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Questions and answers > w3DNA -- web interface to 3DNA

misshapen base ring

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Damien:
Dear all,

I have a long DNA 3D structure that contains 4 bases with misshapen rings. I detected them thanks to visual inspection.

How can I identify these structural deficiencies in a more automatic manner with Web 3DNA? From the list of numbers resulting from "Analysis", can I detect these misshapen bases?

Thanks for your help,

Damien

xiangjun:
Could you post (attach) an example structure to make your point concreate?

Xiang-Jun

Damien:
Hi Xiang-Jun,

Here is the 280 bp circular structure. Bases 275 and 276 of chain E, and 7 and 8 of chain F pose problem.

Thanks

Damien

xiangjun:
Hi Damien,

Thanks for providing a sample PDB file that illustrates the problem you are facing; it helped me to identify the issue.

As shown by the attached image for DT8 on chain F, the base is distorted beyond recognition. For example, C5--C6 distance is only 0.42 Å -- far too short for a covalent bond, whereas N1--C6 = 1.97 Å and C4--C5 = 2.16 Å are far too long. So 3DNA won't recognize it as a DNA base T at all. Same issues exist for the other three nucleotides.

It does not makes much sense to change 3DNA to accommodate such erroneous cases; rather, the mistakes should be fixed in any tool you used to generate this structure in the first place.

HTH,

Xiang-Jun
 

Damien:
Many thanks Xiang-Jun for this reply!

No, I did not suggest to change anything in 3DNA. I'm just looking for a way to avoid the visual inspection of the bases one by one.

I have the answer to my question in your reply: Web 3DNA does not recognize these distorted bases. This explains why the analysis in Web 3DNA results in 277 bp and not 280 (it seems however  that one "bad" base is recognized, DT 8 F).

So, 277 instead of 280 is the indication that something goes wrong. Then, a look at the RMSD in parentheses from the Nucleic acid structural parameter summary file is also a relevant parameter.

Am I right?

Thanks

Damien

ps: the goal of all this is to repair only the distorted base rings (as minimization on such a long structure can be very very long)

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.