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Author Topic: create RNA sequence syn nucleosides  (Read 17841 times)

Offline amirtaghavi

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create RNA sequence syn nucleosides
« on: August 09, 2019, 07:00:14 pm »
Hello,
 
I have a question and I was wondering if you could help.
I want to make a small RNA with the sequence 5' UCAA*GA with the complementary seq. as 3' AGUC*CA. I want to make all four possible combinations of this sequence with the starred  nucleosides (A* and C*) being in the syn-syn, syn-anti, anti-syn & anti-anti (which is the standard form with fiber).
Is there any way that I can create these systems with x3dna.

Thanks in forward.

Best regards,
Amir
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Offline xiangjun

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Re: create RNA sequence syn nucleosides
« Reply #1 on: August 09, 2019, 08:53:09 pm »
Unfortunately, the answer is no within 3DNA. Nevertheless, you may use the 3DNA fiber program to generate a structure in the anti-anti form as a starting point. There exist interactive tools (e.g., PyMOL) to rotate the desired base by its glycosidic bond into the syn form.

Xiang-Jun
« Last Edit: August 20, 2019, 12:15:44 pm by xiangjun »
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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