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I'm working on DNA homopolymers and I have a question about the 'mutate_bases' process. If I use 'fiber' to create a sequence, for example GGGG, the B-DNA structure will add automatically the complementary cytosines, in that case I obtain GC-GC-GC-GC. Because my interest is in DNA-homopolymers, I just use 'mutate_bases' to change the guanines for cytosines, to obtain CC-CC-CC-CC , but I always obtain a 'cisoid' configuration for the C-C pairs. I'd like to know if I can built a DNA-homopolymer sequence where the pairs have a 'transoid' configuration, is it possible?
Best regards,
leo
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The answer is no, if I understand your question correctly. By definition, mutate_bases only mutate bases while keeping the backbone geometry untouched. Since a B-form DNA generated with the 3DNA fiber program contains only Watson-Crick base-pairs which are in 'cisoid', mutate_bases cannot mutate such a pair into 'transoid'.
The NAB (http://casegroup.rutgers.edu) tool from David Case lab may help.
Xiang-Jun
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
