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Author Topic: how is Z-DNA detected by 3DNA and DSSR  (Read 6558 times)

Offline auffinger

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how is Z-DNA detected by 3DNA and DSSR
« on: November 16, 2015, 07:46:35 am »
Hi Xiang-Jun,

We are wondering about how you assigne Z-DNA in your programs.
Will your programs find all Z-DNA fragments even in single strands ?
Furthermore, we wonder about the very specific orientation of the sugars
in Z-DNA CpG motifs. There, the two O4' atoms are pointing one towards the other
(see attached figure). Is there a specific parameter attached to this
type of sugar configuration in your program outputs ?
Thanks for your reply.

Best,

Pascal
pascal auffinger
ibmc-cnrs
15, rue rené descartes
67084 strasbourg cedex
france

web sites:
http://www-ibmc.u-strasbg.fr/arn/Westho ... er_pub.HTM
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Offline xiangjun

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Re: how is Z-DNA detected by 3DNA and DSSR
« Reply #1 on: November 16, 2015, 11:33:03 am »
Hi Pascal,

In 3DNA and DSSR, the classification of Z-DNA is on double-stranded helices, not single strands. Furthermore, in 3DNA (analyze), the classification is on the whole structure, whilst in DSSR, it is on each dinucleotide step.

Regarding the Z-DNA CpG motifs, I am glad that you paid attention to the O4'(C)...G capping interactions. From early on, I realized that it is not just the OP1/OP2 atoms of the phosphate groups that can make capping interactions, and that's why I implemented them all in DSSR. As documented in the manual, you need to specify the --more option to see the capping interactions.

HTH,

Xiang-Jun


Offline xiangjun

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Re: how is Z-DNA detected by 3DNA and DSSR
« Reply #2 on: November 17, 2015, 10:47:01 am »
Hi Pascal,

After further consideration, I now believe that it makes more sense to output the base-capping interactions in DSSR by default (i.e., without needing to specify the --more option). So as of DSSR v1.4.4-2015nov18 (to be released tomorrow), running DSSR on a Z-DNA, e.g. 2dcg, will have the following section:

Code: [Select]
# Running this command:
x3dna-dssr -i=2dcg.pdb

# Pertinent section in the output:
****************************************************************************
List of 6 atom-base capping interactions
    dv: vertical distance of the atom above the nucleotide base
    -----------------------------------------------------------
     type       atom                 nt             dv
   1 sugar      O4'@A.DC1            A.DG2          2.89
   2 sugar      O4'@A.DC3            A.DG4          2.90
   3 sugar      O4'@A.DC5            A.DG6          2.81
   4 sugar      O4'@B.DC7            B.DG8          2.87
   5 sugar      O4'@B.DC9            B.DG10         2.89
   6 sugar      O4'@B.DC11           B.DG12         2.78

Best regards,

Xiang-Jun
« Last Edit: November 17, 2015, 10:48:50 am by xiangjun »

 

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.