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Author Topic: building circular DNA  (Read 1319 times)

Offline x3dna_test

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building circular DNA
« on: July 15, 2019, 06:11:48 pm »
Hi Xiangjun and All,

I am just wondering is it possible to build a circular DNA? I have seen one can analyse circular DNA with x3DNA but not sure how to build them and what parameters to be used.
Thanks.

Offline xiangjun

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Re: building circular DNA
« Reply #1 on: July 15, 2019, 09:36:33 pm »
Hi,

I'm not sure I fully understand your question in a practical sense. Please be specific.

The 3DNA rebuild can generate any structure (at the base-pair level) with a set of prescribed base-pair and step parameters. It's really up to the user to build what they want.

Best regards,

Xiang-Jun
 
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline x3dna_test

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Re: building circular DNA
« Reply #2 on: July 16, 2019, 01:28:56 am »
Hi Xiangjun,

I am just trying to create a DNA ring system and then do some simulations to study some properties.
Am not sure what parameters will be good as I do not have any experimental data.

Offline xiangjun

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Re: building circular DNA
« Reply #3 on: July 16, 2019, 12:06:01 pm »
I understood that you have been "trying to create a DNA ring system". 3DNA does not have a direct solution to this problem, neither will it likely in the general sense.

You may give NAB a try. If you find a way, please post back so other viewers may benefit.

Best regards,

Xiang-Jun
 
« Last Edit: July 16, 2019, 12:52:41 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.