Single Stranded DNA

[aribis77]

A very common query amongst Nucleic acid structural biologists or rather modelling community is that is there a software suitable for single stranded DNA structure modelling. I would like to ask the same here if this software can do the same. If not would first designing the double stranded regions (stem) and then joining them with linear strands separated from double stranded modelling options and then simulating the whole joined structure make sense. I know that separating linear starnds from double stranded structures can be painstaking as that would mean reassignment of charges. But what is this is done on a linear double stranded structure so atleast the problems of conformational bends does not come into the picture. Then finally let the whole structure  ( ss linear regions joined with ds modelled regions) fold within a simulation. Could that be a workable solution?

[xiangjun]

is there a software suitable for single stranded DNA structure modelling

This is a vague question, and I'm not sure how to answer it. Did you know the NAB tool from the David Case laboratory at Rutgers? NAB is a flexible "molecular manipulation language" designed for the "Generation of Models for 'Unusual' DNA and RNA". In principle, NAB in combination with AMBER should do the trick.

As far as 3DNA/DSSR goes, the "fiber" program can generate arbitrary linear double or single-stranded DNA models. The other two programs, "rebuild" and "mutate_bases", can also be applied to certain aspects of modeling studies (see my blogpost "The 3DNA mutate_bases program is cited in Nature").

... Could that be a workable solution?

What you said make sense, in general. However, only doing it will reveal concrete caveats and possible solutions. Please post back if you think 3DNA/DSSR may be of some help along the way, and I'll try my best to help.

As a side note, you may already know "RNA-Puzzles", and the numerous tools available for RNA modeling.

Best regards,

Xiang-Jun