3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: HZW on May 21, 2021, 05:19:10 am

Title: Stacking interactions in G-quadruplexes
Post by: HZW 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.
Title: Re: Stacking interactions in G-quadruplexes
Post by: xiangjun on May 21, 2021, 11:58:26 am: Hi zw Han,

Please start a new thread when the topic changes. For example, the topic on "the pi-pi stacking interactions between nucleotides in the G-quadruplex structure" is clearly distinct from "The definition of glycoside conformation of guanine nucleotide in nucleic acid (http://forum.x3dna.org/general-discussions/the-definition-of-glycoside-conformation-of-guanine-nucleotide-in-nucleic-acid/)". Thus, I've split the original thread into two.

3DNA does not have much to offer on G-quadruplexes, but DSSR does as highlighted in the video overview (http://docs.x3dna.org/dssr-overview/). So far, I've not published any DSSR paper on G-quadruplexes yet, but already offered some resources. User support, however, is only available to DSSR Pro (http://innovation.columbia.edu/technologies/CU20391) users.

Best regards,

Xiang-Jun
Title: Re: Stacking interactions in G-quadruplexes
Post by: HZW 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.
Title: Re: Stacking interactions in G-quadruplexes
Post by: HZW 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.