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1
General discussions (Q&As) / Re: How does 3DNA calculate rise
« Last post by xiangjun on May 21, 2019, 09:43:37 am »
Hi Pascal,

Have a look of $X3DNA/doc/tech-details.pdf, and/or read the source code.

HTH,

Xiang-Jun
2
General discussions (Q&As) / Re: design triple helix
« Last post by xiangjun 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
3
General discussions (Q&As) / How does 3DNA calculate rise
« Last post by Auffinger on May 21, 2019, 05:07:44 am »
Hi Xiang-Jun,

I just have a silly question but I am unable to
find a simple description of how you calculate the rise values
and, incidentally, all other values.

Thanks,

Pascal
4
General discussions (Q&As) / Re: design triple helix
« Last post by mauricio esguerra 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.

5
General discussions (Q&As) / design triple helix
« Last post by sima 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
6
MD simulations / Re: do_x3dna as a plugin for VMD and update in dnaMD
« Last post by Beñat Olave on April 30, 2019, 12:33:50 pm »
Dear Rajendra,

We are a group from Spain, our research is focused in creating different functional DNA nanostructures.

We have just started using computational chemistry and after doing some MD simulations I wanted to study the trajectories of a dsDNA using your tool, I think it can provide very useful information.

Unfortunately, I had issues while installing its plugin for VMD in windows 10 (x86). Even if it seems it is correctly installed:
"package require do_x3dna
1.0"
When I execute any command "do_x3dna WHATEVER", it closes immediately.

I have just solved the closure deleting all the "exit" words from the script but it still gives me this error:

=================== ERROR ======================
 $X3DNA environment variable is not available.
 See below for usage.                           
================================================

I don't understand why, because I have already installed X3DNA correctly, I have used it for other analysis of a single step.

Could you help me?

Best regards,
Beñat Olave
7
General discussions (Q&As) / Re: Tools for connecting two DNAs into one
« Last post by xiangjun on April 21, 2019, 06:09:46 pm »
Have a try, and report back any issues you experience. As a general rule, please remember to be specific with your questions.

Best regards,

Xiang-Jun
8
General discussions (Q&As) / Re: Tools for connecting two DNAs into one
« Last post by xclin on April 21, 2019, 05:57:14 pm »
Hi,

Thanks for your kind response.

What I was trying to do is to connect two separate DNAs, such as two polyA DNAs into one longer DNA. I just realized that the instruction on extending the length of one DNA as illustrated here
http://forum.x3dna.org/users-contributions/build-dna-bulges-and-extend-dna-duplex-at-both-terminals-via-3dna/
can be useful for my purpose.

Best,
Xingcheng
9
General discussions (Q&As) / Re: Tools for connecting two DNAs into one
« Last post by xiangjun on April 21, 2019, 05:38:37 pm »
Hi Xingcheng,

Could you please provide a concrete example to illustrate what you mean by connecting two DNA molecules into one?

Thanks,

Xiang-Jun
10
General discussions (Q&As) / Tools for connecting two DNAs into one
« Last post by xclin on April 21, 2019, 04:11:55 pm »
Hi,

I am a new user to 3DNA. I have two separate DNAs and would like to connect them into one. I am wondering if 3DNA has tools for this purpose?

Thanks,
Xingcheng
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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.