistically weight sequence preferences of different conformational forms and to discover RNA and DNA structural motifs. The alphabet is based on 96 dinucleotide conformational classes, NtC, that were identified by analysis of structures of ~60 thousand RNA and ~60 thousand DNA steps. The resulting automated assignment of the conformational classes to any nucleic acid structure is available at the website dnatco.org [2] and is an extension of our previously published algorithm assigning only DNA structures [3].

[1] Božíková et al., to be published 2020.

[2] Černý et al., Nucleic Acids Research 2016, 44, W284.

[3] Schneider et al., Acta Cryst. D 2018, 74, 52-64.