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Questions and answers => General discussions (Q&As) => Topic started by: sadsubway on May 25, 2011, 07:25:53 am

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Title: change one base pair in a double-strand DNA structure file
Post by: sadsubway on May 25, 2011, 07:25:53 am
Dear sir,

  Thanks for applying the software of 3DNA. Due to my research, here are some questions for using 3DNA:

  Suppose there is a DNA double-strand structure file in PDB format , is there any possible to change just one base-pair in this structure file by 3DNA?

  For example, there is a base pair A-T in a DNA structure file. Now I want to replace the A-T base pair by T-A, C-G, or G-C in the A-T position.

  Due to some other reasons, I don't want to make any difference in the orthogonal coordinates information of other atoms. All I have to do is just replacing one base-pair in this structure file. Could 3DNA handle this case?

  Thanks for your answering!

Sincerely,
Chien-Ho
5/25, 2011
Title: Re: change one base pair in a double-strand DNA structure fi
Post by: xiangjun on May 25, 2011, 09:43:25 pm
Hi Chien-Ho,

Thanks for using 3DNA, and for posting at this forum.

The question on mutating a DNA base (or base-pair) while keeping the backbone untouched has showed up a couple of time in this forum:
Follow the info there, and hopefully, your problem can be solved.


On the other hand, I have added a new component to 3DNA, named "mutate_bases" that does exactly this job. Moreover, it can be applied to RNA structures as well. The program is written in ASNI C, and is commandline-driven, as other major 3DNA components. It has been used internally for a while, and works as designed. If you or others would like to have a try, please post back here. Let me know what OS you use. I will consider to make "mutate_bases" partially available for 'testing' purpose before I include it in a later major 3DNA release (no date specified).

HTH,

Xiang-Jun
Title: Re: change one base pair in a double-strand DNA structure fi
Post by: sadsubway on May 26, 2011, 10:18:34 pm
Dear Dr. Xiang-Jun Lu,

  Thanks for your help!!

  Although the two topics in this forum could be well solutions of my problem, I still want to try the component "mutate_bases" for more experiments. Could you share the component with me please? The OS of my working server is Linux and my 3DNA is version 1.5.

  Thanks for your answer and sharing!

Sincerely,
Chien-Ho,
5/27, 2011
Title: Re: change one base pair in a double-strand DNA structure fi
Post by: xiangjun on May 27, 2011, 10:55:52 pm
Quote from: Chien-Ho
Although the two topics in this forum could be well solutions of my problem, I still want to try the component "mutate_bases" for more experiments. Could you share the component with me please? The OS of my working server is Linux and my 3DNA is version 1.5.
Please upgrade your 3DNA to v2.0, by following "How to download 3DNA v2.0?". The program "mutate_bases" needs 3DNA v2.0 to run. For outside use, I am planning to clean up the code and test it further. Stay tuned ... hopefully I will be able to get the job done by early June.

Xiang-Jun
Title: Re: change one base pair in a double-strand DNA structure fi
Post by: xiangjun on June 04, 2011, 11:16:50 pm
Hi all,

I have finally made the programs ready for distribution. There are actually two variants as detailed below for mutating bases in a nucleic acid structure while keeping the sugar-phosphate backbone untouched. Both the mutate_bp Perl script for base-pair mutations and the more generic/efficient/robust ANSI C program mutate_bases possess the neat and indeed unique feature, i.e., the mutated structures share the same base-pair/step parameters as the original structure.




As always, I welcome users feedback; any questions and comments should be posted in this forum.

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University