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The 2016 January issue of the Computational Crystallography Newsletter (CCN) (https://www.phenix-online.org/newsletter/) contains a short communication titled "Characterization of base pair geometry (https://www.phenix-online.org/newsletter/CCN_2016_01.pdf)" (p.5-8) by Dr. Wilma Olson and me. This essay had been mostly motivated by two publications in the 2015 July issue of CCN by Dr. Jane Richardson: an article titled "A context-sensitive guide to RNA & DNA base pair & base-stack geometry," and an 'Expert advice' of 'Fitting Tip #10' titled "How do your base pairs touch and twist?" In both pieces, Richardson emphasized the importance of base-pair (bp) non-planarity introduced by Buckle and Propeller (see Figure below) for improved fit of DNA/RNA models to X-ray electron density maps. I derived a complete set of six simple bp parameters for a complete qualitative description of bp geometry. The term 'simple' is used because the parameters are more intuitive for non-canonical pairs, and to differentiate them from the existing local bp parameters in 3DNA.
(http://dssr.bio.columbia.edu/data/six-bp-pars.png)
In the CCN short communication, we also highlighted the DSSR-introduced cartoon-block representations of DNA and RNA structures that combine PyMOL cartoon schematics with color-coded rectangular base blocks (See Figure below). The simple, informative cartoon-block representations facilitate understanding of the base interactions in small to mid-sized nucleic acid structures where the base identity, pairing geometry, and stacking interactions are immediately obvious.
(http://dssr.bio.columbia.edu/data/DSSR-cartoon-blocks.png)
A blogpost with the same title "Characterization of base-pair geometry (http://x3dna.org/highlights/CCN-on-base-pair-geometry)" contains details for reproducing the cartoon-block images in the figure above. See also links therein for further information.
Xiang-Jun
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University