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Questions and answers => General discussions (Q&As) => Topic started by: mithun on May 03, 2011, 11:38:23 am

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Title: Base pair step parameters with a missing base pair
Post by: mithun on May 03, 2011, 11:38:23 am

Hi all,

I want to calculate DNA base pair step parameters of nucleosomal DNA
(PDB id: 1kx5) as function of time steps during my MD trajectory.
Applying 'find_pair' and 'analyze' commands on trajectory frames shows that base pairing at nucleotide position 97 (strand I) is non-WC i.e.

 96   (0.094) -:1071_:[THY]T-----A[ADE]:1172_:- (0.071)     |
 97   (0.039) -:1072_:[GUA]Gx*--xC[CYT]:1171_:- (0.046)     x
 98   (0.080) -:1074_:[ADE]A-----T[THY]:1169_:- (0.045)     |

When I compare the pdb frames with the crystal structure, I find that there are actually two consecutive GC pairs (at positions 97 and 98), one forms and breaks during the MD and the other is broken during the entire trajectory.
So, the actual base pairing should be like this:

96  T --- A
97  G --- C
98  G --- C  <--- missing
99  A --- T

In the calculation of helical step parameters the program fails to find values for the step GA/TC :

 96 TG/CA      2.86      0.11      3.79      8.08     27.10     29.71
 97 GA/TC      ----      ----      ----      ----      ----      ----

I am trying to understand why it is so. For the positions '97' and '99' the program should be able to find the 'middle frame' and hence the step parameters for the step GA/TC. Since this value is missing it can only be due to the fact that one base pair is missing in between. But, if 'find_pair' does not recognize this base pair (position '98'), how does it affect the calculation of step parameters ?


Mithun

Title: Re: Base pair step parameters with a missing base pair
Post by: xiangjun on May 03, 2011, 11:43:26 pm

Hi Mithun,

The following info may help:

• 3DNA FAQ "How to fix missing (superfluous) base pairs identified by find_pair? (http://http://3dna.rutgers.edu/x3dna/faqs#find_pair)" You may want to upload (as attachment) the 4-mer duplex fragment (residues 96-98 for one strand) and provide the base pairs found with "find_pair". Then we can discuss specifically why some pair is missed or mis-assigned by "find_pair".
• Search the forum using the term "find_pair".
• Since you are using 3DNA for MD simulations, please see the post "Ruby scripts for the analysis of MD simulation trajectories (http://http://3dna.rutgers.edu:8080/forum/viewtopic.php?f=11&t=195)".

HTH,

Xiang-Jun

Title: Re: Base pair step parameters with a missing base pair
Post by: mithun on May 06, 2011, 07:06:35 am

Hi Xian-Jun,

Thanks for your reply. The problem was related to how 'find_pair' works and the FAQ helped me understanding it.


Regards,

Mithun

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.