modelling ssDNA or ssRNA

[laurap]

Dear Xiang-Jun,

I would like to model an extended conformation of an ssDNA (GT(x15) sequence) and ssRNA (GU(x12) sequence). I mean, is it possible to model single strands without helical configurations (not like the half of a duplex) using 3DNA server/package?

Thanks and regards,

Laura

[xiangjun]

Hi Laura,

Thanks for your interest in 3DNA and for posting on the forum.

I understand what you mean, but I do not think 3DNA (or other tools I know of) can provide you with a straight answer. It all depends -- what specifically is your definition of "an extended conformation", i.e., "single strands without helical configurations"? If you have a starting model, mutate_bases and analyze/rebuild/frame_mol in 3DNA may help.

As always, I am willing to extend 3DNA in ways that make sense to me and are useful to the community. Currently, 3-dimensional nucleic acid structure modeling is one aspect I am interested in.

Xiang-Jun