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Author Topic: generating 10.5 bp/turn B-DNA  (Read 5803 times)

Offline jiomm

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generating 10.5 bp/turn B-DNA
« on: November 10, 2013, 03:55:16 pm »
Dear Xiang

{Sorry, I posted personal mail earlier. Now I am using "New Topic", hope it goes to all}

I explored your online tools and found them  very useful. For Fibre BDNA generic form we can get 36 degree twist and 3.37 rise as default values. I have B-DNA sequence pdb (MY.pdb; also your tool can help to generate directly 10 bp B-DNA) with 10 bp/turn and want same B-DNA sequence as 10.5 bp/turn. Please let me know if following process would be correct to generate 10.5 bp B-DNA:

1) Analyse this MY.pdb (having 10bp/turn) using Analysis tool online.

2) Save the Nucleic Acid Local Base Step Parameters and Local Base-pair Parameters and write on text file. Edit the text file and modify each twist to 34.29 keep rise same as 3.54  (which is obtained as: twist= 360/10.5; and rise = 3.37+ (3.37/2)/10 = 3.5385 ). I am not sure about the rise especially and others. Should I keep other params same?

3) Generate new B-DNA with using this edited parameter file (Reconstruction--> customised model)

Please let me know if this procedure is correct?

kind regards
Jiomm
« Last Edit: November 10, 2013, 04:48:15 pm by jiomm »

Offline xiangjun

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Re: generating 10.5 bp/turn B-DNA
« Reply #1 on: November 10, 2013, 09:13:34 pm »
Hi Jiomm,

Thanks for using 3DNA (w3DNA) and posting your questions on the Forum. The procedure you outlined sounds fine to me. Note that with the 3DNA rebuild program, you can generate an arbitrary structure with any prescribed sequence and associated base-pair and step (or helical) parameters. Since the process is rigorous and reversible, you will get the same parameters back if you analyze the generated structure. It is up to the user to decide whether the structure is meaningful in a particular context.

For your case, you could simply reset twist from 36 degrees to 34.29, while keeping other parameters fixed. I do not understand your rationale of changing rise from 3.37 Å to 3.5385 [i.e., the formula 3.37+ (3.37/2)/10 = 3.5385]. With your settings, the helical pitch is larger than the fiber B-DNA model.

Also note the rebuild structure may have irregular sugar-phosphate backbone connectivity, which can be 'regularized' with restraint optimization using PHENIX.

HTH,

Xiang-Jun

Offline jiomm

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Re: generating 10.5 bp/turn B-DNA
« Reply #2 on: November 11, 2013, 09:27:48 am »
Dear Xiang

Thanks a lot for reply.

>> I do not understand your rationale of changing rise from 3.37 Å to 3.5385

Sorry, I was in wrong impression that with change in base pair per turn (in my case 10 to 10.5) the overall length should also change. But its wrong, overall length should not change and thus rise should be same.

Also regarding PHENIX, I never used that before. Actually I need to use this rebuilt structure for AMBER simulations so before molecular dynamics I will perform minimization with AMBER which should take care of geometric concerns. Do you still think that I should use PHENIX before AMBER minimization?

kind regards
Jiomm

Offline xiangjun

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Re: generating 10.5 bp/turn B-DNA
« Reply #3 on: November 11, 2013, 11:04:02 am »
Quote
Also regarding PHENIX, I never used that before. Actually I need to use this rebuilt structure for AMBER simulations so before molecular dynamics I will perform minimization with AMBER which should take care of geometric concerns. Do you still think that I should use PHENIX before AMBER minimization?
A nice feature about the PHENIX-restraint optimization is that one can fix the base geometry, and minimize the sugar-phosphate backbone only. AMBER should be perfectly fine, it is just that I do not know how to do it in detail. It helps if you could summarize the procedure for the benefit of other 3DNA/AMBER users.

Good luck!

Xiang-Jun

Offline jiomm

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Re: generating 10.5 bp/turn B-DNA
« Reply #4 on: November 11, 2013, 11:25:44 am »
Dear Xiang

Thanks for the support. Regarding AMBER usage and for the benefit of new AMBER users I provide here link (AMBER tutorial) for simulating small fragment of DNA that includes minimization procedure as well

http://ambermd.org/tutorials/basic/tutorial1/

Most of the times more or less this (above link) protocol works with normal DNA.

kind regards
Jiomm

 

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.