3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: auffinger on November 16, 2015, 07:46:35 am

Title: how is Z-DNA detected by 3DNA and DSSR
Post by: auffinger 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
Title: Re: how is Z-DNA detected by 3DNA and DSSR
Post by: xiangjun 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
Title: Re: how is Z-DNA detected by 3DNA and DSSR
Post by: xiangjun 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 (http://www.rcsb.org/pdb/explore/explore.do?structureId=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