changing some of the RNA sequence of an chain to DNA

[Sruthi0412]

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

[xiangjun]

Please be specific: provide an example so that others can reproduce.

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Xiang-Jun

[Sruthi0412]

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.

[xiangjun]

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