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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,
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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)).
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).
"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."
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
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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.
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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
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