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Author Topic: Cannot understand what a base pair type means from web-3DNA output  (Read 7236 times)

Offline sowmya

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Dear Dr. Xiang,

I was analyzing the base pair type distribution among a dataset of RNAs that I have collected for my study using the pair.csv file for those PDB IDs obtained using web-3DNA. When I compiled the list of unique base pair types I noticed certain base pairs with a P, which are: P+A, A-P, P-G, P+G, C-P and P-A.
I got information on the other base pair types from the x3DNA website: http://x3dna.org/highlights/named-base-pairs, but I'm unable to find information on the above mentioned base pairs. Can you share some resources to understand what these named base pairs mean and how they are identified (in terms of the structural orientation of the bases and other parameters)?

Thank you
- Sowmya

Offline xiangjun

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Re: Cannot understand what a base pair type means from web-3DNA output
« Reply #1 on: December 25, 2022, 11:33:44 am »
See the paper "DSSR: an integrated software tool for dissecting the spatial structure of RNA" (https://doi.org/10.1093/nar/gkv716).

Quote
Identification of nucleotides

        Note that pseudouridine (PSU) is shortened to ‘P’, due to its special C1′–C5 glycosidic link- age (Figure 2).

The M–N versus M+N relative base orientations

 

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.