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Questions and answers => General discussions (Q&As) => Topic started by: kailsen on March 17, 2016, 01:07:12 pm

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Title: rebuilding using Modified bases
Post by: kailsen on March 17, 2016, 01:07:12 pm

Hi ,

I'm  using rebuild option for regenerating my sequence.
I wanted to change the nucleotide (base+sugar+backbone) coordinates used to a modified nucleotide.
So as to regenerate a new duplex. Which library file used by rebuild module?

Best,
Kailsen

Title: Re: rebuilding using Modified bases
Post by: xiangjun on March 17, 2016, 01:22:49 pm

Hi Kailsen,

It is possible to generate a duplex with modified nucleotides, using a combination of 3DNA programs (including std_base, rebuild, fiber, mutate_bases etc). For example, you could run rebuild with the primary sequence, and then mutate_bases to get the desired modifications. Please provide a concrete example so we can discuss details.

Xiang-Jun 

Title: Re: rebuilding using Modified bases
Post by: kailsen on March 17, 2016, 01:34:52 pm

Hi 
Thanks for the quick reply.
One way to do will be as u suggested.
But I also want to modify backbone atoms.
I got the answer from your earlier post.

http://forum.x3dna.org/faqs/how-do-i-build-nucleic-acid-structures-with-sugar-phosphate-backbone/msg784/#msg784
Thanks once again,

Best,
kailsen

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University