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General discussions (Q&As) / Zp parameter A/vs B DNA

« on: November 18, 2013, 11:56:21 am »

Dear Xiang-Jun,

I am currently faced with short single strand sequences obtained by ab initio optimizations and I wish to understand if they are A or B  forms. I have read your illuminating NAR03 paper, where the "Zp" criterion to distinguish A from B DNA is discussed. I used the analyze program, eg:

Code: [Select]

analyze -torsion=caa.tor caa.pdb
and obtained

Code: [Select]

[...]
      Dp: perpendicular distance of the 3' P atom to the glycosydic bond
            [as per the MolProbity paper of Richardson et al. (2010)]

              base       v0      v1      v2      v3      v4     tm       P    Puckering    Zp      Dp
   1 A:...1_:[.DA]A   -11.2    28.7   -34.0    28.5   -11.0    34.0   179.8    C2'-endo    2.29    2.01
   2 A:...2_:[.DA]A   -40.8    45.6   -33.4    10.7    18.6    45.3   137.5    C1'-exo     2.51    2.44
   3 A:...3_:[.DC]C   -44.6    43.3   -25.7     0.4    27.4    45.3   124.5    C1'-exo     ---     ---

Now, according to your NAR2003 paper, this should be an A DNA form. To check if I was correct, I worked out the bdl024.pdb B DNA example of the /examples/analyze_rebuild  x3dna folder and, to my surprise, by using the above command I got:

Code: [Select]


[...]
              base       v0      v1      v2      v3      v4     tm       P    Puckering    Zp      Dp
   1 A:...1_:[..C]C   -20.3    33.1   -33.1    22.1    -1.2    34.5   163.5    C2'-endo    1.60    1.87
   2 A:...2_:[..G]G   -23.9    36.6   -34.9    22.3     0.8    37.1   160.0    C2'-endo    1.46    1.59
   3 A:...3_:[..C]C   -24.8     5.6    13.9   -28.7    33.8    33.3    65.3    C4'-exo     2.36    3.05
   4 A:...4_:[..G]G   -25.7    37.1   -33.9    20.1     3.4    37.1   156.2    C2'-endo    2.19    2.01
   5 A:...5_:[..A]A   -20.9    31.2   -29.3    17.7     2.0    31.6   158.0    C2'-endo    1.92    2.02
   6 A:...6_:[..A]A   -22.6    30.8   -27.2    14.8     4.8    30.6   152.6    C2'-endo    1.87    2.02
   7 A:...7_:[..T]T   -34.2    33.1   -20.1     0.8    20.9    34.8   125.2    C1'-exo     2.03    2.27
   8 A:...8_:[..T]T   -35.8    35.4   -22.0     1.8    21.1    36.7   126.9    C1'-exo     2.09    2.31
   9 A:...9_:[..C]C   -21.5    31.7   -29.8    18.0     2.0    32.2   157.9    C2'-endo    1.17    1.63
  10 A:..10_:[..G]G   -36.1    45.1   -36.0    16.8    11.4    43.6   145.6    C2'-endo    1.41    1.25
  11 A:..11_:[..C]C   -21.3    35.1   -35.2    23.4    -1.5    36.6   163.8    C2'-endo    1.11    1.67
[...]

where almost all the "Zp s" are higher than 1.5 Angstroem, even if bdl024.pdb  is a clear example of B DNA.  I have read here http://x3dna.org/highlights/sugar-pucker-correlates-with-phosphorus-base-distance and here: http://forum.x3dna.org/general-discussions/a-dna-definition/ and I realized I am possibly missing something.

Now the questions:
1. Is the "Zp" parameter of NAR03, the same as the one returned by by the analyze -t=myfile.tor myfile.pdb command?  If not, how can I get the correct "Zp"?
2. How can I obtain an output like the one  in http://forum.x3dna.org/general-discussions/a-dna-definition/, where A and B steps are tentatively assigned by 3DNA?

Code: [Select]

[...]
    step       Xp      Yp      Zp     XpH     YpH     ZpH    Form
   1 GC/GC   -4.37    8.77   -1.05   -4.95    8.83   -0.22     B
   2 CG/CG   -2.56    8.63    0.13   -2.38    8.49    1.55     B
   3 GC/GC   -3.74    9.12   -0.62   -4.46    9.06   -1.34     B
[...[

I am sorry if these are old aquestions, but I wasn't able to find answers in the 3DNA site nor in the forum.

As a newbie I would appreciate your help.

Amedeo