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Questions and answers => General discussions (Q&As) => Topic started by: mahesh on August 17, 2013, 12:09:29 am

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Title: Prediction of Non B-DNA structure
Post by: mahesh on August 17, 2013, 12:09:29 am

Hi, is it possible to predict the non B-DNA structure in 3D like cruciforms, hairpin, or G-quadruplex?

Title: Re: Prediction of Non B-DNA structure
Post by: xiangjun on August 17, 2013, 12:28:34 am

3DNA/DSSR is an analyzing/modeling toolset. Overall, it does not make 'predictions'. Nevertheless, some of its functionality could prove useful in testing your ideas.

Xiang-Jun

Title: Re: Prediction of Non B-DNA structure
Post by: mahesh on August 17, 2013, 10:29:42 am

Can we make a 3D model of Non-B-DNA structure using sequence?

Title: Re: Prediction of Non B-DNA structure
Post by: xiangjun on August 17, 2013, 10:54:43 am

The question sounds too general to me. With 3DNA, you can build an arbitrary DNA structure by providing an input file with sequence and desired parameters. See the 2008 3DNA Nature Protocols paper (http://www.nature.com/nprot/journal/v3/n7/abs/nprot.2008.104.html) for details.

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

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