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Questions and answers => General discussions (Q&As) => Topic started by: bciezah1 on April 04, 2017, 08:30:33 pm

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Title: Analysis of dna shape in methylated DNA
Post by: bciezah1 on April 04, 2017, 08:30:33 pm
Hello,

I hope this email finds you well. I have a question. I got some DM trajectories of methylated GC dsDNA. When I tried to use the command "find_pair mypdb stdout | analyze" to calculate shape parameters I received the next message: unknown residue  DM    2  on chain A [#2]. Then what I did is to change the name (in mypdb) of the residue from DM to DC (Because the DM is methylated cytosine) and the command ran without problem. My logic was that since the methylation is not affecting the base pair, and I am interested to get the propeller twist, I can get correct values of the propeller twist. Is this correct?

Thank you,

Basilio.
Title: Re: Analysis of dna shape in methylated DNA
Post by: xiangjun on April 04, 2017, 08:41:17 pm
Hi Basilio,

Generally speaking, 3DNA can handle non-standard bases quite well. For your case, please provide a reproducible example so other can see exactly where the problem is.

Xiang-Jun
Title: Re: Analysis of dna shape in methylated DNA
Post by: bciezah1 on April 04, 2017, 08:46:17 pm
Hi Xiang-Jun,

Thank you for your soon answer. I would be happy to share it, but I would like to know what do you mean when you say "please provide a reproducible example so other can see exactly where the problem is". This means that my solution is correct? and I have to post it?

Thank you,

Basilio.
Title: Re: Analysis of dna shape in methylated DNA
Post by: xiangjun on April 04, 2017, 08:51:21 pm
It'd be very helpful to simply attach a PDB file that illustrates unambiguously what the problem is and how you fixed it.

Xiang-Jun
Title: Re: Analysis of dna shape in methylated DNA
Post by: bciezah1 on April 04, 2017, 09:10:14 pm
Ok, I understand. Ok, here I go:

Regarding the propeller twist, we can calculate this parameter even when the residue is modify. In my case, methylated cytosine. Since the methylation did not affect the atoms used to calculate the propeller twist, we can use 3DNA to calculate the propeller twist in this residue.

In the beginning I received the message of error because my methylated residue (cytosine) was named as DM in my pdb file. However, it seems that 3DNA just recognize the next names DA,DT,DC and DG. Then I just changed the name DM by DC in my pdb file and the software worked without problem. I hope it can be helpful for other persons.

Best,

Basilio.
Title: Re: Analysis of dna shape in methylated DNA
Post by: xiangjun on April 04, 2017, 09:22:15 pm
Again, providing an example PDB file would make things much clearer.

Which version of 3DNA are you using? Methylated cytosine can certainly be handled automatically. However, without a reproducible example, I cannot help any further.

Xiang-Jun
Title: Re: Analysis of dna shape in methylated DNA
Post by: bciezah1 on April 04, 2017, 10:49:58 pm
Ah ok, this is the pdb file. Sorry, I did not understand you in the beginning. The version of 3DNA I am using is 3DNA v2.0. I think this is an old version, but I could not install the new one in my computer in window. I will try tomorrow since the actual version I am using cannot analysis MD trajectories.

Best,

Basilio.
Title: Re: Analysis of dna shape in methylated DNA
Post by: xiangjun on April 04, 2017, 11:07:58 pm
With now.pdb, and 3DNA v2.3 (the current version):

Code: [Select]
find_pair now.pdb now.inp
You will see diagnostic (not error) message like the following:

Code: [Select]
Match ' DM' to 'c' for residue  DM    2  on chain A [#2]
    check it & consider to add line ' DM     c' to file <baselist.dat>
The main output file now.inp has the following content:

Code: [Select]
now.pdb
now.out
    2         # duplex
   40         # number of base-pairs
    1     1    # explicit bp numbering/hetero atoms
    1    40   0 #    1 | ...1>A:...1_:[.DG]G-----c[.DM]:..20_:A<...1   0.40   0.01  25.87   9.03  -3.28
    2    39   0 #    2 | ...1>A:...2_:[.DM]c-----G[.DG]:..19_:A<...1   0.35   0.10  16.33   8.95  -3.63
    3    38   0 #    3 | ...1>A:...3_:[.DG]G-----c[.DM]:..18_:A<...1   0.62   0.58  17.77   8.90  -2.32
    4    37   0 #    4 | ...1>A:...4_:[.DM]c-----G[.DG]:..17_:A<...1   1.05   1.03  21.25   9.11  -0.83
    5    36   0 #    5 | ...1>A:...5_:[.DG]G-----c[.DM]:..16_:A<...1   0.75   0.67   5.95   9.04  -2.63
    6    35   0 #    6 | ...1>A:...6_:[.DM]c-----G[.DG]:..15_:A<...1   0.20   0.15   8.76   9.07  -4.06
    7    34   0 #    7 | ...1>A:...7_:[.DG]G-----c[.DM]:..14_:A<...1   0.65   0.63  22.39   9.00  -1.98
    8    33   0 #    8 | ...1>A:...8_:[.DM]c-----G[.DG]:..13_:A<...1   0.57   0.31  20.15   8.93  -2.81
    9    32   0 #    9 | ...1>A:...9_:[.DG]G-----c[.DM]:..12_:A<...1   1.04   0.55  20.34   8.80  -1.84
   10    31   0 #   10 | ...1>A:..10_:[.DM]c-----G[.DG]:..11_:A<...1   0.42   0.32  30.85   9.18  -2.40
   11    30   0 #   11 | ...1>A:..11_:[.DG]G-----c[.DM]:..10_:A<...1   0.31   0.24  20.12   9.02  -3.20
   12    29   0 #   12 | ...1>A:..12_:[.DM]c-----G[.DG]:...9_:A<...1   0.33   0.23  17.73   8.96  -3.31
   13    28   0 #   13 | ...1>A:..13_:[.DG]G-----c[.DM]:...8_:A<...1   0.11   0.02   4.82   8.99  -4.60
   14    27   0 #   14 | ...1>A:..14_:[.DM]c-----G[.DG]:...7_:A<...1   0.25   0.05  15.58   9.00  -3.87
   15    26   0 #   15 | ...1>A:..15_:[.DG]G-----c[.DM]:...6_:A<...1   0.86   0.64  11.46   9.23  -2.29
   16    25   0 #   16 | ...1>A:..16_:[.DM]c-----G[.DG]:...5_:A<...1   0.08   0.03  17.21   8.95  -4.00
   17    24   0 #   17 | ...1>A:..17_:[.DG]G-----c[.DM]:...4_:A<...1   0.59   0.37  16.52   8.98  -2.84
   18    23   0 #   18 | ...1>A:..18_:[.DM]c-----G[.DG]:...3_:A<...1   0.13   0.13  17.26   9.12  -3.75
   19    22   0 #   19 | ...1>A:..19_:[.DG]G-----c[.DM]:...2_:A<...1   0.31   0.26  11.89   9.12  -3.57
   20    21   9 #   20 x ...1>A:..20_:[.DM]c-----G[.DG]:...1_:A<...1   0.45   0.38  28.30   9.12  -2.38
   41    80   0 #   21 | ...1>B:...1_:[.DG]G-----c[.DM]:..20_:B<...1   0.45   0.13  21.26   8.91  -3.23
   42    79   0 #   22 | ...1>B:...2_:[.DM]c-----G[.DG]:..19_:B<...1   0.46   0.32  24.76   9.07  -2.66
   43    78   0 #   23 | ...1>B:...3_:[.DG]G-----c[.DM]:..18_:B<...1   0.25   0.20  12.01   9.01  -3.75
   44    77   0 #   24 | ...1>B:...4_:[.DM]c-----G[.DG]:..17_:B<...1   0.37   0.32  19.75   9.13  -3.00
   45    76   0 #   25 | ...1>B:...5_:[.DG]G-----c[.DM]:..16_:B<...1   0.20   0.13  19.64   9.12  -3.56
   46    75   0 #   26 | ...1>B:...6_:[.DM]c-----G[.DG]:..15_:B<...1   1.01   1.01  20.99   9.15  -0.93
   47    74   0 #   27 | ...1>B:...7_:[.DG]G-----c[.DM]:..14_:B<...1   0.40   0.37  18.39   9.23  -2.95
   48    73   0 #   28 | ...1>B:...8_:[.DM]c-----G[.DG]:..13_:B<...1   0.88   0.46  20.27   9.05  -2.19
   49    72   0 #   29 | ...1>B:...9_:[.DG]G-----c[.DM]:..12_:B<...1   0.92   0.84  21.58   8.98  -1.31
   50    71   0 #   30 | ...1>B:..10_:[.DM]c-----G[.DG]:..11_:B<...1   0.92   0.89  16.24   9.15  -1.49
   51    70   0 #   31 | ...1>B:..11_:[.DG]G-----c[.DM]:..10_:B<...1   0.33   0.15  18.78   8.97  -3.43
   52    69   0 #   32 | ...1>B:..12_:[.DM]c-----G[.DG]:...9_:B<...1   0.29   0.13  25.28   9.03  -3.20
   53    68   0 #   33 | ...1>B:..13_:[.DG]G-----c[.DM]:...8_:B<...1   0.57   0.47  27.56   8.80  -2.10
   54    67   0 #   34 | ...1>B:..14_:[.DM]c-----G[.DG]:...7_:B<...1   0.62   0.56  20.66   9.09  -2.24
   55    66   0 #   35 | ...1>B:..15_:[.DG]G-----c[.DM]:...6_:B<...1   0.20   0.08  11.63   9.19  -4.05
   56    65   0 #   36 | ...1>B:..16_:[.DM]c-----G[.DG]:...5_:B<...1   0.58   0.51  16.11   9.22  -2.60
   57    64   0 #   37 | ...1>B:..17_:[.DG]G-----c[.DM]:...4_:B<...1   0.91   0.20   8.59   8.75  -3.25
   58    63   0 #   38 | ...1>B:..18_:[.DM]c-----G[.DG]:...3_:B<...1   0.88   0.72  11.69   9.01  -2.10
   59    62   0 #   39 | ...1>B:..19_:[.DG]G-----c[.DM]:...2_:B<...1   0.74   0.70  29.13   8.88  -1.40
   60    61   0 #   40 | ...1>B:..20_:[.DM]c-----G[.DG]:...1_:B<...1   0.17   0.10  19.09   9.01  -3.68
##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.80 [ O N]
##### 0 non-Watson-Crick base-pairs, and 2 helices (0 isolated bps)
##### Helix #1 (20): 1 - 20
##### Helix #2 (20): 21 - 40
So 3DNA is performing as expected.

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University