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Calculate the volume of DNA


Dear Dr. Xiang-Jun,

I am working on nanopore technology for detecting a point mutation.  In my strategy, a mutated DNA hybridizes to a probe DNA, and then the dsDNA is captured in the nanopore, and pass through pore with unzipping strands electrophoretically. I observed a difference in the unzipping duration, which caused by different DNA hybridization energy between WT and mutated DNA, as information to identify point mutation of dsDNA. At the same time, the blocking rates are changed. I wonder why that blocking rates changed. Therefore, I want to calculate the volume of DNA for a deep understanding of the current signal.

May you please guide me how can I calculate the volume of DNA?
Thank you in advance!

Sincerely yours,
Ping Liu
Kawano Laboratory
Department of Food and Energy Systems Science
Tokyo University of Agriculture and Technology

Hi Ping,

3DNA/DSSR does not calculate the volume of a given DNA/RNA structure. It is unlikely that this feature would be implemented in the 3DNA suite either.

There are already tools available for such a purpose. Here are two examples for your reference:

* VOLUME (CCP4: Supported Program)
* 3v website (Volume Calculation and Extraction Procedures)


Dear Dr. Xiang-Jun,

Thank you for your quick response and helpful information.
I will try them. :)

Best regards,


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

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