Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing
· Video Overview· RNA Covers
-
Hi,
On analyzing a RNA/DNA hybrid (RNA--- A/U/G/C and DNA----DA/DT/DG/DC), does x3dna recognizes its a hybrid stucture? Should i give a different designation for RNA strand bases?
Mary Varughese
-
3DNA should be able to automatically analyze a hybrid RNA/DNA structure. See section "(D) Automatic identification of double-helical regions in a DNA–RNA junction (Recipe no. 4, Box 2)" of the 2008 3DNA Nature Protocols paper (http://www.nature.com/nprot/journal/v3/n7/abs/nprot.2008.104.html).
Have a try on your structure, and report back any issues you may have.
Xiang-Jun
-
Hi,
I perform a helical analysis of the RNA/DNA structure.
I got the output file. there seems to be no problem. but it says nothing; like, it recognized a hybrid structure. only says A -like form
Thanking you
Mary varughese
-
That's expected with the analyze program. DSSR provides a classification of each nucleic acid chain (DNA, RNA etc), which may be what you are looking for. Please be specific with a concrete example and tell us what you expect to find.
Xiang-Jun
-
ok sir, i will try DSSR.
i have no access to "2008 3DNA Nature Protocols paper". could you please provide this paper?
Thank you
-
thank you very much sir for the paper
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.