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Questions and answers => General discussions (Q&As) => Topic started by: shengxiehuang on May 10, 2016, 09:35:45 pm

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Title: how to analyze base-stacking interactions with 3dna
Post by: shengxiehuang on May 10, 2016, 09:35:45 pm
Dear Xiang-jun,

      You said that base-stacking interaction could be analyzed with 3dna software (http://x3dna.org/citations/quantification-of-base-stacking-interactions-using-overlap-area). Could you show me how to do it, or which files?

      Best Wishes!

Xiehuang Sheng

-----------------
Shandong Normal University, Shandong, China
Title: Re: how to analyze base-stacking interactions with 3dna
Post by: xiangjun on May 10, 2016, 09:52:18 pm
Hi Xiehuang,

If you try 3DNA on the classic B-DNA dodecamer 355d (http://www.rcsb.org/pdb/explore/explore.do?structureId=355d) as an example,

Code: [Select]
find_pair 355d.pdb | analyze
you will get an output file named 355d.out, which contains the following section:

Code: [Select]
****************************************************************************
Overlap area in Angstrom^2 between polygons defined by atoms on successive
bases. Polygons projected in the mean plane of the designed base-pair step.

Values in parentheses measure the overlap of base ring atoms only. Those
outside parentheses include exocyclic atoms on the ring. Intra- and
inter-strand overlap is designated according to the following diagram:

                    i2  3'      5' j2
                       /|\      |
                        |       |
               Strand I |       | II
                        |       |
                        |       |
                        |      \|/
                    i1  5'      3' j1

     step      i1-i2        i1-j2        j1-i2        j1-j2        sum
   1 CG/CG  1.48( 0.00)  0.00( 0.00)  0.97( 0.00)  0.94( 0.00)  3.39( 0.00)
   2 GC/GC  2.95( 0.63)  0.00( 0.00)  0.00( 0.00)  0.96( 0.04)  3.91( 0.68)
   3 CG/CG  2.66( 0.00)  0.00( 0.00)  0.15( 0.00)  3.44( 0.21)  6.25( 0.21)
   4 GA/TC  3.94( 1.11)  0.00( 0.00)  0.00( 0.00)  4.17( 0.78)  8.11( 1.88)
   5 AA/TT  3.51( 2.16)  0.00( 0.00)  0.00( 0.00)  5.09( 0.08)  8.60( 2.24)
   6 AT/AT  5.91( 2.14)  0.00( 0.00)  0.00( 0.00)  5.65( 1.89) 11.56( 4.03)
   7 TT/AA  5.08( 0.11)  0.00( 0.00)  0.00( 0.00)  3.68( 2.39)  8.76( 2.51)
   8 TC/GA  2.20( 0.00)  0.00( 0.00)  0.00( 0.00)  4.98( 2.19)  7.18( 2.19)
   9 CG/CG  5.50( 1.17)  0.00( 0.00)  0.01( 0.00)  1.56( 0.00)  7.06( 1.17)
  10 GC/GC  0.57( 0.00)  0.00( 0.00)  0.00( 0.00)  5.32( 2.35)  5.89( 2.35)
  11 CG/CG  0.73( 0.00)  0.00( 0.00)  0.54( 0.00)  1.98( 0.03)  3.25( 0.03)
Alternatively, you may give DSSR a try. See the DSSR manual (http://x3dna.bio.columbia.edu/docs/dssr-manual.pdf) for details.

Xiang-Jun
Title: Re: how to analyze base-stacking interactions with 3dna
Post by: shengxiehuang on May 11, 2016, 08:28:14 am
 Dear Xiangjun,
         
Thanks a lot for you reply. I am understand how to do it .

Best Wishes!

xeihuang sheng
----------------------

Shandong Normal University, Shandong,China

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