hybrid analysis

[maryatx3dna]

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

[xiangjun]

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.

Have a try on your structure, and report back any issues you may have.

Xiang-Jun

[maryatx3dna]

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

[xiangjun]

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

[maryatx3dna]

ok sir, i will try DSSR.
i have no access to "2008 3DNA Nature Protocols paper". could you please provide this paper?
Thank you

[maryatx3dna]

thank you very much sir for the paper