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Kolenko P, Svoboda J, Černý J, et al. Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches. Acta Crystallogr D Struct Biol. 2020;76:1233-1243doi: 10.1107/S2059798320014151.
Kolenko, P., Svoboda, J., Černý, J., Charnavets, T., & Schneider, B. (2020). Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches. Acta crystallographica. Section D, Structural biology, 761233-1243. https://doi.org/10.1107/S2059798320014151
Kolenko, Petr, et al. "Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches." Acta crystallographica. Section D, Structural biology vol. 76 (2020): 1233-1243. doi: https://doi.org/10.1107/S2059798320014151
Kolenko P, Svoboda J, Černý J, Charnavets T, Schneider B. Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches. Acta Crystallogr D Struct Biol. 2020 Dec 01;76:1233-1243. doi: 10.1107/S2059798320014151. Epub 2020 Nov 24. PMID: 33263329; PMCID: PMC7709200.
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Acta Crystallogr D Struct Biol. 2020 Dec 01;76:1233-1243. doi: 10.1107/S2059798320014151. Epub 2020 Nov 24.

Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches.

Acta crystallographica. Section D, Structural biology

Petr Kolenko, Jakub Svoboda, Jiří Černý, Tatsiana Charnavets, Bohdan Schneider

Affiliations

  1. Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Brehova 7, 11519 Prague 1, Czech Republic.
  2. Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic.

PMID: 33263329 PMCID: PMC7709200 DOI: 10.1107/S2059798320014151

Abstract

Solution and crystal data are reported for DNA 18-mers with sequences related to those of bacterial noncoding single-stranded DNA segments called repetitive extragenic palindromes (REPs). Solution CD and melting data showed that the CG-rich, near-palindromic REPs from various bacterial species exhibit dynamic temperature-dependent and concentration-dependent equilibria, including architectures compatible with not only hairpins, which are expected to be biologically relevant, but also antiparallel duplexes and bimolecular tetraplexes. Three 18-mer oligonucleotides named Hpar-18 (PDB entry 6rou), Chom-18 (PDB entry 6ros) and its brominated variant Chom-18Br (PDB entry 6ror) crystallized as isomorphic right-handed A-like duplexes. The low-resolution crystal structures were solved with the help of experimental phases for Chom-18Br. The center of the duplexes is formed by two successive T-T noncanonical base pairs (mismatches). They do not deform the double-helical geometry. The presence of T-T mismatches prompted an analysis of the geometries of these and other noncanonical pairs in other DNA crystals in terms of their fit to the experimental electron densities (RSCC) and their geometric fit to the NtC (dinucleotide conformational) classes (https://dnatco.datmos.org/). Throughout this work, knowledge of the NtC classes was used to refine and validate the crystal structures, and to analyze the mismatches.

open access.

Keywords: CD spectra; DNA structure; REPs; T–T mismatch; crystal structure; noncanonical base pairs; repetitive extragenic palindromes

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