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Author Topic: Convert RNA hairpin into DNA  (Read 644 times)

Offline dmiasl

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Convert RNA hairpin into DNA
« on: March 02, 2020, 08:17:53 am »
Hello,
I am currently working on the modelisation of protein interaction with DNA hairpin. Such structures are pretty rare on the PDB, so I'm basing my study on RNA structures. As the title imply, I'm trying to convert RNA hairpin into DNA hairpin. Is there a way to do it in 3DNA ?
Thank you in advance,
DML.

Offline xiangjun

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Re: Convert RNA hairpin into DNA
« Reply #1 on: March 02, 2020, 11:27:56 am »
Hi DML,

Thanks for posting your question on the 3DNA Forum. I understand what you're asking for conceptually. Could you provide a concrete example to show unambiguously the requirements? In writing a useable code, every detail needs to be taken into consideration. 3DNA/DSSR may already have some basic components that could be tailored to your purpose.

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline dmiasl

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Re: Convert RNA hairpin into DNA
« Reply #2 on: March 03, 2020, 02:08:05 am »
Hello, and thank you for taking the time to answer.
The idea is for example to convert the RNA hairpin in 1F27 (extracted and atttached with this post), into DNA, thus converting Uinto T (feasible with mutate), but also altering the backbone's ribose. This can be done "manually", but in a not so clean way, imo.
Thank you very much,
Dominique MIAS-LUCQUIN.

Offline xiangjun

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Re: Convert RNA hairpin into DNA
« Reply #3 on: March 03, 2020, 11:32:29 am »
Quote
The idea is for example to convert the RNA hairpin in 1F27 (extracted and atttached with this post), into DNA, thus converting Uinto T (feasible with mutate), but also altering the backbone's ribose.

As you noted above, the U-->T conversion can be achieved via mutate_bases. This part is clear (to me). However, I still cannot fully understand what you mean by "also altering the backbone's ribose". Idealized DNA sugars can have C2'-endo (B-DNA) or C3'-endo (A-DNA) conformations. In real PDB structures, there are many intermediate sugar puckering as well.

Quote
This can be done "manually", but in a not so clean way, imo.

There is no magic in writing a program to "automate" this process: it is all based on a thorough understanding of the mechanics. It is essential that you provide your "manual" result, in whatever no so clean way. I may then be able to help you (and others in a similar situation) by implementing such a feature in 3DNA.

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline dmiasl

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Re: Convert RNA hairpin into DNA
« Reply #4 on: March 04, 2020, 01:33:13 am »
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However, I still cannot fully understand what you mean by "also altering the backbone's ribose"
By that, I mean converting the ribose into deoxyribose (removing the O2'), or the deoxyribose into ribose (adding the O2').

Offline xiangjun

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Re: Convert RNA hairpin into DNA
« Reply #5 on: March 04, 2020, 10:11:58 am »
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converting the ribose into deoxyribose (removing the O2')

That should be an easy task, right? Together with the U-->T base mutations, the answer to "Convert RNA hairpin into DNA" should be "clean", even if performed manually.


Quote
Could you provide a concrete example to show unambiguously the requirements?

Quote
It is essential that you provide your "manual" result, in whatever no so clean way.

Often times, I wonder how difficult it is to provide a minimal reproducible example that can unambiguously illustrate the question asked.

Xiang-Jun


« Last Edit: March 04, 2020, 10:17:43 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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* DSSR 2.0 has superseded the 3DNA v2.4 suite

Offline dmiasl

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Re: Convert RNA hairpin into DNA
« Reply #6 on: March 04, 2020, 10:35:00 am »
Thank you very much for your help,
Regards,
DML.

 

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.