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Author Topic: Large value of ZpH and inclination for Z-DNA  (Read 6654 times)

Offline drozdzu

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Large value of ZpH and inclination for Z-DNA
« on: December 02, 2012, 06:14:23 am »
Dear Sir,

I would like to know your opinion about the high value of inclination and ZpH in the my structure of  Z-DNA.
For local base-pair number 3 in my first Z-DNA I have values:
      step       X-disp    Y-disp   h-Rise     Incl.       Tip     h-Twist
3 CG/CG     11.88     -0.10      6.56     63.77      1.19     -6.06
    step              Xp      Yp      Zp     XpH     YpH     ZpH    Form
   3 CG/CG    5.82    5.30   -1.92   17.69    4.06    3.91
and for the my second Z-DNA structure I have values:
     step       X-disp    Y-disp   h-Rise     Incl.       Tip     h-Twist
   3 CG/CG    -26.29      0.88      5.98     29.64      2.06     -6.31
 step           Xp      Yp      Zp     XpH     YpH       ZpH    Form
3 CG/CG    5.49    5.42   -2.51  -20.76    5.96    0.50
Is it possible to find something specific by comparing the values of ZpH ​​for the two structures Z-DNA?
Does it matter that the ZpH value is close to 4 A (which in your paper is considered as threshold for TA-DNA (> 4A) ?
Is such a large value of η is associated with a width of the minor groove (8.5 Å for step 3 = 3CG-10GC) ?
What can we say about the differences in X-disp for my two Z-DNA structures ?
It seems to me that X-disp = 11.88 differs from other values for this step in Z-DNA structures. ?
I would like ask one more thing. The average value of helical twist for Z-DNA is around -60.  How to calculate this value having these data ?  :
    step           h-Twist
   1 CG/CG    -6.15
   2 GC/GC       -53.30
   3 CG/CG     -6.31
   4 GC/GC      -53.77
   5 CG/CG        -6.86
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
          ave.     -25.28

As yoou can see I am beginner in the field of explanation the relationship between the helical parameters - therefore can please you to propose me some publication explanatory  for example how depends the width of small groove of the other helical parameters . ?

Thank you for your time and help

Yours sincerely,

paul


Offline xiangjun

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Re: Large value of ZpH and inclination for Z-DNA
« Reply #1 on: December 03, 2012, 12:10:56 am »
Hi paul,

Thanks for using 3DNA and posting your questions on the forum.

As detailed in the 2003 3DNA NAR paper, the set of helical parameters (X-disp, Y-disp, h-Rise, Incl., Tip, h-Twist) parallels that of the stacking parameters (Shift, Slide, Rise, Tilt, Roll, Twist); each represents a rigorous mathematical description of the relative geometry (position and orientation) of the two base pairs involved. You can verify the parameters by rebuilding an atomic model using the output file "bp_helical.par" -- the RMSD of base atoms between 3DNA rebuilt structure and the original one should be virtually zero.

From your list of the parameters, it's clear that two CG/CG steps differ from each other: what is the RMSD between them? Do you see "something specific" there by using a visualization tool (PyMOL/Jmol)? As always, 3DNA outputted parameters should be checked along with other means and your understanding of your structure to make "sense".

As elaborated in the thread "A-DNA definition" on the forum, the Zp vs ZpH parameters are mainly used to distinguish right-handed A-, B- and TA-DNA forms. I have not checked how the ZpH values vary in left-handed Z-DNA.

Z-DNA has dinucleotide as a repeating unit, so you need to add (-6 + -54) or analyze alternating base pairs to get the ~-60° twist angle.

To get started with DNA structures, I highly recommend the book "Understanding DNA: The Molecule and How it Works" by Calladine. You may check publications by Dr. Remo Rohs on DNA shape (minor groove width).

HTH,

Xiang-Jun

Offline drozdzu

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Re: Large value of ZpH and inclination for Z-DNA
« Reply #2 on: December 10, 2012, 08:14:24 pm »
Dear Sir,

Thank you for your answer.

 The rmsd for this base step between my Z-DNA structures (according to superpose program from CCP4) 
is 
RMS     XYZ DISPLACEMENT =   0.355
AVERAGE XYZ DISPLACEMENT =   0.293
 MAXIMUM XYZ DISPLACEMENT =   0.867
and between the entire two structures
is
RMS     XYZ DISPLACEMENT =   0.593

AVERAGE XYZ DISPLACEMENT =   0.409
MAXIMUM XYZ DISPLACEMENT =   4.240
Are these values significantly large ?

I am sending also two figures with superposition of my Z-DNA structures at the local base-pair step number 3.
Are these figures show differences in inclination and X-disp for base-pair step number 3 ?
At this base step we can see ZI to ZII rotation of the phosphate group at this dinucleotide step ?
Is it possible that differences in backbone ZI/ZII conformation would affect how X3DNA calculates some of the parameters (the Zp in
particular) ?

Thank you for your help !
Paul

Offline xiangjun

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Re: Large value of ZpH and inclination for Z-DNA
« Reply #3 on: December 10, 2012, 08:55:22 pm »
Hi Paul,

Thanks for posting back. In addtion to what I said in my previous reply, please note that 3DNA caluclates local step and helical parameters which could thus be strongly influenced by regional distortions. The same argument is true for the derived Xp/Yp/Zp parameters and their corresponding helical variants. The situation is especially noticeable for Z-DNA, as in your case, where the repeating unit is two base pairs but the structure is analyzed the 'normal' way (as in A- and B-DNA).

Other users of the forum may want to comment on your questions. Did you also post your questions on the CCP4 mailing list?

Xiang-Jun

 

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.