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Messages - HZW

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General discussions (Q&As) / Re: How to setup 3DNA
« on: July 08, 2021, 08:55:00 am »
Okay, Thank you very much.

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General discussions (Q&As) / Re: How to setup 3DNA
« on: July 08, 2021, 02:52:10 am »
Dear xiangjun,
 I'm glad to send message to you. I have installed the 3DNA v2.4.4, but I can't use it. Could you please send me the manual of 3DNA. Thank you very much.


Best Regards
Zw Han

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RNA structures (DSSR) / Re: Stacking interactions in G-quadruplexes
« on: May 22, 2021, 09:21:13 am »
 :) I have already analyzed the G4 DNA by web-DSSR. So I will cite it in my article(I'm writing), which is the most basic academic morality.

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RNA structures (DSSR) / Re: Stacking interactions in G-quadruplexes
« on: May 22, 2021, 09:12:43 am »
Thanks for your reply, Dr. Xiang-Jun Lu. I just use Web-DSSR to analyze the studied G4 DNA by uploading the PDB structures.

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RNA structures (DSSR) / Stacking interactions in G-quadruplexes
« on: May 21, 2021, 05:19:10 am »
Dear Dr. Xiang-Jun Lu,
  I would like to ask you how to judge the pi-pi stacking interactions between nucleotides in the G-quadruplex structure. What is the distance between two aromatic bases to judge the strength of stack interactions? For example, the distance between them is considered to have strong stacking interaction in the range of nanometers, and it is considered to be weak stacking force in other ranges. Could you please give me some advice or help? Thank you very much. Looking forward to your reply.
 Best regards,
 zw Han.
 

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

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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.

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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.

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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.