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Hi everyone:
RNA can adpot two sugar-pucker comformations: C3'-endo and C2'-endo. The latter is lower popolation weight. Have someone noticed any reference about statistical analysis of the torsion angle (i.e alpha-zeta) for C2'-endo RNA. Thank you in advance.
Best regards
zhonghe
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Hi Zhonghe,
The following paper may be of (some) interest to you: Sokoloski, Joshua E., et al. "Prevalence of syn nucleobases in the active sites of functional RNAs." RNA 17.10 (2011): 1775-1787.
Other relevant papers? Please chime in.
Best regards,
Xiang-Jun
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Hi Xiang-Jun,
Thanks for your prompt reply. I also found some relevant works (JANE S. RICHARDSON) about torsion angle in C2'-endo RNA, including: "RNA backbone is rotameric" , “RNA backbone: Consensus all-angle conformers and modular string nomenclature", and "Computational methods for RNA structure validation and improvement". Thanks again for your suggestion.
Best regards,
Zhonghe
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Hi Zhonghe,
Thanks for your follow-up. Yes, the Richardson publications you listed are highly relevant. Did you know that DSSR also calculate suiteness? Using 1msy as an example:
x3dna-dssr -i=1msy.pdb
more dssr-torsions.txt
# A2654 and G2655 are in C2'-endo conformation
Using DSSR, it would be straightforward to survey RNA structures (of your choice) and find all nucleotides with C2'-endo sugars. The results could be easily parsed with the --json option. Moreover, DSSR provides context information.
Best regards,
Xiang-Jun
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Hi Xiang-Jun,
Sorry for the delay in replying. It is convenient to use DSSR to charcterize the structural feature of C2'-endo RNA. Thanks for your suggestion.
Best regards
Zhonghe
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.