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Questions and answers => RNA structures (DSSR) => Topic started by: Sruthi0412 on July 19, 2021, 07:29:24 am

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Title: Removing some nucleotides and fixing/reducing the loop in my RNA structure
Post by: Sruthi0412 on July 19, 2021, 07:29:24 am
I have an RNA sequence as below:
5'-GUUUUAGAGCUAUGCUGAAAAGCAUAGCUCUAAAAC-3'

In this, the bold region forms a loop. I want to remove the underlined base pairs( adjacent to the loop) and connect the loop to the rest of the system. In this way my system would be shorter. Is it possible to do such removal and fixing using 3DNA? Kindly guide regarding the same.
After removal my system should look like this

5'-GUUUUAGAGCUAUGAAAAUAGCUCUAAAAC-3'
Title: Re: Removing some nucleotides and fixing/reducing the loop in my RNA structure
Post by: xiangjun on July 19, 2021, 08:08:17 am
In principle, I understand what you're trying to accomplish. However, I am unable to provide any concrete answers due to a lack of information.
Title: Re: Removing some nucleotides and fixing/reducing the loop in my RNA structure
Post by: Sruthi0412 on July 20, 2021, 06:21:06 am
This is an already existing crystal structure sequence upon which we are going to do some molecular dynamics simulations. The given RNA structure interacts with a protein as well. We are trying to establish the effect in protein dynamics and conformations upon shortening our RNA structure. Experimentally the underlines sequences have been removed and studies have been performed. The computational modelling also should be done in a similar methodology. Therefore I want to know if such removal of basepairs and adjusting the loops is possible, taking an existing crystal structure pdb.
5'-GUUUUAGAGCUAUGCUGAAAAGCAUAGCUCUAAAAC-3'

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.