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Author Topic: Intrinsic Curvature of DNA  (Read 10184 times)

Offline laraibrahim

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Intrinsic Curvature of DNA
« on: May 19, 2015, 02:04:21 pm »
Hello,

Thank you for this great program and helpful forum.

Does 3DNA account for the intrinsic sequence dependent curvature of DNA? For example, when I use the reconstruction tool on w3DNA, an A-tract sequence gives a straight segment of DNA. I was expecting something more like this, showing curvature:
http://openi.nlm.nih.gov/imgs/512/281/1176013/1176013_gki699f1.png

Also, is there any way to connect the ends of a linear DNA strand to form a circle?

Thank you in advance,
Lara Ibrahim

Offline xiangjun

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Re: Intrinsic Curvature of DNA
« Reply #1 on: May 19, 2015, 02:26:43 pm »
Hi Lara Ibrahim,

Quote
Thank you for this great program and helpful forum.
Thanks for using 3DNA and your nice words! Over the years, it is enthusiastic users like you that have been driving the project forward.

Quote
Does 3DNA account for the intrinsic sequence dependent curvature of DNA? For example, when I use the reconstruction tool on w3DNA, an A-tract sequence gives a straight segment of DNA. I was expecting something more like this, showing curvature:
http://openi.nlm.nih.gov/imgs/512/281/1176013/1176013_gki699f1.png
As far as the "rebuild" functionality is concerned, 3DNA does "not care" about the intrinsic sequence-dependence at all. It is a mechanistic tool and just does what is told, exactly -- i.e., the rebuilt model is fully defined by the base-pair and step parameters, as specified by a user. There is a long story regarding sequence-dependent DNA bending. Some think that A-tract is curved whilst other believe it is straight. 3DNA is not a tool to solve this puzzle, but helps build models with whatever parameters. From my knowledge, A-tract in x-ray crystal structures is (mostly) straight.

Quote
Also, is there any way to connect the ends of a linear DNA strand to form a circle?
3DNA does not provide a direct recipe for generating a circular DNA. However, as long as you supply it with a set of parameters that form a circle, it will generate one. So if you have a circular DNA to start with, you can "analyze" it to get a set of base-pair and step parameters to regenerate the circle. You can then change base sequence as desired and are still able to build a circle.

HTH,

Xiang-Jun
« Last Edit: May 19, 2015, 03:30:18 pm by xiangjun »

Offline laraibrahim

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Re: Intrinsic Curvature of DNA
« Reply #2 on: May 19, 2015, 02:41:00 pm »
Thank you for your quick reply!
Lara

Offline mauricio esguerra

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Re: Intrinsic Curvature of DNA
« Reply #3 on: May 26, 2015, 05:33:54 am »
Hi Lara,

If your interest is in generating circular DNA then I suggest using the Virtual DNA Viewer plugin of Tom Bishop which comes integrated into the latest versions of VMD.
http://dna.ccs.tulane.edu/vdna/

You can combine this plugin with 3DNA to get your circular DNA models.

One first example of use:

  • Open VMD
  • Go to Extensions/Visualization/Virtual DNA Viewer
  • Notice that there is a box Next to where it says "Draw it". Select Circular DNA there and then click in Draw it.
  • Click on Save Parameters.
  • This will generate a vdna.par file which contains base-pair and step parameters you can use to rebuild using 3dna.
Code: [Select]
x3dna_utils cp_std -d B-DNA
Code: [Select]
rebuild -atomic vdna.par circulardna.pdb
Code: [Select]
pymol circulardna.pdb


    Cheers,

    Mauricio

    Offline laraibrahim

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    Re: Intrinsic Curvature of DNA
    « Reply #4 on: June 02, 2015, 02:17:10 pm »
    Thank you for your advice, I will try this soon!
    Lara

    Offline laraibrahim

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    Re: Intrinsic Curvature of DNA
    « Reply #5 on: June 03, 2015, 07:04:34 pm »
    Hello again,

    I followed the steps using VMD, but when I try to "rebuild" on 3DNA I get "error reading P xyz index".
    How can I fix this?

    Thanks in advance,
    Lara

    Offline xiangjun

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    Re: Intrinsic Curvature of DNA
    « Reply #6 on: June 03, 2015, 08:19:15 pm »
    Could you please post the content of vdna.par file? Either as an attachment or copy-and-paste here.

    Thanks,

    Xiang-Jun

    Offline laraibrahim

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    Re: Intrinsic Curvature of DNA
    « Reply #7 on: June 03, 2015, 08:23:06 pm »
    I have attached the file. Thank you for your help!

    Offline xiangjun

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    Re: Intrinsic Curvature of DNA
    « Reply #8 on: June 03, 2015, 09:58:18 pm »
    Thanks for attaching a sample file which helped me to identify where the problem is. It turns out your data file has DOS-style (Windows) newline character which causes trouble to the parser. I am a bit surprised that this issue did not pop up before. I assume you are using a Windows machine, right?

    I will release an updated 3DNA v2.2 soon. In the meantime, you can verify the result by downloading the following two files. The revised vdna2.par file has Unix-style newline which works in your version of 3DNA. The rebuilt PDB file is called vdna.pdb.

    Xiang-Jun

    Offline xiangjun

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    Re: Intrinsic Curvature of DNA
    « Reply #9 on: June 09, 2015, 02:33:03 pm »
    I've updated 3DNA to v2.2-2015jun09 with a refined parser for the input parameter file of the 'rebuild' program. Now your original attached file can be directly read by the program to generate a 3D PDB file. Please report back if you have further questions.

    Xiang-Jun
     

    Offline laraibrahim

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    Re: Intrinsic Curvature of DNA
    « Reply #10 on: June 23, 2015, 08:22:47 pm »
    Thanks for your reply.
    I created the .par file on a Windows machine but use the 3DNA application on a Mac. I think all the original issues are fixed now.
    Thank you again for all your help!
    Lara

     

    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.