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Author Topic: building a custom dna triplex  (Read 4303 times)

Offline giambasu

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building a custom dna triplex
« on: February 16, 2012, 03:45:31 pm »

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?



Offline xiangjun

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Re: building a custom dna triplex
« Reply #1 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 -- 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,


« Last Edit: February 16, 2012, 04:02:52 pm by xiangjun »


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