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Author Topic: design triple helix  (Read 2843 times)

Offline sima

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design triple helix
« on: May 21, 2019, 02:59:19 am »
Hello . I am a new user
I reviewed the questions of others. Unfortunately, I did not understand how to design triple helix. Using fiber -pauling , I succeeded in making triple helix . But When I use find_pair command, the software shows the following text:
C:\Users\Sima>find_pair triplex-C10C10C10.pdb

handling file <triplex-C10C10C10.pdb>
no base-pairs found for this structure
triplex-C10C10C10.pdb
triplex-C10C10C10.out
    2         # duplex
    0         # number of base-pairs

Time used: 00:00:00:00



i use this link
https://x3dna.org/highlights/pauling-triplex-model-of-nucleic-acids-is-available-in-3dna


thanks for your help
« Last Edit: May 21, 2019, 03:05:52 am by sima »

Offline mauricio esguerra

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Re: design triple helix
« Reply #1 on: May 21, 2019, 03:48:49 am »
Hi Sima,

Note that the command:

Code: [Select]
fiber -pauling insideout.pdb
Will generate a "Pauling" DNA triple helix, that is, one where the inside is out, so to say. That is, the phosphate groups are in the inside and the nitrogenated bases are in the outside, unlike the common in nature DNA Triple Helix. This is why find_pair cannot manage to find any base-pairs, because in a Pauling-Corey triple helix, there are no bases pairing to each other.

You probably want a "normal" DNA Triple Helix. You can generate it with:

Code: [Select]
fiber -31 dnatriplex.pdb
See the attached images at the end of the post.

Note also that there are parallel and antiparallel DNA triple helices. 3DNA generates a fiber model of a parallel triple helix with the fiber -31 command.

An old classic DNA-Triplex review is the one by Frank-Kamenetskii and Mirkin, I suggest getting a hold of it and reading it. Even though old, it's an excellent review of pretty much all possible DNA-Triplexes one might find in biological systems.

Frank-Kamenetskii,M.D. and Mirkin,S.M. (1995) Triplex DNA structures. Annu. Rev. Biochem., 64, 65–95. https://doi.org/10.1146/annurev.bi.64.070195.000433

Also, I suggest our own article on the DNA antiparallel triplex:

Nucleic Acids Research, 2014, Vol. 42, No. 18 11329–11338 http://dx.doi.org/10.1093/nar/gku848
Triple helical DNA in a duplex context and base pair opening
Mauricio Esguerra, Lennart Nilsson and Alessandra Villa*

Good luck with your research into DNA triple helices!

P.S. I've also attached the pdb files I've generated with 3DNA's fiber and which I used for rendering with pymol.

« Last Edit: May 21, 2019, 04:08:47 am by mauricio esguerra »

Offline xiangjun

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Re: design triple helix
« Reply #2 on: May 21, 2019, 09:39:55 am »
Hi,

Sima -- thanks for using 3DNA and for posting your questions on the Forum
Mauricio -- thanks for your insightful response to Sima's question. I already have your 2014 NAR paper on DNA triplex in my file and will have a look at the DNA-triplex review article by Frank-Kamenetskii and Mirkin.

In addition to the Pauling triplex model (no. 56) and the model no. 31, the 3DNA 'fiber' command can also general several other triplex models. The full list is shown below:

30   32.7   3.160  poly d(C) : poly d(I) : poly d(C)
31   30.0   3.260  poly d(T) : poly d(A) : poly d(T)
32   32.7   3.040  poly (U) : poly (A) : poly(U) (11-fold)
33   30.0   3.040  poly (U) : poly (A) : poly(U) (12-fold)
34   30.0   3.290  poly (I) : poly (A) : poly(I)
42   32.7   3.040  poly(U) : poly d(A) : poly(U) [cf. #32]
56  105.0   3.40   Pauling's triplex model (generic sequence: A, C, G, T, U)

Run 'fiber -m' or 'fiber -l' for a full list of regular helical models from 3DNA. See also "Table 4. Selected features of regular DNA and RNA helical models included in 3DNA" of the 2003 3DNA NAR paper.

Best regards,

Xiang-Jun

Offline sima

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Re: design triple helix
« Reply #3 on: May 27, 2019, 10:49:29 am »
Hi Dr.xiangjun and mauricio esguerra :) :)
Thank you for your help and advice.
But I want to design triplex with my own sequence and turn it into a clamp switch. Like this article :

https://pubs.acs.org/doi/abs/10.1021/jacs.6b11470

Offline xiangjun

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Re: design triple helix
« Reply #4 on: May 27, 2019, 11:23:59 am »
It is certainly beyond the scope of 3DNA to design a DNA triplex with your sequence and "turn it into a clamp switch", even though the software may be useful for some specific steps in the whole process.

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.