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Messages - amadeus2

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1
General discussions (Q&As) / Re: Zp parameter A/vs B DNA
« on: November 23, 2013, 01:01:26 pm »
First of all thank you for the suggestion of NAD, I tried PDB database without success.

As to the citation I cannot find it anymore,  but I remember that it was a work by Professor Ignacio Tinoco,  Jr.  Nevertheless, unless you are already aware of, I hope you will find:

1. Achraya et al JACS (2003) vol. 125 p. 9948
2. Isaksoon et al Biochemistry (2004) vol. 43 pag. 15996

useful as well.

Amedeo


2
General discussions (Q&As) / Re: Zp parameter A/vs B DNA
« on: November 23, 2013, 03:56:19 am »
I wish to thank Xiang-Jun for his excellent Single- and double-stranded Zp post which clarifies everything. I also quote his question for Jeff 3D. It should be possible, at leat in principle,  to classify a single strand as A, B, AB or whatever, although strong irregularities are to be expected. Indeed  I have found an example in the literature where even the ss-5'-AAA-3' trimer in solution has been characterized as B-DNA by using  2D-NMR and molecular dynamics simulations. I have not found crystallographic structures of ss-oligonucleotides, but I am not a crystallographer, hence a sligthly off-topic question: « are you aware of examples of "pure" ss-DNA crystals, i.e. without proteins, ligands, etc.? » 

Thank you all

Amedeo



 

3
General discussions (Q&As) / Re: Zp parameter A/vs B DNA
« on: November 18, 2013, 01:36:09 pm »
Thank you very much for yor kind reply,

I was already aware of find_pair -s myfile.pdb stdout | analyze stdin --note the -s option--  and of course I had already tried (I first had to find a way to make my ab initio outputs pdb-compilant, and I also had to write an "analyze" code of my own just to compute  bp_step parameters to test everything was correct in my ab initio generated pdbs), but unfortunately the above procedure (at variance with double strand cases) does not furnish the wished information for my single strands.

Is "Zp" implemented for single strands? And now I am very curious, what is the difference between the two "Zp" , the one stored in myfile.outs and the one located in myfile.tor  obtained using the -t=myfile.tor option of analyze?

Sorry if my first question was badly asked and if I was unclear.

4
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


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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.