3DNA can recognise DNA with S atoms?

[ccaosioc]

In my DNA structure, the P-O bonds in two bases were replaced by P-S bonds, can 3DNA software still identify them?  I began to run 3DNA, it looks sticking.

[xiangjun]

Yes, 3DNA should be able to handle it, except for missing some of the backbone torsion angles.

Xiang-Jun

[ccaosioc]

How to do it? I'm trying to analyzing my structure in the web 3DNA interface.

[xiangjun]

You need to upload your structure to w3DNA, and start from there. Note that w3dna.rutgers.edu is supported by the Dr. Olson lab at Rutgers. You may or may not receive response for your questions posted on the Forum. On the other hand, running 3DNA from command-line should be straightforward, and I am available to promptly address any tecnetical questions.

HTH,

Xiang-Jun