3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: maryatx3dna on September 09, 2013, 10:31:41 am

Title: hybrid analysis
Post by: maryatx3dna on September 09, 2013, 10:31:41 am: 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
Title: Re: hybrid analysis
Post by: xiangjun on September 09, 2013, 10:47:44 am: 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
Title: Re: hybrid analysis
Post by: maryatx3dna on September 10, 2013, 03:42:08 am: 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
Title: Re: hybrid analysis
Post by: xiangjun on September 10, 2013, 10:04:04 am: 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
Title: Re: hybrid analysis
Post by: maryatx3dna on September 10, 2013, 07:29:57 pm: ok sir, i will try DSSR.
i have no access to "2008 3DNA Nature Protocols paper". could you please provide this paper?
Thank you
Title: Re: hybrid analysis
Post by: maryatx3dna on September 11, 2013, 08:12:10 am: thank you very much sir for the paper