Building a DNA superhelix

[molatwork]

Dear 3DNA community,

I wonder if there is a way with 3DNA to generate superhelical DNA given a pitch and a diameter or if anyone could tell me another way of achieving it. I saw in the forum a message expressing interest in adding to 3DNA the capability of analysing superhelices, but nothing about building them.

Thank you very much in advance,


Miguel

[xiangjun]

Dear Miguel,

Thanks for posting your DNA super-helix building question here. Currently, 3DNA does not yet have the functionality. As you noticed, Arvind posted a related question, i.e., analyzing a DNA super-helix to give its pitch and radius.

Essentially, this is the same issue looked from different perspectives, in a sense similar to SCHNAaP/SCHNArP and analyze/rebuild for DNA/RNA duplex. Any rigorous treatment should be mathematically reversible, i.e., given a super-helix, one can derive a set of pitch/radius parameters; conversely, from this same set of parameters, the original super-helix should be rebuilt without loss of information. I would like to hear more on related issues in the literature. Any clues?

Xiang-Jun

[molatwork]

Dear Xiang-Jun,

Thank you for your answer.
The best clue I have found is an analysis of the superhelicity of DNA in nucleosomes. Here is the link:

http://www.cell.com/biophysj/fulltext/S0006-3495(08)70172-3

I have access to this paper if need it be.
My maths are just average, as my programming skills, but if you think that this could be a starting point and you believe I may help, please let me know.

Best regards,


Miguel

[xiangjun]

Thanks for the info. Just to be precise, the link you gave is broken: it should also include the ending characters in the URL. For the benefit of other viewers, here is the correct one with title of the paper as link text: Geometry of the Nucleosomal DNA Superhelix by Thomas C. Bishop. (We all make simple mistakes, and I hope you won't mind my pointing your minor typo out  :roll:. I am hoping you and others will do the same to any 3DNA-related issues. Every bug report or correction etc would be gratefully received!

I have no problem in accessing this paper. I think it is a nice piece of work. It is actually in the 3DNA citation list. I should have read the abstract before, but did not get into the main text. To be realistic, though, I do not think I have that much spare time right now to understand and implement the algorithm to fit your purpose -- it won't be a trivial take, especially to get it done efficiently and robustly. You could contact the author directly for further details. Maybe we could make an arrangement to incorporate Dr. Bishop's method into 3DNA (with proper attributions, of course).

Thanks for your cooperation, and hopefully more 3DNA users would follow your example.

Xiang-Jun