Nucleic Acid Analysis - Experimental vs MD Analysis
Helical Base Pair Steps
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | |||||||||
| 5' | C | - | C | - | C | - | C | - | G | - | G | - | G | - | G | 3' |
| | | x | | | x | | | x | | | x | | | x | | | ||||||
| 3' | G | - | G | - | G | - | G | - | C | - | C | - | C | - | C | 5' |
| 16 | 15 | 14 | 13 | 12 | 11 | 10 | 9 |
[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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CG
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GC
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CG
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GC
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CG
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GC
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CG
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GC
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CG
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GC
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CG
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GC
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CG
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GC
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CG
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GC
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CC
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CG
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GG
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CC
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CG
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GG
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CC
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CG
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GG
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CC
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CG
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GG
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CC
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CG
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GG
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CC
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CG
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GG
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| Mean | Stdev | |
| inclin-2-CG | 3.536 | 9.271 |
| Mean | Stdev | |
| tip-2-CG | -18.773 | 56.186 |
| Mean | Stdev | |
| xdisp-2-CG | -1.094 | 1.241 |
| Mean | Stdev | |
| ydisp-2-CG | 0.013 | 0.698 |
| Mean | Stdev | |
| inclin-3-CG | 6.984 | 5.944 |
| Mean | Stdev | |
| tip-3-CG | 0.237 | 4.761 |
| Mean | Stdev | |
| xdisp-3-CG | -1.206 | 1.068 |
| Mean | Stdev | |
| ydisp-3-CG | -0.501 | 0.671 |
| Mean | Stdev | |
| inclin-4-CG | 5.325 | 5.774 |
| Mean | Stdev | |
| tip-4-CG | -2.359 | 4.855 |
| Mean | Stdev | |
| xdisp-4-CG | -1.673 | 0.981 |
| Mean | Stdev | |
| ydisp-4-CG | -0.425 | 0.697 |
| Mean | Stdev | |
| inclin-5-GC | 6.228 | 5.304 |
| Mean | Stdev | |
| tip-5-GC | -0.143 | 4.687 |
| Mean | Stdev | |
| xdisp-5-GC | -1.431 | 1.082 |
| Mean | Stdev | |
| ydisp-5-GC | 0.067 | 0.607 |
| Mean | Stdev | |
| inclin-6-GC | 4.921 | 5.318 |
| Mean | Stdev | |
| tip-6-GC | -1.566 | 4.458 |
| Mean | Stdev | |
| xdisp-6-GC | -1.482 | 0.857 |
| Mean | Stdev | |
| ydisp-6-GC | -0.359 | 0.740 |
| Mean | Stdev | |
| inclin-7-GC | 6.630 | 5.758 |
| Mean | Stdev | |
| tip-7-GC | -1.542 | 4.606 |
| Mean | Stdev | |
| xdisp-7-GC | -1.993 | 1.101 |
| Mean | Stdev | |
| ydisp-7-GC | -0.613 | 0.748 |
| Mean | Stdev | |
| alpha-1-C | 0.000 | 0.000 |
| Mean | Stdev | |
| beta-1-C | 0.000 | 0.000 |
| Mean | Stdev | |
| chi-1-C | 231.682 | 18.873 |
| Mean | Stdev | |
| diff-1-C | -53.487 | 62.566 |
| Mean | Stdev | |
| epsil-1-C | 200.682 | 20.347 |
| Mean | Stdev | |
| gamma-1-C | 108.248 | 91.161 |
| Mean | Stdev | |
| phase-1-C | 150.442 | 35.193 |
| Mean | Stdev | |
| zeta-1-C | 254.169 | 53.269 |
| Mean | Stdev | |
| alpha-10-C | 283.970 | 23.315 |
| Mean | Stdev | |
| beta-10-C | 175.920 | 13.804 |
| Mean | Stdev | |
| chi-10-C | 240.899 | 14.706 |
| Mean | Stdev | |
| diff-10-C | -63.311 | 45.555 |
| Mean | Stdev | |
| epsil-10-C | 191.451 | 19.411 |
| Mean | Stdev | |
| gamma-10-C | 56.430 | 18.284 |
| Mean | Stdev | |
| phase-10-C | 147.887 | 21.171 |
| Mean | Stdev | |
| zeta-10-C | 254.762 | 28.401 |
| Mean | Stdev | |
| alpha-11-C | 288.575 | 10.906 |
| Mean | Stdev | |
| beta-11-C | 177.023 | 14.985 |
| Mean | Stdev | |
| chi-11-C | 238.622 | 15.628 |
| Mean | Stdev | |
| diff-11-C | -62.568 | 46.622 |
| Mean | Stdev | |
| epsil-11-C | 196.325 | 19.296 |
| Mean | Stdev | |
| gamma-11-C | 53.677 | 10.560 |
| Mean | Stdev | |
| phase-11-C | 142.556 | 28.810 |
| Mean | Stdev | |
| zeta-11-C | 258.893 | 30.459 |
| Mean | Stdev | |
| alpha-12-C | 283.509 | 18.853 |
| Mean | Stdev | |
| beta-12-C | 167.096 | 29.783 |
| Mean | Stdev | |
| chi-12-C | 243.247 | 20.220 |
| Mean | Stdev | |
| diff-12-C | -21.882 | 69.894 |
| Mean | Stdev | |
| epsil-12-C | 213.975 | 25.725 |
| Mean | Stdev | |
| gamma-12-C | 60.762 | 33.736 |
| Mean | Stdev | |
| phase-12-C | 137.405 | 35.283 |
| Mean | Stdev | |
| zeta-12-C | 235.857 | 47.667 |
| Mean | Stdev | |
| alpha-13-G | 282.628 | 14.736 |
| Mean | Stdev | |
| beta-13-G | 163.830 | 14.347 |
| Mean | Stdev | |
| chi-13-G | 258.000 | 16.017 |
| Mean | Stdev | |
| diff-13-G | -16.195 | 77.764 |
| Mean | Stdev | |
| epsil-13-G | 211.099 | 30.743 |
| Mean | Stdev | |
| gamma-13-G | 52.159 | 11.960 |
| Mean | Stdev | |
| phase-13-G | 160.494 | 25.490 |
| Mean | Stdev | |
| zeta-13-G | 227.294 | 49.105 |
| Mean | Stdev | |
| alpha-14-G | 285.750 | 16.000 |
| Mean | Stdev | |
| beta-14-G | 162.002 | 16.992 |
| Mean | Stdev | |
| chi-14-G | 248.187 | 17.580 |
| Mean | Stdev | |
| diff-14-G | -36.745 | 68.351 |
| Mean | Stdev | |
| epsil-14-G | 201.574 | 27.874 |
| Mean | Stdev | |
| gamma-14-G | 52.476 | 14.014 |
| Mean | Stdev | |
| phase-14-G | 154.031 | 32.333 |
| Mean | Stdev | |
| zeta-14-G | 238.319 | 42.593 |
| Mean | Stdev | |
| alpha-15-G | 284.571 | 30.523 |
| Mean | Stdev | |
| beta-15-G | 168.744 | 19.615 |
| Mean | Stdev | |
| chi-15-G | 241.026 | 14.950 |
| Mean | Stdev | |
| diff-15-G | -71.824 | 40.558 |
| Mean | Stdev | |
| epsil-15-G | 188.307 | 18.215 |
| Mean | Stdev | |
| gamma-15-G | 57.235 | 27.773 |
| Mean | Stdev | |
| phase-15-G | 155.824 | 22.312 |
| Mean | Stdev | |
| zeta-15-G | 260.131 | 24.983 |
| Mean | Stdev | |
| alpha-16-G | 286.898 | 22.426 |
| Mean | Stdev | |
| beta-16-G | 179.234 | 15.400 |
| Mean | Stdev | |
| chi-16-G | 241.819 | 15.494 |
| Mean | Stdev | |
| diff-16-G | 0.000 | 0.000 |
| Mean | Stdev | |
| epsil-16-G | 0.000 | 0.000 |
| Mean | Stdev | |
| gamma-16-G | 53.569 | 22.602 |
| Mean | Stdev | |
| phase-16-G | 147.423 | 24.920 |
| Mean | Stdev | |
| zeta-16-G | 0.000 | 0.000 |
| Mean | Stdev | |
| alpha-2-C | 263.568 | 60.769 |
| Mean | Stdev | |
| beta-2-C | 177.489 | 14.266 |
| Mean | Stdev | |
| chi-2-C | 239.038 | 15.976 |
| Mean | Stdev | |
| diff-2-C | -65.910 | 42.434 |
| Mean | Stdev | |
| epsil-2-C | 193.010 | 18.055 |
| Mean | Stdev | |
| gamma-2-C | 57.971 | 24.768 |
| Mean | Stdev | |
| phase-2-C | 149.817 | 23.444 |
| Mean | Stdev | |
| zeta-2-C | 258.920 | 27.624 |
| Mean | Stdev | |
| alpha-3-C | 286.167 | 19.651 |
| Mean | Stdev | |
| beta-3-C | 174.862 | 15.215 |
| Mean | Stdev | |
| chi-3-C | 243.565 | 16.476 |
| Mean | Stdev | |
| diff-3-C | -36.415 | 68.936 |
| Mean | Stdev | |
| epsil-3-C | 203.064 | 27.933 |
| Mean | Stdev | |
| gamma-3-C | 54.666 | 18.355 |
| Mean | Stdev | |
| phase-3-C | 145.285 | 23.014 |
| Mean | Stdev | |
| zeta-3-C | 239.479 | 43.123 |
| Mean | Stdev | |
| alpha-4-C | 284.006 | 31.988 |
| Mean | Stdev | |
| beta-4-C | 166.330 | 26.524 |
| Mean | Stdev | |
| chi-4-C | 241.495 | 16.073 |
| Mean | Stdev | |
| diff-4-C | -64.842 | 42.866 |
| Mean | Stdev | |
| epsil-4-C | 198.983 | 17.301 |
| Mean | Stdev | |
| gamma-4-C | 61.890 | 35.577 |
| Mean | Stdev | |
| phase-4-C | 146.547 | 31.580 |
| Mean | Stdev | |
| zeta-4-C | 263.825 | 29.019 |
| Mean | Stdev | |
| alpha-5-G | 282.905 | 13.132 |
| Mean | Stdev | |
| beta-5-G | 169.969 | 11.711 |
| Mean | Stdev | |
| chi-5-G | 263.880 | 13.135 |
| Mean | Stdev | |
| diff-5-G | -31.811 | 71.885 |
| Mean | Stdev | |
| epsil-5-G | 211.371 | 25.911 |
| Mean | Stdev | |
| gamma-5-G | 50.844 | 10.122 |
| Mean | Stdev | |
| phase-5-G | 149.713 | 19.707 |
| Mean | Stdev | |
| zeta-5-G | 243.182 | 48.909 |
| Mean | Stdev | |
| alpha-6-G | 266.369 | 41.310 |
| Mean | Stdev | |
| beta-6-G | 108.771 | 52.274 |
| Mean | Stdev | |
| chi-6-G | 216.657 | 29.430 |
| Mean | Stdev | |
| diff-6-G | -68.880 | 38.495 |
| Mean | Stdev | |
| epsil-6-G | 203.300 | 17.886 |
| Mean | Stdev | |
| gamma-6-G | 125.963 | 62.485 |
| Mean | Stdev | |
| phase-6-G | 149.553 | 66.811 |
| Mean | Stdev | |
| zeta-6-G | 272.180 | 28.120 |
| Mean | Stdev | |
| alpha-7-G | 246.325 | 74.433 |
| Mean | Stdev | |
| beta-7-G | 175.652 | 13.542 |
| Mean | Stdev | |
| chi-7-G | 241.236 | 17.530 |
| Mean | Stdev | |
| diff-7-G | -66.234 | 44.876 |
| Mean | Stdev | |
| epsil-7-G | 191.645 | 19.624 |
| Mean | Stdev | |
| gamma-7-G | 82.538 | 54.443 |
| Mean | Stdev | |
| phase-7-G | 153.680 | 22.107 |
| Mean | Stdev | |
| zeta-7-G | 257.878 | 28.510 |
| Mean | Stdev | |
| alpha-8-G | 283.808 | 28.051 |
| Mean | Stdev | |
| beta-8-G | 167.563 | 38.069 |
| Mean | Stdev | |
| chi-8-G | 235.466 | 19.804 |
| Mean | Stdev | |
| diff-8-G | 0.000 | 0.000 |
| Mean | Stdev | |
| epsil-8-G | 0.000 | 0.000 |
| Mean | Stdev | |
| gamma-8-G | 67.438 | 47.710 |
| Mean | Stdev | |
| phase-8-G | 150.085 | 23.134 |
| Mean | Stdev | |
| zeta-8-G | 0.000 | 0.000 |
| Mean | Stdev | |
| alpha-9-C | 0.000 | 0.000 |
| Mean | Stdev | |
| beta-9-C | 0.000 | 0.000 |
| Mean | Stdev | |
| chi-9-C | 231.474 | 19.603 |
| Mean | Stdev | |
| diff-9-C | -67.329 | 37.940 |
| Mean | Stdev | |
| epsil-9-C | 196.700 | 16.657 |
| Mean | Stdev | |
| gamma-9-C | 109.027 | 91.690 |
| Mean | Stdev | |
| phase-9-C | 141.828 | 46.079 |
| Mean | Stdev | |
| zeta-9-C | 264.028 | 26.736 |
| Mean | Stdev | |
| majd-2-CCGG | 0.000 | 0.000 |
| Mean | Stdev | |
| majw-2-CCGG | 0.000 | 0.000 |
| Mean | Stdev | |
| mind-2-CCGG | 0.000 | 0.000 |
| Mean | Stdev | |
| minw-2-CCGG | 0.000 | 0.000 |
| Mean | Stdev | |
| majd-3-CCGG | 0.215 | 1.215 |
| Mean | Stdev | |
| majw-3-CCGG | 14.130 | 1.697 |
| Mean | Stdev | |
| mind-3-CCGG | 4.472 | 0.764 |
| Mean | Stdev | |
| minw-3-CCGG | 6.081 | 1.469 |
| Mean | Stdev | |
| majd-4-CGCG | 3.702 | 2.004 |
| Mean | Stdev | |
| majw-4-CGCG | 12.920 | 1.596 |
| Mean | Stdev | |
| mind-4-CGCG | 4.043 | 0.934 |
| Mean | Stdev | |
| minw-4-CGCG | 8.042 | 1.150 |
| Mean | Stdev | |
| majd-5-GGCC | 2.938 | 1.626 |
| Mean | Stdev | |
| majw-5-GGCC | 13.332 | 1.715 |
| Mean | Stdev | |
| mind-5-GGCC | 4.427 | 1.094 |
| Mean | Stdev | |
| minw-5-GGCC | 7.415 | 1.538 |
| Mean | Stdev | |
| majd-6-GGCC | -0.464 | 1.293 |
| Mean | Stdev | |
| majw-6-GGCC | 12.684 | 3.031 |
| Mean | Stdev | |
| mind-6-GGCC | 4.287 | 0.666 |
| Mean | Stdev | |
| minw-6-GGCC | 6.157 | 1.524 |
| Mean | Stdev | |
| buckle-2-CG | -2.157 | 12.274 |
| Mean | Stdev | |
| opening-2-CG | 1.453 | 3.508 |
| Mean | Stdev | |
| propel-2-CG | -8.491 | 9.490 |
| Mean | Stdev | |
| shear-2-CG | 0.028 | 0.317 |
| Mean | Stdev | |
| stagger-2-CG | -0.101 | 0.454 |
| Mean | Stdev | |
| stretch-2-CG | 0.013 | 0.117 |
| Mean | Stdev | |
| buckle-3-CG | -9.225 | 9.408 |
| Mean | Stdev | |
| opening-3-CG | 0.848 | 3.123 |
| Mean | Stdev | |
| propel-3-CG | -4.392 | 8.661 |
| Mean | Stdev | |
| shear-3-CG | -0.005 | 0.313 |
| Mean | Stdev | |
| stagger-3-CG | 0.041 | 0.405 |
| Mean | Stdev | |
| stretch-3-CG | 0.025 | 0.110 |
| Mean | Stdev | |
| buckle-4-CG | -9.609 | 9.103 |
| Mean | Stdev | |
| opening-4-CG | 1.197 | 3.253 |
| Mean | Stdev | |
| propel-4-CG | -2.599 | 8.513 |
| Mean | Stdev | |
| shear-4-CG | -0.062 | 0.310 |
| Mean | Stdev | |
| stagger-4-CG | 0.188 | 0.362 |
| Mean | Stdev | |
| stretch-4-CG | 0.041 | 0.108 |
| Mean | Stdev | |
| buckle-5-GC | 5.797 | 9.235 |
| Mean | Stdev | |
| opening-5-GC | 1.108 | 3.152 |
| Mean | Stdev | |
| propel-5-GC | 0.571 | 8.601 |
| Mean | Stdev | |
| shear-5-GC | 0.051 | 0.312 |
| Mean | Stdev | |
| stagger-5-GC | 0.066 | 0.398 |
| Mean | Stdev | |
| stretch-5-GC | 0.037 | 0.107 |
| Mean | Stdev | |
| buckle-6-GC | 6.305 | 9.132 |
| Mean | Stdev | |
| opening-6-GC | 0.659 | 3.278 |
| Mean | Stdev | |
| propel-6-GC | -6.866 | 8.528 |
| Mean | Stdev | |
| shear-6-GC | 0.008 | 0.325 |
| Mean | Stdev | |
| stagger-6-GC | 0.107 | 0.402 |
| Mean | Stdev | |
| stretch-6-GC | 0.022 | 0.114 |
| Mean | Stdev | |
| buckle-7-GC | -0.803 | 11.491 |
| Mean | Stdev | |
| opening-7-GC | 1.447 | 3.533 |
| Mean | Stdev | |
| propel-7-GC | -7.570 | 9.157 |
| Mean | Stdev | |
| shear-7-GC | -0.061 | 0.319 |
| Mean | Stdev | |
| stagger-7-GC | -0.203 | 0.432 |
| Mean | Stdev | |
| stretch-7-GC | -0.004 | 0.118 |
| Mean | Stdev | |
| rise-2-CCGG | 3.533 | 0.352 |
| Mean | Stdev | |
| roll-2-CCGG | 3.154 | 5.573 |
| Mean | Stdev | |
| shift-2-CCGG | 0.109 | 0.773 |
| Mean | Stdev | |
| slide-2-CCGG | -0.720 | 0.798 |
| Mean | Stdev | |
| tilt-2-CCGG | -0.116 | 4.652 |
| Mean | Stdev | |
| twist-2-CCGG | 34.082 | 4.727 |
| Mean | Stdev | |
| rise-3-CCGG | 3.403 | 0.293 |
| Mean | Stdev | |
| roll-3-CCGG | 1.221 | 5.866 |
| Mean | Stdev | |
| shift-3-CCGG | -0.109 | 1.003 |
| Mean | Stdev | |
| slide-3-CCGG | -0.263 | 0.718 |
| Mean | Stdev | |
| tilt-3-CCGG | -0.537 | 4.626 |
| Mean | Stdev | |
| twist-3-CCGG | 34.830 | 5.356 |
| Mean | Stdev | |
| rise-4-CGCG | 2.986 | 0.319 |
| Mean | Stdev | |
| roll-4-CGCG | 4.949 | 6.596 |
| Mean | Stdev | |
| shift-4-CGCG | 0.458 | 0.907 |
| Mean | Stdev | |
| slide-4-CGCG | 0.075 | 0.553 |
| Mean | Stdev | |
| tilt-4-CGCG | 1.762 | 5.364 |
| Mean | Stdev | |
| twist-4-CGCG | 30.812 | 7.390 |
| Mean | Stdev | |
| rise-5-GGCC | 3.388 | 0.312 |
| Mean | Stdev | |
| roll-5-GGCC | 1.058 | 6.077 |
| Mean | Stdev | |
| shift-5-GGCC | 0.209 | 1.005 |
| Mean | Stdev | |
| slide-5-GGCC | -0.707 | 0.816 |
| Mean | Stdev | |
| tilt-5-GGCC | -0.831 | 4.611 |
| Mean | Stdev | |
| twist-5-GGCC | 28.839 | 7.231 |
| Mean | Stdev | |
| rise-6-GGCC | 3.542 | 0.348 |
| Mean | Stdev | |
| roll-6-GGCC | 3.421 | 5.553 |
| Mean | Stdev | |
| shift-6-GGCC | 0.081 | 0.678 |
| Mean | Stdev | |
| slide-6-GGCC | -0.994 | 0.711 |
| Mean | Stdev | |
| tilt-6-GGCC | 2.621 | 4.348 |
| Mean | Stdev | |
| twist-6-GGCC | 34.357 | 4.797 |








































