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Author Topic: changing some of the RNA sequence of an chain to DNA  (Read 88 times)

Offline Sruthi0412

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changing some of the RNA sequence of an chain to DNA
« on: September 27, 2020, 03:28:47 pm »
I am beginner in x3dna and wanted to know how to change a few of the RNA sequences in my RNA into DNA sequences. There are 20 nt in my chain and I want the bases 4-8 to be DNA. Could you give some guidelines regarding changing this

Offline xiangjun

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Re: changing some of the RNA sequence of an chain to DNA
« Reply #1 on: September 27, 2020, 05:18:15 pm »
Please be specific: provide an example so that others can reproduce.

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Dr. Xiang-Jun Lu [律祥俊]
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Offline Sruthi0412

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Re: changing some of the RNA sequence of an chain to DNA
« Reply #2 on: September 27, 2020, 06:04:55 pm »
Sorry for not being clear in my first query.
 I have a single strand of RNA with the sequence
5'- GCGCAUAAAGAUGAGACGCG -3' .
I want to change the CAUA region to DNA bases. Basically, I want the sequence to be changed as DC DA DT DA (Nucleotides 4-8) , while all the other nucleotides are the same RNA sequences. I wanted to know if it is possible to do so in x3dna. I want to run some MD simulations on this sequences to observe how well the DNA substitutions can stay within an RNA strand. I am attaching the RNA pdb here.

Offline xiangjun

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Re: changing some of the RNA sequence of an chain to DNA
« Reply #3 on: September 28, 2020, 11:10:37 am »
Hi,

Thanks for your followup -- it helps clarify previous ambiguities.

In 3DNA, you could perform base mutations without changing backbone geometry using the mutate_bases program. As an example, to mutate U6 to DT, you can do the following:

Code: [Select]
mutate_bases 'chain=A snum=6 m=DT' rna2.pdb mutated-U6DT.pdb
You may mutate all four bases simultaneously. Check mutate_bases -h. You then need to remove O2' atoms manually.

DSSR 2.0 has a much powerful modeling module that supersedes mutate_bases, with many more features.

HTH,

Xiang-Jun

« Last Edit: September 28, 2020, 11:14:35 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

 

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.