Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: About the mutation in DNA  (Read 4024 times)

Offline espinosaleal

  • with-posts
  • *
  • Posts: 2
    • View Profile
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,

"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

  • Administrator
  • with-posts
  • *****
  • Posts: 1505
    • View Profile
    • 3DNA homepage
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.

Dr. Xiang-Jun Lu [律祥俊]

* Click "NOTIFY" to receive email notifications
* Original Poster, please provide a summary


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.