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Questions and answers => General discussions (Q&As) => Topic started by: gzt on June 03, 2013, 01:42:43 pm

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Title: Single stranded DNA simulation
Post by: gzt on June 03, 2013, 01:42:43 pm

Dear All,

I need to simulate the behaviour (with 3D visualization) of many arbitrary designed variable sized single stranded DNA in solution. This includes double helix formation among single stranded DNA, hairy pin in one single stranded DNA, etc.

I am new to 3DNA and I would like to know if it is possible to do what I need with this software. If not, what would you suggest ? Probably any kinetic Monte Carlo implementation around ?

Kind regards and many thanks in advance.

Title: Re: Single stranded DNA simulation
Post by: xiangjun on June 03, 2013, 09:19:49 pm

With 3DNA, you can build a straight single-stranded DNA (ssDNA) of arbitrary sequence using fiber as shown below:

Code: [Select]

fiber -seq=aaatttt -single fb.pdb
or a sequence-dependent ssDNA structure by providing a sequence and associated step parameters.

Note that 3DNA's model building facility is purely geometry-based, employing base-pair parameters, and it takes no consideration of energetics. Overall, you may find 3DNA useful in certain aspects of  your project, and need to try other tools (e.g., NAB/AMBER etc from the Case lab (http://casegroup.rutgers.edu)) as well.

HTH,

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