Nucleic Acid Analysis - Experimental vs MD Analysis
Helical Base Pair Steps
[Image courtesy of Neidle, S. (2007). Principles of nucleic acid structure.] |
[Image courtesy of Neidle, S. (2007). Principles of nucleic acid structure.] 
[Image courtesy of Neidle, S. (2007). Principles of nucleic acid structure.] |
MD BI/BII Population
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Experimental BI/BII Population
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MD Puckering
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Experimental Puckering
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AT 
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CG 
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GC 
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TA 
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AT 
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CG 
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GC 
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TA 
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AT 
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CG 
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GC 
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TA 
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AT 
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CG 
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GC 
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TA 
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AT 
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CG 
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GC 
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TA 
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AT 
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CG 
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GC 
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TA 
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AT 
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CG 
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GC 
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TA 
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AT 
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CG 
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GC 
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TA 
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AC 
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GT 
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TA 
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AC 
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GT 
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TA 
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AC 
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GT 
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TA 
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AC 
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GT 
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TA 
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AC 
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GT 
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TA 
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AC 
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GT 
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TA 
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| Mean | Stdev | |
| inclin-2-GC | 2.980 | 9.909 |
| Mean | Stdev | |
| tip-2-GC | 1.193 | 9.340 |
| Mean | Stdev | |
| xdisp-2-GC | 0.483 | 1.178 |
| Mean | Stdev | |
| ydisp-2-GC | 0.097 | 1.115 |
| Mean | Stdev | |
| inclin-3-TA | 1.925 | 7.698 |
| Mean | Stdev | |
| tip-3-TA | 1.026 | 9.458 |
| Mean | Stdev | |
| xdisp-3-TA | -0.208 | 1.260 |
| Mean | Stdev | |
| ydisp-3-TA | -0.260 | 1.082 |
| Mean | Stdev | |
| inclin-4-AT | 0.535 | 7.151 |
| Mean | Stdev | |
| tip-4-AT | -2.646 | 8.409 |
| Mean | Stdev | |
| xdisp-4-AT | -0.274 | 1.389 |
| Mean | Stdev | |
| ydisp-4-AT | 0.175 | 1.023 |
| Mean | Stdev | |
| inclin-5-CG | 0.848 | 8.073 |
| Mean | Stdev | |
| tip-5-CG | -2.701 | 6.729 |
| Mean | Stdev | |
| xdisp-5-CG | 0.622 | 1.341 |
| Mean | Stdev | |
| ydisp-5-CG | -0.063 | 1.108 |
| Mean | Stdev | |
| alpha-1-C | 0.000 | 0.000 |
| Mean | Stdev | |
| beta-1-C | 0.000 | 0.000 |
| Mean | Stdev | |
| chi-1-C | 221.497 | 14.909 |
| Mean | Stdev | |
| diff-1-C | -56.392 | 41.203 |
| Mean | Stdev | |
| epsil-1-C | 223.474 | 20.994 |
| Mean | Stdev | |
| gamma-1-C | 117.271 | 97.074 |
| Mean | Stdev | |
| phase-1-C | 158.066 | 20.327 |
| Mean | Stdev | |
| zeta-1-C | 279.866 | 33.164 |
| Mean | Stdev | |
| alpha-10-A | 287.531 | 17.560 |
| Mean | Stdev | |
| beta-10-A | 170.582 | 16.945 |
| Mean | Stdev | |
| chi-10-A | 249.905 | 13.120 |
| Mean | Stdev | |
| diff-10-A | -72.586 | 34.312 |
| Mean | Stdev | |
| epsil-10-A | 194.424 | 14.601 |
| Mean | Stdev | |
| gamma-10-A | 56.354 | 13.658 |
| Mean | Stdev | |
| phase-10-A | 162.699 | 32.183 |
| Mean | Stdev | |
| zeta-10-A | 267.011 | 22.523 |
| Mean | Stdev | |
| alpha-11-C | 287.152 | 10.677 |
| Mean | Stdev | |
| beta-11-C | 166.491 | 11.236 |
| Mean | Stdev | |
| chi-11-C | 261.067 | 12.577 |
| Mean | Stdev | |
| diff-11-C | -6.419 | 63.760 |
| Mean | Stdev | |
| epsil-11-C | 233.025 | 19.705 |
| Mean | Stdev | |
| gamma-11-C | 53.824 | 9.241 |
| Mean | Stdev | |
| phase-11-C | 144.988 | 12.252 |
| Mean | Stdev | |
| zeta-11-C | 239.444 | 54.878 |
| Mean | Stdev | |
| alpha-12-G | 262.191 | 73.487 |
| Mean | Stdev | |
| beta-12-G | 187.034 | 30.672 |
| Mean | Stdev | |
| chi-12-G | 212.429 | 55.086 |
| Mean | Stdev | |
| diff-12-G | 0.000 | 0.000 |
| Mean | Stdev | |
| epsil-12-G | 0.000 | 0.000 |
| Mean | Stdev | |
| gamma-12-G | 218.018 | 115.925 |
| Mean | Stdev | |
| phase-12-G | 173.886 | 28.310 |
| Mean | Stdev | |
| zeta-12-G | 0.000 | 0.000 |
| Mean | Stdev | |
| alpha-2-G | 286.955 | 17.740 |
| Mean | Stdev | |
| beta-2-G | 172.405 | 14.028 |
| Mean | Stdev | |
| chi-2-G | 252.798 | 14.094 |
| Mean | Stdev | |
| diff-2-G | -34.325 | 79.047 |
| Mean | Stdev | |
| epsil-2-G | 200.479 | 32.172 |
| Mean | Stdev | |
| gamma-2-G | 57.350 | 16.730 |
| Mean | Stdev | |
| phase-2-G | 165.525 | 19.938 |
| Mean | Stdev | |
| zeta-2-G | 234.803 | 48.104 |
| Mean | Stdev | |
| alpha-3-T | 290.783 | 11.384 |
| Mean | Stdev | |
| beta-3-T | 169.191 | 18.920 |
| Mean | Stdev | |
| chi-3-T | 250.691 | 13.167 |
| Mean | Stdev | |
| diff-3-T | -24.382 | 64.993 |
| Mean | Stdev | |
| epsil-3-T | 204.064 | 28.952 |
| Mean | Stdev | |
| gamma-3-T | 53.405 | 9.889 |
| Mean | Stdev | |
| phase-3-T | 155.916 | 16.474 |
| Mean | Stdev | |
| zeta-3-T | 228.446 | 37.932 |
| Mean | Stdev | |
| alpha-4-A | 284.506 | 29.814 |
| Mean | Stdev | |
| beta-4-A | 167.885 | 21.596 |
| Mean | Stdev | |
| chi-4-A | 248.642 | 13.420 |
| Mean | Stdev | |
| diff-4-A | -73.994 | 29.951 |
| Mean | Stdev | |
| epsil-4-A | 195.092 | 13.521 |
| Mean | Stdev | |
| gamma-4-A | 59.668 | 26.120 |
| Mean | Stdev | |
| phase-4-A | 163.954 | 29.411 |
| Mean | Stdev | |
| zeta-4-A | 269.086 | 19.931 |
| Mean | Stdev | |
| alpha-5-C | 284.694 | 18.091 |
| Mean | Stdev | |
| beta-5-C | 165.958 | 15.602 |
| Mean | Stdev | |
| chi-5-C | 262.552 | 14.211 |
| Mean | Stdev | |
| diff-5-C | 36.545 | 59.097 |
| Mean | Stdev | |
| epsil-5-C | 235.226 | 22.871 |
| Mean | Stdev | |
| gamma-5-C | 55.225 | 19.010 |
| Mean | Stdev | |
| phase-5-C | 144.964 | 13.517 |
| Mean | Stdev | |
| zeta-5-C | 198.682 | 43.607 |
| Mean | Stdev | |
| alpha-6-G | 251.818 | 83.810 |
| Mean | Stdev | |
| beta-6-G | 184.231 | 30.183 |
| Mean | Stdev | |
| chi-6-G | 257.453 | 28.343 |
| Mean | Stdev | |
| diff-6-G | 0.000 | 0.000 |
| Mean | Stdev | |
| epsil-6-G | 0.000 | 0.000 |
| Mean | Stdev | |
| gamma-6-G | 127.047 | 110.416 |
| Mean | Stdev | |
| phase-6-G | 180.419 | 38.529 |
| Mean | Stdev | |
| zeta-6-G | 0.000 | 0.000 |
| Mean | Stdev | |
| alpha-7-C | 0.000 | 0.000 |
| Mean | Stdev | |
| beta-7-C | 0.000 | 0.000 |
| Mean | Stdev | |
| chi-7-C | 220.677 | 16.361 |
| Mean | Stdev | |
| diff-7-C | -50.055 | 28.326 |
| Mean | Stdev | |
| epsil-7-C | 234.209 | 21.649 |
| Mean | Stdev | |
| gamma-7-C | 130.286 | 102.938 |
| Mean | Stdev | |
| phase-7-C | 158.602 | 26.769 |
| Mean | Stdev | |
| zeta-7-C | 284.263 | 16.665 |
| Mean | Stdev | |
| alpha-8-G | 284.461 | 17.843 |
| Mean | Stdev | |
| beta-8-G | 168.552 | 15.362 |
| Mean | Stdev | |
| chi-8-G | 258.541 | 15.346 |
| Mean | Stdev | |
| diff-8-G | 8.498 | 90.926 |
| Mean | Stdev | |
| epsil-8-G | 216.638 | 37.600 |
| Mean | Stdev | |
| gamma-8-G | 54.198 | 17.274 |
| Mean | Stdev | |
| phase-8-G | 157.512 | 20.071 |
| Mean | Stdev | |
| zeta-8-G | 208.140 | 54.593 |
| Mean | Stdev | |
| alpha-9-T | 288.702 | 18.860 |
| Mean | Stdev | |
| beta-9-T | 160.795 | 21.916 |
| Mean | Stdev | |
| chi-9-T | 247.084 | 14.105 |
| Mean | Stdev | |
| diff-9-T | -33.648 | 60.275 |
| Mean | Stdev | |
| epsil-9-T | 200.839 | 26.341 |
| Mean | Stdev | |
| gamma-9-T | 53.933 | 15.966 |
| Mean | Stdev | |
| phase-9-T | 155.306 | 21.195 |
| Mean | Stdev | |
| zeta-9-T | 234.488 | 35.895 |
| Mean | Stdev | |
| majd-2-GTAC | 0.000 | 0.000 |
| Mean | Stdev | |
| majw-2-GTAC | 0.000 | 0.000 |
| Mean | Stdev | |
| mind-2-GTAC | 0.000 | 0.000 |
| Mean | Stdev | |
| minw-2-GTAC | 0.000 | 0.000 |
| Mean | Stdev | |
| majd-3-TATA | 0.188 | 1.250 |
| Mean | Stdev | |
| majw-3-TATA | 12.762 | 1.133 |
| Mean | Stdev | |
| mind-3-TATA | 4.521 | 0.568 |
| Mean | Stdev | |
| minw-3-TATA | 6.736 | 1.038 |
| Mean | Stdev | |
| majd-4-ACGT | -0.336 | 1.790 |
| Mean | Stdev | |
| majw-4-ACGT | 12.555 | 1.624 |
| Mean | Stdev | |
| mind-4-ACGT | 4.491 | 0.558 |
| Mean | Stdev | |
| minw-4-ACGT | 6.779 | 1.004 |
| Mean | Stdev | |
| buckle-2-GC | -13.912 | 8.463 |
| Mean | Stdev | |
| opening-2-GC | 3.085 | 3.639 |
| Mean | Stdev | |
| propel-2-GC | 2.878 | 8.165 |
| Mean | Stdev | |
| shear-2-GC | -0.246 | 0.325 |
| Mean | Stdev | |
| stagger-2-GC | -0.080 | 0.352 |
| Mean | Stdev | |
| stretch-2-GC | 0.036 | 0.128 |
| Mean | Stdev | |
| buckle-3-TA | -1.210 | 8.925 |
| Mean | Stdev | |
| opening-3-TA | 1.801 | 5.189 |
| Mean | Stdev | |
| propel-3-TA | -4.660 | 7.424 |
| Mean | Stdev | |
| shear-3-TA | -0.224 | 0.281 |
| Mean | Stdev | |
| stagger-3-TA | 0.219 | 0.349 |
| Mean | Stdev | |
| stretch-3-TA | 0.032 | 0.118 |
| Mean | Stdev | |
| buckle-4-AT | 1.324 | 8.922 |
| Mean | Stdev | |
| opening-4-AT | 1.588 | 5.372 |
| Mean | Stdev | |
| propel-4-AT | -5.193 | 7.477 |
| Mean | Stdev | |
| shear-4-AT | 0.263 | 0.285 |
| Mean | Stdev | |
| stagger-4-AT | 0.244 | 0.350 |
| Mean | Stdev | |
| stretch-4-AT | 0.038 | 0.120 |
| Mean | Stdev | |
| buckle-5-CG | 14.493 | 8.334 |
| Mean | Stdev | |
| opening-5-CG | 3.046 | 3.649 |
| Mean | Stdev | |
| propel-5-CG | 4.287 | 8.298 |
| Mean | Stdev | |
| shear-5-CG | 0.206 | 0.316 |
| Mean | Stdev | |
| stagger-5-CG | -0.140 | 0.366 |
| Mean | Stdev | |
| stretch-5-CG | 0.042 | 0.129 |
| Mean | Stdev | |
| rise-2-GTAC | 3.124 | 0.258 |
| Mean | Stdev | |
| roll-2-GTAC | 1.572 | 4.476 |
| Mean | Stdev | |
| shift-2-GTAC | -0.695 | 0.583 |
| Mean | Stdev | |
| slide-2-GTAC | -0.341 | 0.384 |
| Mean | Stdev | |
| tilt-2-GTAC | -1.542 | 3.626 |
| Mean | Stdev | |
| twist-2-GTAC | 27.322 | 4.300 |
| Mean | Stdev | |
| rise-3-TATA | 3.227 | 0.256 |
| Mean | Stdev | |
| roll-3-TATA | -2.172 | 6.855 |
| Mean | Stdev | |
| shift-3-TATA | -0.030 | 0.822 |
| Mean | Stdev | |
| slide-3-TATA | 0.186 | 0.566 |
| Mean | Stdev | |
| tilt-3-TATA | -0.372 | 4.639 |
| Mean | Stdev | |
| twist-3-TATA | 42.803 | 4.984 |
| Mean | Stdev | |
| rise-4-ACGT | 3.122 | 0.262 |
| Mean | Stdev | |
| roll-4-ACGT | 0.419 | 4.771 |
| Mean | Stdev | |
| shift-4-ACGT | 0.870 | 0.592 |
| Mean | Stdev | |
| slide-4-ACGT | -0.267 | 0.395 |
| Mean | Stdev | |
| tilt-4-ACGT | 2.223 | 3.662 |
| Mean | Stdev | |
| twist-4-ACGT | 27.947 | 4.339 |
