The 3DNA suite includes the mutate_bases program, which, as its name suggests, mutates bases while maintaining the backbone conformation. This feature was incorporated into the suite following user feedback and has been utilized in several studies before being formally published in the Li et al. (2019) paper. A key advantage is that the mutation process preserves both the geometry of the sugar-phosphate backbone and the base reference frame, encompassing position and orientation. Consequently, re-analyzing the mutated model yields identical base-pair and step parameters as those of the original structure.

In DSSR, the standalone mutate_bases program has become the mutate sub-command with enhanced functionality and improved usability, as documented in the User Manual. The mutate module allows users to perform base mutations efficiently and effectively by taking advantage of the powerful DSSR analysis engine.

To further expand the modeling capabilities of the DSSR, v2.5.3 introduced the --mutate-type option to allow for backbone mutations, based on the base reference frame. Furthermore, the target can be any fragment, regardless of length or composition, rather than just a single nucleotide. When combined with the rebuild module, this feature significantly enhances DSSR’s ability to model nucleic acid structures.

Here is an example of modeling PDB entry 1msy, a 27-nt structure (1msy.pdb) that mimics the sarcin/ricin loop from E. coli 23S ribosomal RNA.

x3dna-dssr analyze -i=1msy.pdb --ss --rebuild -o=1msy-expt.out
mv dssr-ssStepPars.txt 1msy-step.txt
x3dna-dssr rebuild --backbone=RNA --par-file=1msy-step.txt -o=1msy-step.pdb

x3dna-dssr -i=1msy.pdb --select-resi='A 2654' -o=1msy-A2654.pdb
x3dna-dssr -i=1msy.pdb --select-resi='A 2655' -o=1msy-G2655.pdb
x3dna-dssr -i=1msy-A2654.pdb --frame=2654 -o=frame___A.pdb
x3dna-dssr -i=1msy-G2655.pdb --frame=2655 -o=frame___G.pdb

x3dna-dssr mutate -i=1msy-step.pdb --entry='num=8 to=A; num=9 to=G' -o=1msy-C2endo.pdb --mutate-part=whole
x3dna-dssr --connect-file -i=1msy-C2endo.pdb -o=1msy-C2endo-cnt.pdb --po-bond=5.0

1. The analyze step uses options --ss and --rebuild to generate the file dssr-ssStepPars.txt (containing base-step parameters), which is then renamed to 1msy-step.txt. The rebuild step employs 1msy-step.txt to construct a structure (1msy-step.pdb) with regular C3'-endo sugar RNA backbone conformation. Note that the rebuilt structure has nucleotides numbered from 1 to 27, while in the PDB 1msy, they correspond to 2647 to 2673, respectively.
2. However, the A2654 and G2655 dinucleotides in 1msy are actually in C2'-endo sugar conformation, creating the S-shaped structure around the GpU platform. The above rebuilt structure does not reflect this distortion. So we extract A2654 and G2655 with --select-resi and then put each in its standard base reference frame, named frame___A.pdb and frame___G.pdb, respectively.
3. Now we mutate A8 and G9 in the rebuilt structure 1msy-step.pdb to A and G with option --mutate-part=backbone to ensure the backbone conformations are changed according to those in frame___A.pdb and frame___G.pdb, respectively. The resulting structure is named 1msy-C2endo.pdb. Now the S-shape around the GpU platform is preserved, even though the backbone are not always covalently connected, due to large O3'(i-1) to P(i) distances between neighboring nucleotides. The last step is to generate CONECT records with --connect-file option to connect the backbone atoms explicitly, resulting in more smooth backbone cartoon representation in PyMOL as shown below.

As noted in the Li et al. (2019) paper, users can optimize this approximate backbone connection using Phenix, while keeping the base atoms fixed. The 3DNA-Phenix combination leads to a model where the base geometry strictly follows the parameters prescribed in the user-specified file, and the backbone is regularized with improved stereochemistry and a ‘smooth’ appearance in ribbon representation.

There are other variants of the DSSR mutate module, including for building Z-DNA backbones. However, the above example is sufficient to demonstrate the power of the integrated approach enabled by DSSR for the analysis and modeling of nucleic acid structures. See the DSSR User Manual for more details.

References

Li,S. et al. (2019) Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures. Nucleic Acids Res., 47, W26–W34.