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Questions and answers => General discussions (Q&As) => Topic started by: sudipta on July 26, 2012, 06:36:33 pm

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Title: how to bend a big DNA soomthly?
Post by: sudipta on July 26, 2012, 06:36:33 pm
Hi,

I want to make a smooth circular bend structure of DNA using 3DNA. The DNA contains 88 base pairs.  I can't able to control the roll parameters that actually produce a smooth circular bend structure of this DNA. How do I choose the roll parameters. Is there any way to choose those parameters? I have followed the same procedure (the roll parameters chosen as sinusoidal) which as proposed in nature protocol paper. However, I have failed to put those parameters in the correct position of bp_step.par file. As a result I get a bend structure but the structure is zigzag type. In this regard if you have any suggestion please let me know.

Looking forward to hear from you soon.

Thanks in advance
Sudipta
Title: Re: how to bend a big DNA soomthly?
Post by: xiangjun on July 27, 2012, 10:29:11 am
3DNA per se does not provide a prescription "to bend a big DNA smoothly". How to choose roll angles to fit a smooth curve is problem specific; 3DNA is mechanical and rigorous in that it constructs a structure corresponding to the parameters you fed into "rebuild", or (reversibly) it can "analyze" a given DNA structure to provide parameters that fully describe its base geometry.

As mentioned previously, and made clear in the 2008 3DNA Nature Protocols paper, the various prescriptions of roll-introduced DNA bending in Figure 3 are based on the classic work of Calladine and Drew. That protocol was intended to illustrate 3DNA's capability of building structures, in schematic representation, based on user-supplied parameters, not to show how to derive roll angles for any desired DNA bending.

That said, 3DNA is handy for constructing and visualizing a DNA structure in three dimensions to help verify if a roll prescription fulfills one's assumptions -- seeing is believing as well as understanding. For example, by noticing a bend structure in zigzag type, you immediately realized that your roll parameters (as sinusoidal) were not chosen correctly.

There are literature publications on how to fit a smooth ribbon to curved DNA. Pubmed or Google Scholar is your friend; it helps if you could share your findings.

HTH,

Xiang-Jun
 
Title: Re: how to bend a big DNA soomthly?
Post by: mauricio esguerra on July 28, 2012, 07:39:18 am
Hi Sudipta,

You might find Tom Bishop's VDNA plugin for VMD useful:

http://dx.doi.org/10.1093/bioinformatics/btp566 (http://dx.doi.org/10.1093/bioinformatics/btp566)

You will find it by default in new versions of VMD at:
Extensions -> Visualization -> Virtual DNA Viewer.

The good thing about the plugin is that it allows you to produce various sets of step-parameters which you can later use with 3DNA rebuild for a full-atom reconstruction. For example, you can tell the GUI to make a dna-circle of 88 centers and to "save parameters" which you can later use.

I could make a step-by-step example if you have a hard time finding your way around.

Cheers,

Mauricio

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.