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

[Sunera]

Hi Dr. Jun,

Sorry for the late reply. Yes, I definitely think the idea in the FAQ is relevant. But I do not have a PDB structure with the m3C modification, I was hoping that we would be able to generate the PDB (and PSF) using 3DNA/DSSR by specifying the residues.

As a side question, what would be a good force field that can allow us to perform a phase separation simulation with the methylated ssDNA and IDR sequence?

[xiangjun]

Welcome back.

But I do not have a PDB structure with the m3C modification, I was hoping that we would be able to generate the PDB (and PSF) using 3DNA/DSSR by specifying the residues.

Are you expecting 3DNA/DSSR to "generate the PDB" by specifying the residues, including unknown ones?  3DNA/DSSR can build DNA/RNA structures with standard bases (A,C,G,T,U), or modified ones with *known* building block as illustrated in 5-methylcytosine in the FAQ. It does not generate structures for ligands like m3C. It is up to the user to provide such building blocks for 3DNA/DSSR to proceed. CCP4 and Phenix may have utilities to generate new ligands.

By the way, what does PSF stand for?

As a side question, what would be a good force field that can allow us to perform a phase separation simulation with the methylated ssDNA and IDR sequence?

Sorry, I'm not familiar with this field, and I cannot offer any valuable suggestions. Overall, this question is out of the scope of the Forum.

Best regards,

Xiang-Jun