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Author Topic: 2D DNA structure  (Read 1390 times)

Offline luka86

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2D DNA structure
« on: February 01, 2024, 09:57:09 am »
Dear Dr. Xiang-Jun,
I am working on single stranded DNA aptamers and would like to be able to retrieve the 2D DNA structure of single-stranded DNA based on the PDB file. I would like to obtain the output in .ct or dot-bracket format, the same format as it is created by Mfold from the sequence. Is this feature already included in some of the tools?
Thank you in advance,
Best regards, Luka

Offline xiangjun

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Re: 2D DNA structure
« Reply #1 on: February 01, 2024, 10:07:44 am »
Hi Luka,

Please use a specific to illustrate unambiguously what you want to achieve. What you have tried and the results you got.

Xiang-Jun

Offline luka86

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Re: 2D DNA structure
« Reply #2 on: February 01, 2024, 10:58:43 am »
I have run the find_pair program combined with analyze on a PDB file of the single stranded DNA of this sequence GCGCGAATAAACGCGC. The exact command that I run was this: find_pair AATAAA_dna.pdb | analyze and I got some output files from which I believe that AATAAA_dna.out is the main output with some base pair information. It contains a section like this that is somewhat similar to .ct file:

****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

            Strand I                    Strand II          Helix
   1   (0.022) ....>-:...1_:[.DG]G-----C[.DC]:..16_:-<.... (0.021)     |
   2   (0.024) ....>-:...2_:[.DC]C-----G[.DG]:..15_:-<.... (0.044)     |
   3   (0.042) ....>-:...3_:[.DG]G-----C[.DC]:..14_:-<.... (0.025)     |
   4   (0.025) ....>-:...4_:[.DC]C-----G[.DG]:..13_:-<.... (0.024)     |
   5   (0.024) ....>-:...5_:[.DG]G-----C[.DC]:..12_:-<.... (0.030)     |
   6   (0.029) ....>-:...8_:[.DT]T-**+-A[.DA]:..11_:-<.... (0.020)     |
   7   (0.030) ....>-:...7_:[.DA]A-*---A[.DA]:..10_:-<.... (0.023)     |

Note: This structure contains 2[1] non-Watson-Crick base-pairs.
****************************************************************************

I would like to get the output in the .ct format like this:
     1 G      0      2     16       1
     2 C      1      3     15       2
     3 G      2      4     14       3
     4 C      3      5     13       4
     5 G      4      6     12       5
     6 A      5      7      0       6
     7 A      6      8      0       7
     8 T      7      9      0       8
     9 A      8     10      0       9
    10 A      9     11      0      10
    11 A     10     12      0      11
    12 C     11     13      5      12
    13 G     12     14      4      13
    14 C     13     15      3      14
    15 G     14     16      2      15
    16 C     15      0      1      16

or in dot-bracket format like this:

(((((......)))))

Offline xiangjun

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Re: 2D DNA structure
« Reply #3 on: February 01, 2024, 11:05:25 am »
Please attach the file: AATAAA_dna.pdb

Offline luka86

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Re: 2D DNA structure
« Reply #4 on: February 02, 2024, 09:20:33 am »
Thank you, I am sending the file in the attachment of the PDB file and also of the .out file that I got. But I am on mac, I am not sure if I have successfully uploaded the files.
« Last Edit: February 02, 2024, 09:28:15 am by luka86 »

Offline xiangjun

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Re: 2D DNA structure
« Reply #5 on: February 02, 2024, 12:13:19 pm »
Hi Luka,

Thanks for attaching file AATAAA_dna.pdb (no need to copy-and-paste the content). DSSR does what you want, as shown below:

Code: [Select]
x3dna-dssr -i=AATAAA_dna.pdb -o=AATAAA_dna.out

# dssr-2ndstrs.dbn
>AATAAA_dna nts=16 [AATAAA_dna] -- secondary structure derived by DSSR
GCGCGAATAAACGCGC
(((((......)))))

# dssr-2ndstrs.ct
   16 ENERGY = 0.0 [AATAAA_dna] -- secondary structure derived by DSSR
    1 G     0     2    16     1
    2 C     1     3    15     2
    3 G     2     4    14     3
    4 C     3     5    13     4
    5 G     4     6    12     5
    6 A     5     7     0     6
    7 A     6     8     0     7
    8 T     7     9     0     8
    9 A     8    10     0     9
   10 A     9    11     0    10
   11 A    10    12     0    11
   12 C    11    13     5    12
   13 G    12    14     4    13
   14 C    13    15     3    14
   15 G    14    16     2    15
   16 C    15     0     1    16

It generates output file AATAAA_dna.out, and a few auxiliary files including dssr-2ndstrs.ct and dssr-2ndstrs.dbn which are all attached.

See the post [No more grant funding for 3DNA/DSSR](http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/).

Xiang-Jun

Offline luka86

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Re: 2D DNA structure
« Reply #6 on: February 05, 2024, 09:36:24 am »
Thank you, but it seems that there is no free version of dssr. Is there any option to parse the x3dna output or some other way that is free of charge?
Thanks in advance.

 

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.