how is Z-DNA detected by 3DNA and DSSR

[auffinger]

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

[xiangjun]

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

[xiangjun]

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