# 3DNA Forum

## Questions and answers => General discussions (Q&As) => Topic started by: deligkaris on November 01, 2016, 02:07:17 pm

Title: intra base pair and inter base pair step parameters
Post by: deligkaris on November 01, 2016, 02:07:17 pm
dear 3dna community,

If I have the AT intra base pair parameters (shear, stretch, stagger, etc), will these parameters be exactly the same for a TA base pair, or will they have the opposite sign? (the absolute values will be the same but I am not sure about the sign).

Similarly, if I have the AA base pair step parameters (shift, slide, rise etc) will these parameters be exactly the same for a TT base pair step, or will their values have the opposite sign?

Thank you,
Title: Re: intra base pair and inter base pair step parameters
Post by: xiangjun on November 01, 2016, 02:26:39 pm
Thanks for posting your questions on the 3DNA Forum.

The specific points you raised have been mentioned in the initial 2003 3DNA NAR paper (http://nar.oxfordjournals.org/content/31/17/5108.full), and more recently in the 2015 DSSR NAR paper (http://nar.oxfordjournals.org/content/43/21/e142.full)).

Quote
If I have the AT intra base pair parameters (shear, stretch, stagger, etc), will these parameters be exactly the same for a TA base pair, or will they have the opposite sign? (the absolute values will be the same but I am not sure about the sign).

See the section titled "Base pair parameters" in the 2003 3DNA NAR paper (http://nar.oxfordjournals.org/content/31/17/5108.full).

Quote
"To calculate the six complementary base pair parameters of an M–N pair (Shear, Stretch, Stagger, Buckle, Propeller and Opening), where the two z‐axes run in opposite directions, the reference frame of the complementary base N is rotated about the x2‐axis by 180°, i.e. reversing the y2‐ and z2‐axes in Figure 2a. Under this convention, if the base pair is reckoned as an N–M pair, rather than an M–N pair, the x‐axis parameters (Shear and Buckle) reverse their signs. For an M+N pair, e.g. the Hoogsteen A+U in Figure 2b, the x2‐, y2‐ and z2‐axes do not change sign; thus all six parameters for an N+M pair are of opposite sign from those for an M+N pair."

Quote
Similarly, if I have the AA base pair step parameters (shift, slide, rise etc) will these parameters be exactly the same for a TT base pair step, or will their values have the opposite sign?

Similar to above. Shift/Tilt change signs while the other four parameters remain the same.

You could easily verify the results yourself by analyzing a DNA duplex (e.g., 355d) by swapping its two strands in the input PDB file. It helps if you do this exercise and post back your findings.

HTH,

Xiang-Jun

Title: Re: intra base pair and inter base pair step parameters
Post by: deligkaris on November 09, 2016, 12:33:59 pm
Thank you.

The parameters that change sign are: shear, buckle, shift, tilt.

I switched helices in 355D. Here is the comparison:

1   12 # base-pairs ORIGINAL
2    0 # ***local base-pair & step parameters***
3 #        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     Shift     Slide     Rise      Tilt      Roll      Twist
4 C-G      0.276    -0.140     0.073     6.930   -17.308    -0.606     0.000     0.000     0.000     0.000     0.000     0.000
5 G-C     -0.236    -0.182     0.491     9.341   -14.302    -2.077     0.087     0.039     3.200    -3.216     8.520    32.731
6 C-G      0.244    -0.171     0.159    -4.433    -5.405     0.434     0.496     0.668     3.691     2.847    -9.055    43.879
7 G-C     -0.255    -0.115     0.008    10.806    -9.449     1.012    -0.138     0.593     3.000     0.967    11.300    25.114
8 A-T     -0.037    -0.107     0.011     4.724   -15.314     1.601    -0.453    -0.139     3.388    -1.585     1.373    37.500
9 A-T      0.051    -0.050     0.065     0.442   -15.001     6.233     0.171    -0.325     3.298    -0.330     0.459    37.520
10 T-A     -0.037    -0.117     0.173    -0.264   -16.744     3.928    -0.011    -0.601     3.219    -0.311    -2.675    32.403
11 T-A     -0.108    -0.120    -0.004    -1.561   -16.364     5.120    -0.082    -0.397     3.216     1.681    -0.974    33.744
12 C-G      0.209    -0.127     0.003   -12.410   -10.274    -1.223    -0.267    -0.226     3.465     0.684    -1.686    42.136
13 G-C     -0.106    -0.053     0.239     4.205    -9.603     3.206     0.700     0.776     3.068    -3.656     4.180    26.581
14 C-G      0.156    -0.130     0.208     0.283   -17.417    -1.755    -1.311     0.360     3.371    -2.853    -9.368    41.601
15 G-C     -0.244    -0.069     0.254     4.671    -4.954    -1.620    -0.309     0.211     3.174    -0.679     6.692    33.310
16
17
18
19
20
21
22
23
24   12 # base-pairs SWITCHED
25    0 # ***local base-pair & step parameters***
26 #        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     Shift     Slide     Rise      Tilt      Roll      Twist
27 C-G      0.244    -0.069     0.254    -4.671    -4.954    -1.620     0.000     0.000     0.000     0.000     0.000     0.000
28 G-C     -0.156    -0.130     0.208    -0.283   -17.417    -1.755     0.309     0.211     3.174     0.679     6.692    33.310
29 C-G      0.106    -0.053     0.239    -4.205    -9.603     3.206     1.311     0.360     3.371     2.853    -9.368    41.601
30 G-C     -0.209    -0.127     0.003    12.410   -10.274    -1.223    -0.700     0.776     3.068     3.656     4.180    26.581
31 A-T      0.108    -0.120    -0.004     1.561   -16.364     5.120     0.267    -0.226     3.465    -0.684    -1.686    42.136
32 A-T      0.037    -0.117     0.173     0.264   -16.744     3.928     0.082    -0.397     3.216    -1.681    -0.974    33.744
33 T-A     -0.051    -0.050     0.065    -0.442   -15.001     6.233     0.011    -0.601     3.219     0.311    -2.675    32.403
34 T-A      0.037    -0.107     0.011    -4.724   -15.314     1.601    -0.171    -0.325     3.298     0.330     0.459    37.520
35 C-G      0.255    -0.115     0.008   -10.806    -9.449     1.012     0.453    -0.139     3.388     1.585     1.373    37.500
36 G-C     -0.244    -0.171     0.159     4.433    -5.405     0.434     0.138     0.593     3.000    -0.967    11.300    25.114
37 C-G      0.236    -0.182     0.491    -9.341   -14.302    -2.077    -0.496     0.668     3.691    -2.847    -9.055    43.879
38 G-C     -0.276    -0.140     0.073    -6.930   -17.308    -0.606    -0.087     0.039     3.200     3.216     8.520    32.731

Thank you Xiang-Jun.
Title: Re: intra base pair and inter base pair step parameters
Post by: xiangjun on November 10, 2016, 11:29:10 am
Thanks for posting back your worked example on 355d (http://www.rcsb.org/pdb/explore/explore.do?structureId=355d) regarding signs of 3DNA-derived base-pair parameters. Just for the record, I wrote a blogpost titled "Effect of reversing strands of a DNA duplex on 3DNA calculated parameters (http://x3dna.org/articles/effect-of-reversing-strands-of-a-dna-duplex-on-3dna-calculated-parameters)" dated 2012-08-02.

Best regards,

Xiang-Jun

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.