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Hi,
I would like to quantify overwinding for an RNA double-helical structure in pdb-format.
How can I achieve that with the 3DNA output?
Thanks for your help,
Claus D. Kuhn
Cold Spring Harbor Laboratory
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You may want to have a look of twist angles in 3DNA output. For comparison, you can generate a regular fiber A-RNA model, such as (replace the sequence with your choice):
fiber -rna -seq=AAGGUU fiber-rna.pdb
Early publications on TBP-DNA complexes discussed the under-winding of TATA-box regions in detail: e.g., "Crystal structure of a yeast TBP/TATA-box complex (http://www.ncbi.nlm.nih.gov/pubmed/8413604)" and "Co-crystal structure of TBP recognizing the minor groove of a TATA element (http://www.ncbi.nlm.nih.gov/pubmed/8413605)". See also the section on "TA DNA (http://nar.oxfordjournals.org/content/31/17/5108.full)" in the 2003 3DNA NAR paper.
THT,
Xiang-Jun
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Thanks for your insights Xiang-Jun,
however, I did look at the twist values of the 2 helices in question and there do not seem to be gross differences, or are differences of about 1deg already significant?
I noticed that the RNA helix gets wider upon the screw-like motion that I observe in my structures. This then leads to RNA compression by a one base pair step.
Isnt it possible that the twist angles stay the same when the helix gets wider during screw-like compression??
Thanks for your help.
Claus
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Hi Claus,
I understand your concerns. For perfectly regular structures (as in fiber models) or dramatically deformed TATA-boxes in TBP-bound complexes, the differences in twist angles are easy to discern. Normally, there are no noticeable "gross differences" as in your structures. It is advisiable not to make a big point of the ~1 degree differences, unless backed up by other evidences.
I do not know exactly what you mean by "the RNA helix gets wider upon the screw-like motion", and how that "leads to RNA compression by a one base pair step". In my experience, 3D RNA structures are complicated, and fully of surprises. 3DNA, and other programs alike, is just a tool to help users make sense of their structures. Its output parameters may not be applicable in a particular situation. I am open to expand 3DNA's scope that is of general interest.
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