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Questions and answers => General discussions (Q&As) => Topic started by: giambasu on February 16, 2012, 03:45:31 pm

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Title: building a custom dna triplex
Post by: giambasu on February 16, 2012, 03:45:31 pm

Hi,

I am trying to build a standard dna triplex which is a mixture of TAT and CGC(+) triples.
Can I use the x3dna rebuild (or other) facility to generate such a structure from the
helical parameters that I get from, for example, analysing the TAT or CIC DNA triplexes?

thanks,

George

Title: Re: building a custom dna triplex
Post by: xiangjun on February 16, 2012, 04:00:59 pm

Hi George,

Thanks for posting at the new 3DNA forum!

One way to build a standard DNA triplex with a mixture of TAT and CGC(+) triples would be first to build a Poly (U) : poly (A) : poly(U) triplex, using fiber model #32, or another one as you see fit. Run fiber -l for a list of possible fiber models available from 3DNA, and read the 3DNA 2003 NAR paper for details.

Next, you can use mutate_bases to mutate A/U to the bases you need. See the documentation for details (http://forum.x3dna.org/programs/mutate_bases/) -- currently mutate_bases is the only program I have documented.

Third, you need to download 3DNA v2.1beta (http://x3dna.org/download/) which has mutate_bases incorporated as an integral part of the new distribution.

Note that 3DNA v2.1 is only in beta test version. If you notice any issues, please report back.

Best regards,

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.