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Questions and answers > RNA structures (DSSR)
How to look for abasic site using DSSR
lvelve0901:
Hi Xiangjun,
Long time no contact. I hope you had a good time recently.
I have a question about DSSR. Can DSSR detect abasic site?
For example, in 1l2c.pdb and 1l2d.pdb, there is a abasic site HPD18DG7. I thought this could be written in internal loop; however, the internal loop only detect a lower base pair open (DA23DT2).
Best,
Honglue
xiangjun:
Hi Honglue,
As shown in Fig.1 (see below) of the DSSR paper, "Nucleotides are recognized using standard atom names and base planarity." Since abasic sites (e.g., HPD18 in chain C of PDB id 1l2c) do not have proper base atoms, they are not recognized as nucleotides by DSSR to begin with. Naturally, they do not appear in later analysis results of DSSR output. This is just the way DSSR works and you may take it as a deficiency. Please let me know if you have a better way to handle such cases.
Hope this clarifies your confusions.
Xiang-Jun
lvelve0901:
Does that mean DSSR cannot detect abasic site, since there is no base atom?
Thanks.
Best,
Honglue
xiangjun:
Hi Honglue,
I've added an option --abasic to DSSR to take abasic sites as nucleotides, as long as main-chain backbone atoms are preserved: P, O5', C5', C4', C3', and O3'. Quick tests on 1l2c and 1l2d show that this new DSSR feature is working as designed (e.g., C.HPD18 is listed in an internal loop). Understandably, the abasic nucleotides won't be involved in base pairing and stacking interactions.
The DSSR on the download page (still labeled v1.6.8-2017mar28) has been updated. Have a try and report back if it solves your problem.
Xiang-Jun
kazi956:
--- Quote from: xiangjun on May 01, 2017, 11:35:39 pm ---Hi Honglue,
I've added an option --abasic to DSSR to take abasic sites as nucleotides, as long as main-chain backbone atoms are preserved: P, O5', C5', C4', C3', and O3'. Quick tests on 1l2c and 1l2d show that this new DSSR feature is working as designed (e.g., C.HPD18 is listed in an internal loop). Understandably, the abasic nucleotides won't be involved in base pairing and stacking interactions.
The DSSR on the download page (still labeled v1.6.8-2017mar28) has been updated. Have a try and report back if it solves your problem.
Xiang-Jun
--- End quote ---
Hi, I am trying to use --abasic command (./x3dna-dssr --abasic -i=test.pdb) on version 1.9.8(2019Oct16), but it's not recognizing the abasic site even if I have P, O5', C5', C4', and C3' atoms. Wondering if --abasic works properly only on the DSSR v1.7.2-2017nov20 release; if so, how can I download the older version? Thank you!
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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.
