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Author Topic: About the mutation in DNA  (Read 3676 times)

Offline espinosaleal

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About the mutation in DNA
« on: April 17, 2014, 05:24:13 pm »
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
"If you want to build a ship, don't drum up people together to collect wood and don't assign them tasks and work, but rather teach them to long for the endless immensity of the sea"  Antoine de Saint-Exupéry

Offline xiangjun

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Re: About the mutation in DNA
« Reply #1 on: April 17, 2014, 06:07:35 pm »
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 tool from David Case lab may help.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.