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Author Topic: Z-steps  (Read 36 times)

Offline Auffinger

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Z-steps
« on: September 28, 2017, 12:04:38 pm »
Hi Xiang-Jun,

I am not sure since I havent' checked 3DNA pages for a while
if you implemented a feature to detect Z-steps in RNA and DNA systems
as defined in:
(if not, I think it would be nice to have and probably pretty easy to do for you).

Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops.
D'Ascenzo L, Leonarski F, Vicens Q, Auffinger P.
RNA. 2017 Mar;23(3):259-269. doi: 10.1261/rna.059097.116. Epub 2016 Dec 20.

and

'Z-DNA like' fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response.
D'Ascenzo L, Leonarski F, Vicens Q, Auffinger P.
Nucleic Acids Res. 2016 Jul 8;44(12):5944-56. doi: 10.1093/nar/gkw388. Epub 2016 May 5.

Thanks for your reply,

All the best,

Pascal
pascal auffinger
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Offline xiangjun

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Re: Z-steps
« Reply #1 on: September 28, 2017, 02:08:06 pm »
Hi Pascal,

I read both of your papers mentioned above, and like the thoroughness of your analyses. 3DNA/DSSR certainly contains features for characterizating Z-steps in DNA/RNA, and I could consolidate them into a more user-friendly form.

For the benefit of other users, and to avoid any potential technical caveats, please provide concrete examples with defining features of Z-steps, presumably based on your publications.

Best regards,

Xiang-Jun
« Last Edit: September 29, 2017, 12:21:46 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.