Ideal bond lengths and angles in nucleic acid structures: an update for the 2020s

摘要

In this issue of Acta Crystallographica Section B, a toolkit for analysis of nucleic acid structures is reported byMariusz Jaskolski and co-workers (Gilski et al., 2019). This paper is a valuable addition to the toolkit for analysis of nucleic acid structures. It alters the specific optimal values for bond-length and bond-angle restraint values in Watson-Crick base pairs. It also reduces the variability in those values beyond what is currently available, which are based on a study by Parkinson et al (1996). The approach taken here, incorporating Cambridge Structural Database (CSD; Groom et al., 2016) structures, quantum-mechanical calculations, and two ultra-high resolution nucleic acid crystal structures in the Protein Data Bank (PDB; Berman et al., 2000), provides a robust basis for both the ideal bond-length and bond-angle values and for the estimated variability in those values. The Parkinson study was based only on CSD structures available in 1996; the Gilski study has ten times as many CSD structures from which to draw, and the authors are combining the CSD analyses with these other two sources of information. They provide tables of bond lengths and angles not only for CG and AT pairs, but also for the isolated bases, for an isocytosine-isoguanine base pair, and for isocytosine and isoguanine alone. The authors subject the data to an elaborate statistical analysis that provides further justification for their values. They also inquire into whether the bond lengths and angles found in isolated bases differ significantly from those found in base pairs: the answer is that the differences are small but discernable.