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Author Topic: which parameter shall I change to produce bend DNA  (Read 6258 times)

Offline sudipta

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which parameter shall I change to produce bend DNA
« on: July 05, 2012, 03:33:36 pm »
Hi,
Is it possible to rebuild a  new bend DNA using 3DNA? if so, which parameter should I change? I have seen in the documentation that the changing of  parameter, 'roll' can produce the bend DNA. However, there is no  step by step procedure in the documentation for that. Please explain figure 2 in the documentation. How to obtain that bend DNA with  curvature of 45^o by changing the roll parameter.
Thanks in advance
Sudipta

Offline xiangjun

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Re: which parameter shall I change to produce bend DNA
« Reply #1 on: July 05, 2012, 03:51:01 pm »
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Please explain figure 2 in the documentation.
Are you referring to recipe #2 of the 2008 3DNA Nature Protocols paper, "command-line script to create a 22 base-pair long schematic duplex structure with a 45° curvature per helical turn"? It was Figure 3, instead of 2.

All the (step-by-step) details about how to generate Roll-introduce DNA curvature are presented there. Just try to reproduce recipe #2, as another user recently went through. If you have any technical problems, please post back to the forum.

Xiang-Jun

Offline sudipta

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Re: which parameter shall I change to produce bend DNA
« Reply #2 on: July 05, 2012, 04:10:06 pm »
Hi,
Thank you very much for your reply.

Actually, I was asking about the figure 2 in the documentation file named as, 'x3dna_v1.5.pdf' .

Yes, I have seen the recipe 2 of that paper. But I don't understand what is the relation between roll angles and DNA bending angle. In that paper, I have seen there are four different possibility to obtain the same curvature. So, my question is what is the basis of choosing roll parameters for a specific DNA bending angle?

Thanking you
Sudipta

Offline xiangjun

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Re: which parameter shall I change to produce bend DNA
« Reply #3 on: July 05, 2012, 04:53:22 pm »
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So, my question is what is the basis of choosing roll parameters for a specific DNA bending angle?

Good question. However, that's what 3DNA cannot answer directly. As is made clear in the manual you referred to and in the 2008 3DNA Nature Protocols (NP) paper, the formulae for roll-introduced DNA curvature were based on the work of Calladine & Drew.

3DNA's usefulness in this area is described in the 2008 NP paper:

Quote
The complicated three-dimensional nature of local bending makes it difficult, even for a seasoned scientist, to visualize how the variation in roll at different dinucleotide steps leads to global curvature. With 3DNA, one simply prepares a data file with any prescribed set of parameters and builds the structure to see what it looks like (Fig. 3). The matrix-based scheme adopted in the 3DNA analysis/rebuilding programs makes this a completely reversible and rigorous process.


HTH,

Xiang-Jun

Offline sudipta

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Re: which parameter shall I change to produce bend DNA
« Reply #4 on: July 05, 2012, 05:56:37 pm »
Hi,

Thank you very much for your reply.

Another thing, if I want to perform a molecular dynamics simulation of a bend DNA (crated by 3DNA) using standard AMBER or CHARMM force field then is it possible. Are these force field parametrized for bend DNA? In other way, if I use standard CHARMM or AMBER force field for that then simulation be stable. Do you have any idea for that?

Thanking you
Sudipta

 

Offline xiangjun

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Re: which parameter shall I change to produce bend DNA
« Reply #5 on: July 05, 2012, 06:23:21 pm »
No idea if AMBER or CHARMM is parametrized for (strongly) bend DNA. Large DNA bending angle is normally found in protein-DNA complexes, e.g. IHF or CAP.

You will get more pertinent advice on this question in the AMBER or CHARMM mailing list.

Xiang-Jun

Offline sudipta

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Re: which parameter shall I change to produce bend DNA
« Reply #6 on: July 05, 2012, 07:24:48 pm »
Hi,

Thank you very much for your reply. Yes, I have seen some papers on protein influenced DNA bending.

Thanks again
Sudipta

 

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.