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General discussions (Q&As) / Single Stranded DNA

« on: September 13, 2017, 08:12:10 am »

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?