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Questions and answers => RNA structures (DSSR) => Topic started by: jmmmggg on July 06, 2023, 03:04:18 pm

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Title: Classification of helix versus loops
Post by: jmmmggg on July 06, 2023, 03:04:18 pm

Hello,
I am an undergraduate student interested in studying tetraloops.
My partner created a file using DSSR containing all hairpin loops, and now we are trying to determine which loops qualify as tetraloops.
We have some 6-nucleotide hairpin loops where it appears as if the first and last nucleotides are interacting as if they were a tetraloop, but we could not tell for sure. Thus, we are wondering what DSSR constitutes as a base pair, as well as how it defines helices versus hairpin loops.

Thank you!
-Julia

Title: Re: Classification of helix versus loops
Post by: xiangjun on July 06, 2023, 08:20:52 pm

Hi Julia,

Please read the 2015 NAR paper "DSSR, an integrated software tool for dissecting the spatial structure of RNA" (https://nar.oxfordjournals.org/content/43/21/e142.full) and the thread "Reproducing results published in the DSSR-NAR paper" (http://forum.x3dna.org/dssr-nar-paper/reproducing-results-published-in-the-dssr-nar-paper/).

When asking questions, please be specific so other can understand exactly what you mean. I am glad the know that DSSR is being used by undergraduate students. Your instructor may provide you better help on the topics.

Also read the thread "No more grant funding for 3DNA/DSSR" (http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/).

Best regards,

Xiang-Jun

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.