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Author Topic: hybrid analysis  (Read 24748 times)

Offline maryatx3dna

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hybrid analysis
« 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
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Offline xiangjun

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Re: hybrid analysis
« Reply #1 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.

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

Xiang-Jun
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Offline maryatx3dna

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Re: hybrid analysis
« Reply #2 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
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Offline xiangjun

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Re: hybrid analysis
« Reply #3 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
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Offline maryatx3dna

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Re: hybrid analysis
« Reply #4 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
« Last Edit: September 10, 2013, 07:34:17 pm by maryatx3dna »
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Offline maryatx3dna

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Re: hybrid analysis
« Reply #5 on: September 11, 2013, 08:12:10 am »
thank you very much sir for the paper
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Funded by X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids (R24GM153869)

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University