building a custom dna triplex

[giambasu]

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

[xiangjun]

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 -- currently mutate_bases is the only program I have documented.

Third, you need to download 3DNA v2.1beta 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