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Questions and answers => General discussions (Q&As) => Topic started by: HZW on May 19, 2021, 02:31:23 am

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Title: The definition of glycoside conformation of guanine nucleotide in nucleic acid
Post by: HZW on May 19, 2021, 02:31:23 am

Recently, I have been struggling with a problem, that is, the definition of glycoside dihedral angle. I saw it the definition of glycosidic torsions( syn:(-90,90), anti:([-180,-90]&[90,180]) on the website(http://x3dna.org/). However, The book(Stephen Neidle - Principles of Nucleic Acid Structure-Elsevier_ Academic Press) has defined the glycosidic angles :
Anti: −120 > χ >180°
Syn: 0 < χ < 90°

So I wonder what the definition of glycoside angle is. Could you please give me some answers about glycoside angle? Thank you very much.

Title: Re: The definition of glycoside conformation of guanine nucleotide in nucleic acid
Post by: xiangjun on May 19, 2021, 09:24:28 am

Hi,

The definition of the glycosidic bond and the corresponding chi (χ) torsion angle which characterizes the relative base/sugar orientation is unambiguous: O4′-C1′-N1-C2 for pyrimidines (C, T and U), and O4′-C1′-N9-C4 for purines (A and G). However, there are different conventions in literature about anti and syn conformations. In addition to Neidle's definition you mentioned, please also see:

• http://jenalib.leibniz-fli.de/ImgLibDoc/nana/chi.gif
• Sokoloski et al. (2011): "Prevalence of syn nucleobases in the active sites of functional RNAs" (https://dx.doi.org/10.1261%2Frna.2759911)
• Dvorkin et al. (2018): "Encoding canonical DNA quadruplex structure" (https://advances.sciencemag.org/content/4/8/eaat3007)

As many other things, a simple concept in principle could be mess in practice. To really get the bottom of it, you could perform a survey of high-resolution, representative DNA/RNA structures in the PDB to see what you get.

HTH,

Xiang-Jun

Title: Re: The definition of glycoside conformation of guanine nucleotide in nucleic acid
Post by: HZW on May 20, 2021, 10:03:40 am

Thank you for your reply, Dr. Xiang-Jun Lu. I have known it. The system I studied is G4 DNA(MD simulation). Recently, I was thinking about how to analyze the dynamic changes of glycoside conformations between syn and anti in my article. So I need to understand the definition of glycoside conformations. However, there is another new question. That is how to define the glycosidic torsions in the DSSR or 3DNA. Could you please give me a answer? Thank you very much.
 Best regards,
 zw Han.

Title: Re: The definition of glycoside conformation of guanine nucleotide in nucleic acid
Post by: xiangjun on May 20, 2021, 10:26:25 am

Quote

However, there is another new question. That is how to define the glycosidic torsions in the DSSR or 3DNA. Could you please give me a answer?

See my previous response.

Xiang-Jun

Title: Re: The definition of glycoside conformation of guanine nucleotide in nucleic acid
Post by: HZW on May 21, 2021, 02:50:24 am

Okay, thank you vey much, Dr. Xiang-Jun Lu.

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.