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Hi Xiang-Jun,
We are wondering about how you assigne Z-DNA in your programs.
Will your programs find all Z-DNA fragments even in single strands ?
Furthermore, we wonder about the very specific orientation of the sugars
in Z-DNA CpG motifs. There, the two O4' atoms are pointing one towards the other
(see attached figure). Is there a specific parameter attached to this
type of sugar configuration in your program outputs ?
Thanks for your reply.
Best,
Pascal
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Hi Pascal,
In 3DNA and DSSR, the classification of Z-DNA is on double-stranded helices, not single strands. Furthermore, in 3DNA (analyze), the classification is on the whole structure, whilst in DSSR, it is on each dinucleotide step.
Regarding the Z-DNA CpG motifs, I am glad that you paid attention to the O4'(C)...G capping interactions. From early on, I realized that it is not just the OP1/OP2 atoms of the phosphate groups that can make capping interactions, and that's why I implemented them all in DSSR. As documented in the manual, you need to specify the --more option to see the capping interactions.
HTH,
Xiang-Jun
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Hi Pascal,
After further consideration, I now believe that it makes more sense to output the base-capping interactions in DSSR by default (i.e., without needing to specify the --more option). So as of DSSR v1.4.4-2015nov18 (to be released tomorrow), running DSSR on a Z-DNA, e.g. 2dcg (http://www.rcsb.org/pdb/explore/explore.do?structureId=2dcg), will have the following section:
# Running this command:
x3dna-dssr -i=2dcg.pdb
# Pertinent section in the output:
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List of 6 atom-base capping interactions
dv: vertical distance of the atom above the nucleotide base
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type atom nt dv
1 sugar O4'@A.DC1 A.DG2 2.89
2 sugar O4'@A.DC3 A.DG4 2.90
3 sugar O4'@A.DC5 A.DG6 2.81
4 sugar O4'@B.DC7 B.DG8 2.87
5 sugar O4'@B.DC9 B.DG10 2.89
6 sugar O4'@B.DC11 B.DG12 2.78
Best regards,
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