Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: DSSR output - Base pair characteristics  (Read 5609 times)

Offline jctoledo

  • with-posts
  • *
  • Posts: 2
    • View Profile
DSSR output - Base pair characteristics
« on: March 26, 2013, 11:19:15 am »
Hi all,

Loving DSSR for analyzing RNA structures! I was wondering what are all the qualitative parameters about base pairs that are captured by this tool are. For example I ran DSSR on PDBID 3OXO the and following (abridged) sample base pair details are given:

Code: [Select]
3 A.C3             A.G86            [C-G] WC           19-XIX    cWW cW-W
...
8 A.G7             B.A64            [G+A] Linker       00-n/a    tSS tm+m
...
9 A.G8             A.A81            [G-A]              00-n/a    tSH tm-M
...
22 A.G32            A.A71            [G+A]              00-n/a    cH. cM+.


Where for the case of base pair #3, I have recognized the following annotations:
- "3": Base pair number
- "A.C3": Chain 1, residue identifier 1, residue position 1
- "A.G86": Chain 2, residue identifier 2, residue position 2
- "[C-G] WC": A descriptive label for this base pair
- "19-XIX": The Saenger class for this base pair (00-n/a when not available)
- "cWW": The Leontis-Westhof nomenclature for interacting edges (cis Watson-Crick/Watson-Crick -> Class #1)

However what does the last column refer to? For example:
Base pair #3: "cW-W"
Base pair #8: "tm+m"
Base pair #9: "tm-M"
Base pair #22: "cM+."

Also, what does the "." signify when found in either of the last two columns of this output?

Regards,
Jose

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1509
    • View Profile
    • 3DNA homepage
Re: DSSR output - Base pair characteristics
« Reply #1 on: March 26, 2013, 01:33:06 pm »
Hi Jose,

Thanks for trying out DSSR and for your kind comment about the program. User feedback like yours is a great incentive for me to make DSSR a better tool to serve the RNA structure community.

To start with, I have tried hard to made DSSR easy to set up and play with. Based on my reading of literature in structural biology, I've made the DSSR output more intuitive (compared to previous 3DNA programs). For example, A.U2647 means U2647 on chain A. So far, I have not heard of any installation problem yet, and I am glad that you can make sense of most items in the DSSR output.

Your question regarding the meaning of the last column is well expected. It represents my own notation to specify a base pair, as elaborated below:
  • Each base has three edges: W for the Watson-Crick edge, M for the major groove edge, and m for the minor groove edge. M corresponds to the Hoogsteen (or C-H) edge of the Leontis-Westhof nomenclature, and for the majority of cases (where the glycosidic bond is anti) m agrees with the 'sugar' edge. Note that in DSSR, the edges are defined purely on the geometry of the base plane as would be in a Watson-Crick base pair, and it is not related to sugar. See my post "The chi (χ) torsion angle characterizes base/sugar relative orientation". The DSSR definition applies to RNA as well as DNA, with either syn or anti glycosidic bond.
  • In some boundary cases, the two bases in a pair may not be directly interacting edge-to-edge, where it is not straightforward to clearly designate which edge is involved. This is where the '.' comes in.
  • The DSSR notation contains 4 characters of the pattern: [ct][WMm.][+-][WMm.]. The third position is either '+' or '-', and it designates the relative orientation of the two bases (flipped or normal) as has been consistently used in 3DNA. For example, see the difference in A+U Hoogsteen pair vs. A-U Watson-Crick pair.
  • The first position is either 'c' for cis and 't' for trans of the two glycosidic bonds. It is defined by the 'virtual' torsion angle tor(N1-C1'-C1'-N9) reported in the DSSR output.

HTH,

Xiang-Jun

PS. Does "PDBID 3OXO" correspond to an RNA structure?
« Last Edit: March 26, 2013, 02:34:23 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

* Click "NOTIFY" to receive email notifications
* Original Poster, please provide a summary

Offline jctoledo

  • with-posts
  • *
  • Posts: 2
    • View Profile
Re: DSSR output - Base pair characteristics
« Reply #2 on: March 26, 2013, 01:56:53 pm »
Thank you for the prompt response. This cleared things up!

FYI, I had a typo in my original post. The basepairs were extracted from PDBID: 3OX0 [http://www.rcsb.org/pdb/explore.do?structureId=3OX0] (got my O's and 0's confused)

Jose

 

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.