Generation of ssDNA PDB with m3C modification using 3DNA webserver

[Sunera]

Is it possible to generate a PDB of a single stranded DNA containing a 3-methylated cytosine using the 3DNA Web Server? Could you please advise on the best way to generate an all-atom PDB containing this modification if it cannot be generated using 3DNA?

[xiangjun]

Hi,

Thanks for your interesting in using 3DNA and for posting your questions on the Forum.

The http://web.x3dna.org has features to build regular fiber models or customized structures (including single-stranded structure as detailed in the supplemental PDF). However, the web-server does not allow you to generate  single-stranded DNA containing a 3-methylated cytosine. The web server simply does not have 'knowledge' of what a 3-methylated cytosine is. I know of no other tools that can do this automatically.

However, 3DNA/DSSR has features that would allow for such modeling from the command line. I need more details of exactly what you want to achieve to be of further help.

See the FAQ: How can I mutate cytosine to 5-methylcytosine?

Best regards,

Xiang-Jun

[Sunera]

Hello Dr. Jun,

Thank you so much for your reply. So, my intention is to conduct an all-atom intrinsically disordered protein - ssDNA phase separation simulation using the OpenMM MD suite. I was wondering how to generate the PDB for a custom DNA sequence that contains the (m3C) modification on one of the bases.

Best,
Sunera

[xiangjun]

Hi Sunera,

Thanks for your follow up. Is the idea in FAQ "How can I mutate cytosine to 5-methylcytosine?" relevant? Do you have a PDB structure with m3C modification?

Best regards,

Xiang-Jun