Calculating the angle of DNA curvature

[wkagawa]

Hi all.
I am trying to calculate the angle of curvature of a particular DNA.  Is this possible to do using X3DNA?  I read the recent Nature Protocol paper by Xiang-Jun Lu and Wilma Olson, which said,

"The 3DNA software also lets the user take advantage of the unique capability of Curves to find a global curvilinear helical axis and related global parameters, such as the widths and depths of the major and minor grooves, ..."

Does this imply that the angle of DNA curvature can only be calculated with Curves?  I do not know the basics behind how to calculate the angle of DNA curvature, so any help to point me towards the right direction will be greatly appreciated.

[xiangjun]

Thanks for reading the 3DNA Nature Protocols 2008 paper (NP2008).

The quota you cited refers to the section titled "Relationship to other programs", more specifically the "-c" option of "find_pair" designed to make Curves users' life a bit more straightforward. Curves is certainly a well-known program in quantifying DNA curvature, as evidenced clearly in literature where DNA bending angles are reported.

In the 3DNA NP2008 paper, protocol (recipe) no. 4 is on "Automatic identification of double-helical regions in a DNA–RNA junction", which provides detailed steps on calculating the angle between helices #1 and #3.  If that's what you want, you may find it worthwhile to (re)read the relevant parts more carefully.

Given the many similar questions recently popped up in the forum, it seems fair to say that quantifying DNA bending angle or curvature is still an open issue,  at least not well-understood by non-experts in the community. From my experience (not just in nucleic acid structures), this is not surprising at all. A seemingly long-solved problem still could bug you down when you try to get to the bottom of it.

HTH,

Xiang-Jun

[wkagawa]

Hi Xiang-Jun,

Thank you for the reply. The recipes in your Nature Protocol paper are very helpful.
I have been trying to compare DNA bending angles of several, structurally related protein-DNA complexes. However, after working with 3DNA and CURVES for awhile, I noticed that the problem is complex, because these DNA have different structures, and thus it is difficult to compare bending angles between them. With your comments, I have convinced myself that even if the bending angles can be quantified in a certain way, the calculated angles would be difficult to interpret and may not have much meaning.