RNA overwinding

[ClausKuhn]

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

[xiangjun]

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" and "Co-crystal structure of TBP recognizing the minor groove of a TATA element". See also the section on "TA DNA" in the 2003 3DNA NAR paper.

THT,

Xiang-Jun

[ClausKuhn]

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

[xiangjun]

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