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Questions and answers => General discussions (Q&As) => Topic started by: rodrigopontiggia on February 16, 2009, 02:41:54 pm

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Title: Base Pair Step Parameters
Post by: rodrigopontiggia on February 16, 2009, 02:41:54 pm
I´m analyzing an double helix RNA with a modified nucleotide. The effect of the modification pushes one of the bases but doesnt affect complementary one. stragger, proppeler and Buckle are very affected. Since  it affects only one base of the base pair I dont know if  it is correct two analyze roll and tilt. May be its a wrong average of a non-averageble structure.
It would be great If you could tell me if I should take in consideration the base pair step parameters in my analysis.

  Thanks

Regads
Title: Re: Base Pair Step Parameters
Post by: xiangjun on February 17, 2009, 10:09:53 pm
Quote from: "rodrigopontiggia"
I´m analyzing an double helix RNA with a modified nucleotide. The effect of the modification pushes one of the bases but doesnt affect complementary one. stragger, proppeler and Buckle are very affected. Since it affects only one base of the base pair I dont know if it is correct two analyze roll and tilt. May be its a wrong average of a non-averageble structure.

Again, it would make life easier for me and other viewers of this forum to understand exactly what you mean if you have provided more details,  i. e., the PDB file containing the fragment you are having trouble with and corresponding 3DNA output. Remember to help as much as possible to others so they can help you!

In a general sense, I believe I know what you mean, and I am glad that you bring up this issue. There is still confusions in the literature regarding analysis of non-Watson-Crick base-pairs and their associated helical regions, which are prevalent in RNA structures. Without going into specific details, I would suggest that you leave out each such pair and its two associated steps from averaging with other normal WC pairs/steps. A comparison is meaningful only if its parts are comparable, which is not the case for a WC vs non-WC pairs.

However, such non-WC pairs should not be ignored  -- instead, they should be treated separately and with more care. 3DNA can help in pursuing such cases further, especially in the context of the structural database (NDB/PDB), with its various visualization and analysis tools.

HTH,

Xiang-Jun
Title: Re: Base Pair Step Parameters
Post by: rodrigopontiggia on February 18, 2009, 03:59:55 pm
Thanks for your answer and sorry for the little info.

    Maybe I should make myself more clear. I simulated a 12 mer A-RNA with one modified nucleotide in the middle.  The modification caused a perturbation in the following base-pair which is still watson-Crick. One of them is quite appart from its natural position (compared to the wild-type ) . The base-pair parameters are quite different from the control specially propeller, stragger and bucke. I don´t know if such values allow me to use the   step parameters (Roll , Rise, Tilt) since they are calculated from irregular  base pairs .


 I´m sending an attachment the output of  modified duplex to explain my point. THe modification is the U7 of Strand II, notice that  the effect is seen in the base of the C6 of strand 2 which shows to be quite affected.

  Hope this help u to understand my problem

Best Reagads.

Rodrigo
Title: Re: Base Pair Step Parameters
Post by: xiangjun on February 21, 2009, 01:05:55 pm
Hi Rodrigo,

Your case is yet another example of the importance to be specific when asking questions and in discussions.

From your attached 3DNA output file, the H-bonds are normal for what would be expected for Watson-Crick pairs:
Code: [Select]
****************************************************************************
Detailed H-bond information: atom-name pair and length [ON]
   1 G-----C  [3]  O6 - N4  2.86  N1 - N3  2.90  N2 - O2  2.81
   2 A-----U  [2]  N6 - O4  3.03  N1 - N3  2.90
   3 A-----U  [2]  N6 - O4  2.98  N1 - N3  2.91
   4 A-----U  [2]  N6 - O4  2.94  N1 - N3  2.95
   5 A-----U  [2]  N6 - O4  2.89  N1 - N3  2.96
   6 G-----C  [3]  O6 - N4  2.95  N1 - N3  2.93  N2 - O2  2.85
   7 A-----U  [2]  N6 - O4  3.05  N1 - N3  2.92
   8 A-----U  [2]  N6 - O4  3.03  N1 - N3  2.94
   9 A-----U  [2]  N6 - O4  2.96  N1 - N3  2.92
  10 G-----C  [3]  O6 - N4  2.91  N1 - N3  2.91  N2 - O2  2.80
  11 A-----U  [2]  N6 - O4  3.00  N1 - N3  2.89
  12 A-----U  [2]  N6 - O4  2.95  N1 - N3  2.96
****************************************************************************

Naturally, the six base-pair parameters have mean and std values in ranges reported in the literature:
Code: [Select]
****************************************************************************
Local base-pair parameters
     bp        Shear    Stretch   Stagger    Buckle  Propeller  Opening
    1 G-C      -0.23     -0.18     -0.63    -20.29     -2.28     -0.66
    2 A-U       0.09     -0.04     -0.48    -13.64    -10.06      4.26
    3 A-U       0.06     -0.06     -0.53    -11.24    -12.42      2.82
    4 A-U       0.09     -0.03     -0.62    -13.46    -13.99      0.86
    5 A-U       0.18      0.01     -0.56    -15.56    -12.75     -1.66
    6 G-C      -0.05     -0.03     -0.69    -25.26    -19.76      2.36
    7 A-U       0.06      0.01     -0.35     -7.49     -7.94      4.36
    8 A-U       0.14     -0.00     -0.49     -8.36    -11.15      3.57
    9 A-U       0.09     -0.04     -0.34     -6.42    -10.45      1.32
   10 G-C      -0.11     -0.13     -0.33     -9.45    -12.75      1.08
   11 A-U       0.08     -0.08     -0.36     -9.60    -12.41      3.48
   12 A-U       0.16     -0.09     -0.35     -1.29    -11.67      0.95
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      ave.      0.05     -0.06     -0.48    -11.84    -11.47      1.89
      s.d.      0.12      0.06      0.13      6.42      4.05      1.91
****************************************************************************
Thus, from what I have in hand, nothing appears (to me) really unusual here. Of course, it would also be helpful to analyze your structure with other programs, e.g., Curves, to see what you get.

HTH,

Xiang-Jun

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