Structural variability of base pairs in DNA

D. Berdár1, J. Svoboda1, P. Kolenko1,2, B. Schneider1

1Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic

2Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University, Břehová 78/7, 115 19 Prague, Czech Republic

Base pairing is an important feature of nucleic acid structure with fundamental implication for the flow of the genetic code. Base pairing is realized via distinct hydrogen bond edges and results in canonical and non-canonical geometries as described in Leontis-Westhof nomenclature [1]. We decided to analyze geometries of “mismatched” DNA base pairs, i.e. base pairs in non-Watson-Crick topologies by solving of crystal structures with mismatched pairs in 18-mer DNA duplexes. Previously crystallized 18-mer DNA oligonucleotide contained double thymine mismatch in the central positions [2], now we obtained nine additional variants covering both canonical and non-canonical base pairing. The refinement and validation stages of solving all our structures benefited from using the NtC dinucleotide classes ( [3]. Firstly, we used NtCs as refinement targets and secondly for annotation of solved structures. We present a comprehensive structural annotation of the base pairs in the ten solved 18-mer duplexes.


1. Leontis NB, Westhof E. Geometric nomenclature and classification of RNA base pairs. RNA. 2001;7(4):499-512.

2. 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;76(Pt 12):1233-1243.

3. Černý J, Božíková P, Svoboda J, Schneider B. A unified dinucleotide alphabet describing both RNA and DNA structures. Nucleic Acids Res. 2020;48(11):6367-6381