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Author Topic: Can 3DNA be used to build a miRNA-target structure?  (Read 6295 times)

Offline GuidoLeoni

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Can 3DNA be used to build a miRNA-target structure?
« on: November 21, 2012, 03:10:21 am »
Thank for your work with 3DNA.
Might it be possible to reproduce with 3DNA a structure of a mirna target pairment?
Best regards

Offline xiangjun

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Re: Can 3DNA be used to build a miRNA-target structure?
« Reply #1 on: November 21, 2012, 10:33:48 am »
Could you be more specific, better with an example (or reference), to illustrate exactly what want to achieve?

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline GuidoLeoni

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Re: Can 3DNA be used to build a miRNA-target structure?
« Reply #2 on: November 21, 2012, 11:26:59 am »
Of course  :D
I ought to perform some docking studies on a experimentally validated (luciferase assay) pair mirna-target.
According to the assay, I can't determine the portion of the target that is bound by the mirna. Therefore I ran a mirna binding-site predictor on the mrna sequence of the target highlighting some interesting candidate positions. 
In order to further characterize my binding i thought to perform some dockings between the complex formed by mirna with the portion of target highlighted by predictors  and the Argonaute protein.
The central point is that i need to rebuild the pair mirna- target as highlighted by my predictors in order to use it as input for docking.
Here is an example  with part of the 2 sequences. The first sequence is the mirna and the second is the target


U A A A G U G C U U A U
 |  |   |  |  |   |   |   |         |  |
A U U UC  A C  G       U A

I hope that my explanation is enough clear and sorry for the "naif" representation of the mirna-target pairment
Thank you very much
Guido Leoni

Offline GuidoLeoni

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Re: Can 3DNA be used to build a miRNA-target structure?
« Reply #3 on: November 21, 2012, 11:29:36 am »
The empty spaces in alignment are mismatches


U A A A G U G C U U A U
 |  |   |  |  |   |   |   |         |  |
A U U UC  A C  G C C U A

Offline xiangjun

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Re: Can 3DNA be used to build a miRNA-target structure?
« Reply #4 on: November 21, 2012, 12:25:59 pm »
Hi Guido Leoni,

Thanks for providing such a detailed explanation of your miRNA-mRNA pairment question. I can now clearly see what you want to achieve, and I understand the importance of your research area.

Am I right to assume that the RNA structure you want to build is (with code tag for monospace)?
Code: [Select]
U A A A G U G C U U A U
| | | | | | | |     | |
A U U U C A C G C C U A

There are many tools dedicated to building three-dimensional RNA structures, see for example "RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction". You may want to check some of the tools included in the evaluation paper, or try other (newer) ones.

If you want to try out 3DNA, here are the procedures to build an approximate structure with the above sequence and secondary structure:

# build an RNA duplex with Watson-Crick base pairs
fiber -se=UAAAGUGCUUAU -r RNA-WC-duplex.pdb
find_pair RNA-WC-duplex.pdb stdout
# as shown below:

NA-WC-duplex.pdb
RNA-WC-duplex.out
    2         # duplex
   12         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   24  0 #    1 | ....>A:...1_:[..U]U-----A[..A]:..24_:B<....  0.11  0.06 10.52  8.94 -4.24
    2   23  0 #    2 | ....>A:...2_:[..A]A-----U[..U]:..23_:B<....  0.11  0.06 10.52  8.94 -4.24
    3   22  0 #    3 | ....>A:...3_:[..A]A-----U[..U]:..22_:B<....  0.11  0.06 10.52  8.94 -4.24
    4   21  0 #    4 | ....>A:...4_:[..A]A-----U[..U]:..21_:B<....  0.11  0.06 10.51  8.94 -4.24
    5   20  0 #    5 | ....>A:...5_:[..G]G-----C[..C]:..20_:B<....  0.24  0.07 10.52  8.94 -4.10
    6   19  0 #    6 | ....>A:...6_:[..U]U-----A[..A]:..19_:B<....  0.11  0.06 10.52  8.95 -4.24
    7   18  0 #    7 | ....>A:...7_:[..G]G-----C[..C]:..18_:B<....  0.24  0.07 10.52  8.94 -4.09
    8   17  0 #    8 | ....>A:...8_:[..C]C-----G[..G]:..17_:B<....  0.24  0.07 10.52  8.95 -4.10
    9   16  0 #    9 | ....>A:...9_:[..U]U-----A[..A]:..16_:B<....  0.11  0.06 10.52  8.94 -4.24
   10   15  0 #   10 | ....>A:..10_:[..U]U-----A[..A]:..15_:B<....  0.11  0.06 10.52  8.94 -4.24

   11   14  0 #   11 | ....>A:..11_:[..A]A-----U[..U]:..14_:B<....  0.11  0.06 10.52  8.94 -4.24
   12   13  0 #   12 | ....>A:..12_:[..U]U-----A[..A]:..13_:B<....  0.11  0.06 10.52  8.94 -4.24
##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.50 [ O N]
##### 0 non-Watson-Crick base-pairs, and 1 helix (0 isolated bps)
##### Helix #1 (12): 1 - 12

# now mutate A15 and A16 on chain B to C
mutate_bases 'c=B s=16 m=C; c=B s=15 m=C' RNA-WC-duplex.pdb RNA-ok-duplex.pdb
find_pair RNA-ok-duplex.pdb stdout
# now you get the desired miRNA-mRNA duplex with two U--C mis-matches:

RNA-ok-duplex.pdb
RNA-ok-duplex.out
    2         # duplex
   12         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   24  0 #    1 | ....>A:...1_:[..U]U-----A[..A]:..24_:B<....  0.11  0.06 10.52  8.94 -4.24
    2   23  0 #    2 | ....>A:...2_:[..A]A-----U[..U]:..23_:B<....  0.11  0.06 10.52  8.94 -4.24
    3   22  0 #    3 | ....>A:...3_:[..A]A-----U[..U]:..22_:B<....  0.11  0.06 10.52  8.94 -4.24
    4   21  0 #    4 | ....>A:...4_:[..A]A-----U[..U]:..21_:B<....  0.11  0.06 10.51  8.94 -4.24
    5   20  0 #    5 | ....>A:...5_:[..G]G-----C[..C]:..20_:B<....  0.24  0.07 10.52  8.94 -4.10
    6   19  0 #    6 | ....>A:...6_:[..U]U-----A[..A]:..19_:B<....  0.11  0.06 10.52  8.95 -4.24
    7   18  0 #    7 | ....>A:...7_:[..G]G-----C[..C]:..18_:B<....  0.24  0.07 10.52  8.94 -4.09
    8   17  0 #    8 | ....>A:...8_:[..C]C-----G[..G]:..17_:B<....  0.24  0.07 10.52  8.95 -4.10
    9   16  0 #    9 | ....>A:...9_:[..U]U-**--C[..C]:..16_:B<....  0.11  0.06 10.52  8.99  0.76
   10   15  0 #   10 | ....>A:..10_:[..U]U-**--C[..C]:..15_:B<....  0.11  0.06 10.51  8.99  0.76

   11   14  0 #   11 | ....>A:..11_:[..A]A-----U[..U]:..14_:B<....  0.11  0.06 10.52  8.94 -4.24
   12   13  0 #   12 | ....>A:..12_:[..U]U-----A[..A]:..13_:B<....  0.11  0.06 10.52  8.94 -4.24
##### Base-pair criteria used:     4.00     0.00    15.00     2.50    65.00     4.50     7.50 [ O N]
##### 2 non-Watson-Crick base-pairs, and 1 helix (0 isolated bps)
##### Helix #1 (12): 1 - 12

Note that you need to use the current version of 3DNA v2.1 from the download page. For your reference, attached below are the two PDB files RNA-WC-duplex.pdb and RNA-ok-duplex.pdb mentioned above.
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline GuidoLeoni

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Re: Can 3DNA be used to build a miRNA-target structure?
« Reply #5 on: November 22, 2012, 06:56:09 am »
Thank for your tips.
Your solution is the most practical to solve my challenge considering that i don't need of precise and minimized structure as initial input for my docking calculations.
Best regards

 

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.