DSSR-enabled cartoon block images for G-quadruplex

Via Google Scholar, I noticed the recent publication in Nucleic Acids Research by Meier et al. titled Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge. Reading through the article, I am pleased to see the section “Nucleic acid geometry and visualization” under MATERIALS AND METHODS:

We used the program DSSR (53) of the 3DNA suite (54) to analyse the nucleic acid backbone and the base pair geometry from the 3D structures. We reported the ‘simple’ base-pair parameters for buckle, propeller twist and stagger which are more intuitive for non-canonical base-pairs than the classic base-pair parameters as explained in the program manual and the 3DNA website (http://home.x3dna.org/highlights/details-on-the-simple-base-pair-parameters, http://home.x3dna.org/articles/simple-parameters-for-non-Watson-Crick-base-pairs). We wrote an R (55) script that automatically creates a backbone angle plot from the output of the DSSR program. The script can be downloaded from the 3DNA forum at http://home.x3dna.org. The nucleic acid was visualized in PyMOL and the dssr block plugin (The PyMOL Molecular Graphics Sys- tem, Version 2.0, Schro ̈dinger, LLC, https://pymol.org/). …

This is the first time (I’m aware of) that the ‘simple’ base-pair parameters introduced in 3DNA v2.3 is cited in a peer-reviewed journal article. I’m also glad to know that the blog posts on the 3DNA homepage are read, and even referenced in a publication — which surely will prompt me to write more. This is also the first time that the dssr_block PyMOL plugin is cited. I must say that Figures 1, 5, and 6 from the paper look gorgeous. Among other things, the G-tetrads and the surrounding base identity are immediately obvious using the simple color code: A, red; T, blue, C, yellow, and G, green. See Fig. 1 below.

DSSR-enabled block images [Fig. 1 of Meier18-nar-gky307]

In the section on “DATA AVAILABILITY”, the authors further noted:

Our R (55) script that automatically creates backbone angle plots from the output of the DSSR program can be downloaded from the 3DNA forum at http://home.x3dna.org.

I communicated with Markus Meier (the lead author) on the 3DNA Forum, on the thread DSSR: Analyzing NMR structures – overwritten output files. Checking the thread right now, I found that the R script (backbone_torsions_plot-1.0.tar.bz2) has been downloaded 263 times. I appreciate Markus’s effort in contributing the R script with a working example to the DSSR user community. It has always been my hope that more DSSR users would share their scripts and examples via the 3DNA Forum.

As a side note, I met Markus in Los Angles at the 60th Annual Meeting. It was a nice experience chatting with him, and had a lunch together. We’ve kept in touch following the meeting.





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