Effect of reversing strands of a DNA duplex on 3DNA calculated parameters

From a pure structural perspective, the designation of the two strands in an anti-parallel DNA duplex is sort of arbitrary. Thus, for a given PDB file, let’s assume that the atomic coordinates of chain A (strand I) come before those of chain B (strand II). We can swap the order of the two chains as they appear in the PDB file, i.e., list first the atomic coordinates of chain B and then those of chain A.

Structurally, the two settings corresponding to exactly the same DNA molecule. As far as 3DNA goes, however, the different orderings do make a different in calculated parameters. Using the Dickerson B-DNA dodecamer CGCGAATTCGCG solved at high resolution (PDB entry 355d) as an example, running 3DNA find_pair and analyze on ‘355d.pdb’ gives the results (abbreviated) below:

find_pair 355d.pdb 355d.bps
    # contents of file '355d.bps':
------------------------------------------------------------------
355d.pdb
355d.out
    2         # duplex
   12         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   24  0 #    1 | ....>A:...1_:[.DC]C-----G[.DG]:..24_:B<....
    2   23  0 #    2 | ....>A:...2_:[.DG]G-----C[.DC]:..23_:B<....
    3   22  0 #    3 | ....>A:...3_:[.DC]C-----G[.DG]:..22_:B<....
    4   21  0 #    4 | ....>A:...4_:[.DG]G-----C[.DC]:..21_:B<....
    5   20  0 #    5 | ....>A:...5_:[.DA]A-----T[.DT]:..20_:B<....
    6   19  0 #    6 | ....>A:...6_:[.DA]A-----T[.DT]:..19_:B<....
    7   18  0 #    7 | ....>A:...7_:[.DT]T-----A[.DA]:..18_:B<....
    8   17  0 #    8 | ....>A:...8_:[.DT]T-----A[.DA]:..17_:B<....
    9   16  0 #    9 | ....>A:...9_:[.DC]C-----G[.DG]:..16_:B<....
   10   15  0 #   10 | ....>A:..10_:[.DG]G-----C[.DC]:..15_:B<....
   11   14  0 #   11 | ....>A:..11_:[.DC]C-----G[.DG]:..14_:B<....
   12   13  0 #   12 | ....>A:..12_:[.DG]G-----C[.DC]:..13_:B<....
------------------------------------------------------------------

analyze 355d.bps
    # generate output file '355d.out', with base-pair step parameters:
****************************************************************************
    step       Shift     Slide      Rise      Tilt      Roll     Twist
   1 CG/CG      0.09      0.04      3.20     -3.22      8.52     32.73
   2 GC/GC      0.50      0.67      3.69      2.85     -9.06     43.88
   3 CG/CG     -0.14      0.59      3.00      0.97     11.30     25.11
   4 GA/TC     -0.45     -0.14      3.39     -1.59      1.37     37.50
   5 AA/TT      0.17     -0.33      3.30     -0.33      0.46     37.52
   6 AT/AT     -0.01     -0.60      3.22     -0.31     -2.67     32.40
   7 TT/AA     -0.08     -0.40      3.22      1.68     -0.97     33.74
   8 TC/GA     -0.27     -0.23      3.47      0.68     -1.69     42.14
   9 CG/CG      0.70      0.78      3.07     -3.66      4.18     26.58
  10 GC/GC     -1.31      0.36      3.37     -2.85     -9.37     41.60
  11 CG/CG     -0.31      0.21      3.17     -0.68      6.69     33.31
****************************************************************************

Reversing the order of chains A and B in ‘355d.pdb’ as ‘355d-reversed.pdb’ and repeating the above procedure, we have the following results:

find_pair 355d-reversed.pdb 355d-reversed.bps
    # contents of file '355d-reversed.bps':
------------------------------------------------------------------
355d-reversed.pdb
355d-reversed.out
    2         # duplex
   12         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
    1   24  0 #    1 | ....>B:..13_:[.DC]C-----G[.DG]:..12_:A<....
    2   23  0 #    2 | ....>B:..14_:[.DG]G-----C[.DC]:..11_:A<....
    3   22  0 #    3 | ....>B:..15_:[.DC]C-----G[.DG]:..10_:A<....
    4   21  0 #    4 | ....>B:..16_:[.DG]G-----C[.DC]:...9_:A<....
    5   20  0 #    5 | ....>B:..17_:[.DA]A-----T[.DT]:...8_:A<....
    6   19  0 #    6 | ....>B:..18_:[.DA]A-----T[.DT]:...7_:A<....
    7   18  0 #    7 | ....>B:..19_:[.DT]T-----A[.DA]:...6_:A<....
    8   17  0 #    8 | ....>B:..20_:[.DT]T-----A[.DA]:...5_:A<....
    9   16  0 #    9 | ....>B:..21_:[.DC]C-----G[.DG]:...4_:A<....
   10   15  0 #   10 | ....>B:..22_:[.DG]G-----C[.DC]:...3_:A<....
   11   14  0 #   11 | ....>B:..23_:[.DC]C-----G[.DG]:...2_:A<....
   12   13  0 #   12 | ....>B:..24_:[.DG]G-----C[.DC]:...1_:A<....
------------------------------------------------------------------

analyze 355d-reversed.bps
    # generate output file '355d-reversed.out', with base-pair step parameters:
****************************************************************************
    step       Shift     Slide      Rise      Tilt      Roll     Twist
   1 CG/CG      0.31      0.21      3.17      0.68      6.69     33.31
   2 GC/GC      1.31      0.36      3.37      2.85     -9.37     41.60
   3 CG/CG     -0.70      0.78      3.07      3.66      4.18     26.58
   4 GA/TC      0.27     -0.23      3.47     -0.68     -1.69     42.14
   5 AA/TT      0.08     -0.40      3.22     -1.68     -0.97     33.74
   6 AT/AT      0.01     -0.60      3.22      0.31     -2.67     32.40
   7 TT/AA     -0.17     -0.33      3.30      0.33      0.46     37.52
   8 TC/GA      0.45     -0.14      3.39      1.59      1.37     37.50
   9 CG/CG      0.14      0.59      3.00     -0.97     11.30     25.11
  10 GC/GC     -0.50      0.67      3.69     -2.85     -9.06     43.88
  11 CG/CG     -0.09      0.04      3.20      3.22      8.52     32.73
****************************************************************************

Comparing the base-pair step parameters between ‘355d.out’ and ’355d-reversed.out’, one would notice that while slide/rise/roll/twist simply switch orders, shift/tilt (the x-axis parameters) also flip their signs. On the other hand, the nucleotide serial numbers specifying base pairs (the left two columns) are identical in ‘355d.bps’ and ’355d-reversed.bps’.

Apart from explicitly swapping the two strands in PDB data file, one can simply switch around the nucleotide serial numbers generated with find_pair in order to analyze a DNA duplex based on its complementary sequence instead of the primary one. For example, starting from the same PDB file ‘355d.pdb’, we change ‘355d.bps’ to ’355d-cs.bps’ as below,

------------------------------------------------------------------
355d.pdb
355d-cs.out
    2         # duplex
   12         # number of base-pairs
    1    1    # explicit bp numbering/hetero atoms
   13   12
   14   11
   15   10
   16    9
   17    8
   18    7
   19    6
   20    5
   21    4
   22    3
   23    2
   24    1
------------------------------------------------------------------

Run analyze 355d-cs.bps, one would get exactly the same parameters in output file ’355d-cs.out’ as in ’355d-reversed.out’.

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