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Author Topic: Analysis of helical parameter of DNA with unnatural  (Read 13 times)

Offline priyabrata das

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We are trying to use the 3DNA to analyze helical parameters in our DNA MD simulations. However, the base pair  DX:DY was not be recognized when I used “find_pair”. Notably, the unrecognized base-pair ( DX, DY ) are not typical purine or pyrimidine. How can I analysis the confirmation parameters with 3DNA in such case? 

  The PDB files of DX, DY,  and a frame of MD simulations(XY.pdb) are given in the attachment. Thank you very much!

Thanks and Best wishes

Priyabrata Das

Offline xiangjun

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Re: Analysis of helical parameter of DNA with unnatural
« Reply #1 on: Today at 10:33:13 am »
Hi Priyabrata Das,

Thanks for using 3DNA and reporting the unidentified pairing issue you experienced on the Forum.

The problem is due to DY, which is a special modified case that cannot be properly recognized by 3DNA. More specifically, it is the N7 atom (see the attached image below) that causes the trouble.

I may consider refining the algorithm in 3DNA v2.4 for base identification in special cases like this. For now, simply renaming N7 to NX (for example) would do the trick. Alternatively (and better yet), you may want to give DSSR a try (see below).

Best regards,

Xiang-Jun


PS. The issue is fixed in DSSR v1.8.8, released today. Here is an excerpt of the DSSR output on your structure (XY.pdb).

Code: [Select]
List of 4 types of 12 modified nucleotides
      nt    count  list
   1  DP-g    4    DP6,DP7,DP22,DP23
   2  DZ-c    4    DZ10,DZ11,DZ26,DZ27
   3 DP4-g    2    DP4/8,DP4/24
   4 DZ5-c    2    DZ5/9,DZ5/25
    total number of base pairs: 16
    total number of helices: 1
    total number of stems: 1

****************************************************************************
List of 16 base pairs
     nt1            nt2            bp  name        Saenger   LW   DSSR
   1 DC5/1          DG3/32         C-G WC          19-XIX    cWW  cW-W
   2 DT2            DA31           T-A WC          20-XX     cWW  cW-W
   3 DT3            DA30           T-A WC          20-XX     cWW  cW-W
   4 DA4            DT29           A-T WC          20-XX     cWW  cW-W
   5 DT5            DA28           T-A WC          20-XX     cWW  cW-W
   6 DP6            DZ27           g-c WC          19-XIX    cWW  cW-W
   7 DP7            DZ26           g-c WC          19-XIX    cWW  cW-W
   8 DP4/8          DZ5/25         g-c WC          19-XIX    cWW  cW-W
   9 DZ5/9          DP4/24         c-g WC          19-XIX    cWW  cW-W
  10 DZ10           DP23           c-g WC          19-XIX    cWW  cW-W
  11 DZ11           DP22           c-g WC          19-XIX    cWW  cW-W
  12 DA12           DT21           A-T WC          20-XX     cWW  cW-W
  13 DT13           DA20           T-A WC          20-XX     cWW  cW-W
  14 DA14           DT19           A-T WC          20-XX     cWW  cW-W
  15 DA15           DT18           A-T WC          20-XX     cWW  cW-W
  16 DG3/16         DC5/17         G-C WC          19-XIX    cWW  cW-W
« Last Edit: Today at 02:32:07 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.