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Author Topic: Noncanonical base pair standards  (Read 578 times)

Offline m.bruist

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Noncanonical base pair standards
« on: May 26, 2019, 12:10:55 pm »
I am characterizing variations in noncanonical RNA base pairs created by molecular dynamics. I wish to have a standard against which to compare my observed pair structures. Is there a table of local base pair parameters and/or simple base pair parameters for the pairs in the twelve families of Leontis-Westhof base pairs? For example, has anyone run each of the exemplars found in the Nucleic Acid Data Bank or Bowling Green catalog (http://ndbserver.rutgers.edu/ndbmodule/services/BPCatalog/bpCatalog.html) through DSSR?

Mike Bruist

Offline xiangjun

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Re: Noncanonical base pair standards
« Reply #1 on: May 26, 2019, 12:26:33 pm »
Hi Mike,

Thanks for posting on the 3DNA Forum. I sort of understand of your point, but I do not think there exists a table of "local base pair parameters and/or simple base pair parameters for the pairs in the twelve families of Leontis-Westhof base pairs". The LW notation of 12 base-pair classes is intuitive in concept, qualitative in nature, and incomplete in practice.

For example, have a close look at the "1MSY FR3D basepairs pairwise interaction annotations" compiled by the Leontis-Zirbel group. Can you figure out what ncWW and ntSH in the following two entries mean?

Code: [Select]
1MSY|1|A|U|2647             ncWW             1MSY|1|A|G|2673
1MSY|1|A|U|2653             ntSH             1MSY|1|A|C|2667

As another example, the Watson-Crick (WC) and the G–U wobble pairs all belong to the cWW class. Nevertheless, WC and wobble pairs are obviously different. Moreover, and the G–U and U–G wobble pairs are also dissimilar above the base-pair level. See the recent review article "The multiple flavors of GoU pairs in RNA" by  Westhof et al. in which the LW notation is not mentioned at all. Also, there are more variants of G∙U pairs than those wobble-like  "GoU pairs" mentioned in the Westhof review.

For a comprehensive, and quantitative classification of base pairs in DNA or RNA, please see our recent article "Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G∙ A Pairs". See also read the section "3.2.2 Base pairs" in the DSSR User Manual.

HTH,

Xiang-Jun
« Last Edit: May 28, 2019, 10:53:31 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline mauricio esguerra

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Re: Noncanonical base pair standards
« Reply #2 on: August 01, 2019, 11:13:54 am »
Hi Mike,

There was a webserver at: http://bps.rutgers.edu, which was based on a database of collected information for base-pair parameters for the PDB as of 2008. Unfortunately that webserver was not kept maintained by the Chemistry Department at Rutgers University where it used to be hosted.

One can see just the landing page of what it was, at waybackmachine:

https://web.archive.org/web/20150827153608/http://bps.rutgers.edu/bps

The corresponding reference to the paper which accompanied the database-webserver is:

BPS: a database of RNA base-pair structures
Yurong Xin, Wilma K. Olson
Nucleic Acids Research, Volume 37, Issue suppl_1, 1 January 2009, Pages D83–D88, https://doi.org/10.1093/nar/gkn676

It had precisely the type of information you're interested in.

Best,

Mauricio Esguerra Neira




Offline xiangjun

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Re: Noncanonical base pair standards
« Reply #3 on: August 01, 2019, 11:30:40 am »
Hi Mauricio,

Thanks for chiming in. With DSSR, it won't be difficult to compile a list of all types of base-pairs (bp) in the PDB (or any user-selected dataset) with corresponding bp parameters. It is important to note, however, that no one-to-one correspondence exists between the 12 LW qualitative bp classes and the far more abundant types in reality. The outdated and dysfunctional BPS database, compiled based on 3DNA results, does not contain LW classification information.

Best regards,

Xiang-Jun
« Last Edit: August 01, 2019, 03:16:28 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.