The base morphology parameters were calculated using the program by M. Babcock (Babcock, M.S. and Olson, W.K., 1994, J. Mol. Biol., 237, 98-156). This is the GGA structure the first output is the RMS deviation of the standard bases (ideal) to the experimental (modeled) structures. The way a coordinate frame is fixed to each base is by a least squares fitting of an ideal base with a coordinate frame which is appropriate by base pairing partner type in your case all Watson Crick. Like most modeled structures the rms is fine. 1.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Checking Numbers and RMS Values CHAIN a BASE 1 G RMS = 0.347479E-01 CHAIN a BASE 2 G RMS = 0.348711E-01 CHAIN a BASE 3 A RMS = 0.143589E-01 CHAIN a BASE 4 G RMS = 0.347964E-01 CHAIN a BASE 5 G RMS = 0.348218E-01 CHAIN a BASE 6 A RMS = 0.142539E-01 CHAIN a BASE 7 G RMS = 0.346955E-01 CHAIN a BASE 8 G RMS = 0.347759E-01 CHAIN a BASE 9 A RMS = 0.144043E-01 CHAIN a BASE 10 G RMS = 0.347999E-01 CHAIN a BASE 11 G RMS = 0.349270E-01 CHAIN a BASE 12 A RMS = 0.143281E-01 CHAIN a BASE 13 T RMS = 0.798844E-02 CHAIN a BASE 14 C RMS = 0.203942E-01 CHAIN a BASE 15 C RMS = 0.202791E-01 CHAIN a BASE 16 T RMS = 0.799491E-02 CHAIN a BASE 17 C RMS = 0.202718E-01 CHAIN a BASE 18 C RMS = 0.204511E-01 CHAIN a BASE 19 T RMS = 0.777361E-02 CHAIN a BASE 20 C RMS = 0.203331E-01 CHAIN a BASE 21 C RMS = 0.206016E-01 CHAIN a BASE 22 T RMS = 0.783716E-02 CHAIN a BASE 23 C RMS = 0.203674E-01 CHAIN a BASE 24 C RMS = 0.203499E-01 This next region gives the rotational and translational relationship of each base to it's complement. The order is rotation (X,Y,Z), angle between base planes, and then translational (XYZ) and finally the dist-sqrt of the sum of the squares of the x, y, and z components. =linear distance in space. 1.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN YOUR PIVOT POINT WAS: 0.000 1.808 0.000 Calculations Across a Basepair #Ch Base #Ch Base Buckle Prop Open Angle Shear Stretch Stagger Dist -------------------------------------------------------------------------------------------- 1a G 24a C 8.568 1.680 4.867 8.729 -0.038 0.109 0.165 0.201 2a G 23a C 0.156 -5.493 4.414 5.494 -0.080 0.080 -0.053 0.125 3a A 22a T 1.746 -6.064 6.932 6.307 0.081 -0.003 0.002 0.081 4a G 21a C 2.156 3.556 4.737 4.158 -0.091 0.086 0.011 0.126 5a G 20a C -1.024 -2.006 5.461 2.251 -0.112 0.081 -0.124 0.186 6a A 19a T 2.460 -5.049 5.997 5.614 0.092 -0.019 0.067 0.115 7a G 18a C 8.673 4.813 5.922 9.915 -0.039 0.101 0.185 0.214 8a G 17a C -1.146 -5.878 4.836 5.987 -0.017 0.100 -0.039 0.109 9a A 16a T 6.092 -3.237 10.040 6.889 0.197 0.063 0.334 0.393 10a G 15a C 3.195 3.793 6.777 4.956 -0.181 0.104 0.060 0.217 11a G 14a C -11.767 -8.500 5.578 14.510 -0.053 0.084 -0.217 0.238 12a A 13a T -9.271 1.989 3.296 9.481 0.225 0.043 -0.028 0.231 THE NUMBER OF SAMPLES= 12 -------------------------------------------------------------------------------------------- MEAN= 0.820 -1.700 5.738 7.024 -0.001 0.069 0.030 0.186 STANDARD DEVIATION= 5.975 4.435 1.620 3.090 0.119 0.040 0.141 0.081 The mean for buckle in DNA is 2.02+/- 7.35, for propeller it's 14.12 +/- 6.69 and for Opening it's 5.58 +/- 4.42. I will check this weekend for the specifics for your subfragments in this and the other sequences, I remember that the last time I looked the numbers were less than desireabl for the triplets you have so will need to look at the newest structures to up the numbers. More next week but as you can see, only the opening is close in mean to the experimental. However, from experience minimized structures can be lower than experimental data for many reasons, the subsequences if I can get enough may prove closer to the results you see here, but in general the minimized structures are slightly lower in parameter deviation from planarity. 1.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Calculations of Basepairs #Ch: #Ch #Ch: #Ch Tilt Roll Twist Angle Shift Slide Rise Dist ------------------------------------------------------------------------------------------------- 1a: 24a 2a: 23a 1.178 3.212 35.629 3.367 0.121 -0.903 3.021 3.155 2a: 23a 3a: 22a 1.396 -1.766 38.272 2.210 0.426 -0.654 2.951 3.052 3a: 22a 4a: 21a -1.711 -6.020 35.907 6.156 -0.015 -0.923 3.102 3.236 4a: 21a 5a: 20a 2.902 -4.652 37.849 5.384 -0.002 -0.850 3.195 3.306 5a: 20a 6a: 19a -0.249 -3.894 39.091 3.826 0.182 -0.459 2.993 3.033 6a: 19a 7a: 18a -2.416 -6.935 37.196 7.216 0.068 -0.767 3.065 3.161 7a: 18a 8a: 17a 4.062 -9.984 38.776 10.573 0.066 -0.810 3.420 3.516 8a: 17a 9a: 16a -1.125 -15.493 40.653 15.207 0.452 -0.478 3.169 3.236 9a: 16a 10a: 15a -0.034 -17.916 35.993 17.620 -0.130 -0.949 3.484 3.613 10a: 15a 11a: 14a 6.021 -8.811 38.442 10.472 -0.029 -1.045 3.474 3.628 11a: 14a 12a: 13a -0.305 -7.111 39.888 6.974 0.018 -0.622 3.082 3.144 THE NUMBER OF SAMPLES= 11 ------------------------------------------------------------------------------------------------- MEAN= 0.884 -7.215 37.972 8.091 0.105 -0.769 3.178 3.280 STANDARD DEVIATION= 2.452 5.647 1.577 4.685 0.176 0.184 0.185 0.203 Here you see more roll than tilt which is as it should be, the twist is slightly higher than the normal B-DNA mean but not bad, well within limits. the distances are good. 1.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Calculations of Adjacent Single Bases #Ch Base #Ch Base Tilt Roll Twist Angle Shift Slide Rise Dist -------------------------------------------------------------------------------------------- 1a G 2a G -2.215 1.111 35.324 2.439 -1.001 -0.766 3.011 3.264 2a G 3a A 4.034 -1.855 39.411 4.353 -0.579 -0.635 3.060 3.178 3a A 4a G -1.293 -0.681 34.869 1.439 -1.233 -0.787 3.074 3.405 4a G 5a G 0.852 -7.227 38.266 7.142 -1.261 -0.801 3.217 3.547 5a G 6a A 2.406 -5.165 39.363 5.586 -0.877 -0.438 3.110 3.261 6a A 7a G 0.429 -0.315 37.314 0.523 -1.209 -0.511 3.071 3.339 7a G 8a G -1.021 -13.916 38.678 13.688 -1.153 -0.628 3.479 3.719 8a G 9a A 3.049 -13.427 43.498 13.438 -0.663 -0.360 3.362 3.446 9a A 10a G -2.642 -12.954 34.947 13.016 -1.536 -0.691 3.377 3.774 10a G 11a G -1.050 -16.271 37.379 16.015 -1.128 -1.129 3.525 3.869 11a G 12a A 1.751 -5.670 38.108 5.826 -1.044 -0.885 3.126 3.412 13a T 14a C 2.359 -8.446 41.749 8.576 -1.072 -0.286 3.066 3.261 14a C 15a C -12.670 -0.967 39.456 12.456 -1.063 -0.851 3.490 3.746 15a C 16a T -2.935 -22.716 36.849 22.506 -1.290 -1.016 3.582 3.941 16a T 17a C 5.049 -17.769 37.622 18.139 -1.580 -0.435 3.054 3.466 17a C 18a C -8.961 -5.833 39.078 10.486 -1.292 -0.882 3.386 3.730 18a C 19a T 4.912 -13.686 36.788 14.291 -1.359 -0.891 3.041 3.448 19a T 20a C 2.955 -2.754 38.751 3.963 -1.243 -0.368 2.937 3.211 20a C 21a C -4.834 -1.986 37.442 5.134 -1.255 -0.791 3.162 3.493 21a C 22a T 1.868 -11.388 36.874 11.341 -1.207 -0.936 3.154 3.505 22a T 23a C 1.181 -1.796 37.003 2.112 -1.433 -0.566 2.948 3.326 23a C 24a C -4.475 5.433 36.092 6.923 -1.243 -0.951 3.080 3.455 THE NUMBER OF SAMPLES= 22 -------------------------------------------------------------------------------------------- MEAN= -0.511 -7.194 37.948 9.063 -1.169 -0.709 3.196 3.491 STANDARD DEVIATION= 4.301 7.017 2.009 5.767 0.236 0.229 0.193 0.214 This gives the rotational and translational relationship of base to base along a single strand. These numbers are always wilder than base pair calculations and again within normal ranges. 1.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Local Helical Calculations of Basepairs #Ch: #Ch #Ch: #Ch Incl Tip H-Twist DX DY DZ ------------------------------------------------------------------------------- 1a: 24a 2a: 23a 5.150 -1.889 35.793 -1.904 -0.037 2.930 2a: 23a 3a: 22a -2.641 -2.088 38.338 -0.787 -0.483 2.992 3a: 22a 4a: 21a -9.511 2.702 36.448 -0.636 -0.214 3.209 4a: 21a 5a: 20a -6.993 -4.363 38.244 -0.695 0.379 3.265 5a: 20a 6a: 19a -5.688 0.363 39.285 -0.238 -0.300 3.022 6a: 19a 7a: 18a -10.547 3.675 37.914 -0.298 -0.412 3.143 7a: 18a 8a: 17a -14.389 -5.855 40.247 0.093 0.421 3.503 8a: 17a 9a: 16a -20.857 1.515 43.520 0.916 -0.722 3.119 9a: 16a 10a: 15a -26.463 0.050 40.206 1.023 0.185 3.542 10a: 15a 11a: 14a -12.811 -8.754 39.895 -0.370 0.836 3.574 11a: 14a 12a: 13a -10.107 0.434 40.518 -0.104 -0.061 3.143 THE NUMBER OF SAMPLES= 11 ------------------------------------------------------------------------------- MEAN= -10.442 -1.292 39.128 -0.273 -0.037 3.222 STANDARD DEVIATION= 8.123 3.605 2.032 0.769 0.437 0.215 Once again these numbers are within range. This calculation uncouples the rotations to the helical axis alone, same with the translation, uou can think of it in terms of a pendulum motion to get from one base to the next while simultaneoulsy moving up the helical axixis in a screw type motion (not surprisingly the mathematics is based upon something called screw theory). The helical axis is defined as the uniqu axis which exists such that the orientation to the helical axis (tip and inclination) and distance from the axis (dx and dy) are the same for both basepairs being considered. It is like the global helical axis except in the global case the choice of atoms to consider and wether a curved or linear axis is used leads to different results. In the local frame there is only a linear choice and a mathematically unique axis. There is a place for global calculations but I am unhappy with the available methods (which is why I have been developing one of my own but still needs a bit of work so did not include) 1.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Local Helical Calculations of Adjacent Single Bases #Ch Base #Ch Base Incl Tip H-Twist DX DY DZ -------------------------------------------------------------------------- 1a G 2a G 1.800 3.587 35.411 -1.415 -0.475 3.042 2a G 3a A -2.686 -5.840 39.661 -0.725 -0.498 3.011 3a A 4a G -1.118 2.123 34.899 -1.211 0.057 3.133 4a G 5a G -10.693 -1.260 38.952 -0.289 0.190 3.282 5a G 6a A -7.466 -3.478 39.773 -0.049 -0.242 3.082 6a A 7a G -0.483 -0.659 37.318 -0.758 0.137 3.061 7a G 8a G -19.784 1.452 41.117 0.842 -0.294 3.514 8a G 9a A -17.128 -3.889 45.625 0.824 -0.660 3.267 9a A 10a G -20.305 4.142 37.364 0.846 0.197 3.507 10a G 11a G -23.518 1.518 40.781 0.541 -0.329 3.710 11a G 12a A -8.458 -2.612 38.567 -0.635 -0.010 3.171 13a T 14a C -11.425 -3.192 42.660 0.441 -0.101 2.998 14a C 15a C -1.358 17.800 41.452 -1.081 -1.889 3.667 15a C 16a T -31.602 4.082 43.387 1.400 -0.422 3.662 16a T 17a C -25.156 -7.147 41.912 1.200 0.915 2.735 17a C 18a C -8.348 12.825 40.514 -0.526 -1.091 3.679 18a C 19a T -20.299 -7.286 39.557 0.275 0.771 2.968 19a T 20a C -4.058 -4.353 38.961 -0.245 0.385 2.853 20a C 21a C -3.019 7.350 37.804 -0.957 -0.515 3.334 21a C 22a T -17.149 -2.812 38.637 0.039 0.255 3.228 22a T 23a C -2.778 -1.826 37.065 -0.666 0.594 2.925 23a C 24a C 8.518 7.016 36.772 -2.230 -0.433 3.034 THE NUMBER OF SAMPLES= 22 -------------------------------------------------------------------------- MEAN= -10.296 0.797 39.463 -0.199 -0.157 3.221 STANDARD DEVIATION= 10.039 6.182 2.552 0.907 0.607 0.283 Again, the helical calculations along each strand are larger than for the base pair plane and these are within range. Thwe next calculation gives the relative unequal distribution of the complementary parameters as a function of triplet class. The regular calculated value is also given for comparison. The normal method of calculation assumes that each base moves an equal amount away from ideality, a mathematical simplification used to ensure comparability, the distribution of course need not be equal and this calculation tries to measure the unequal nature of the distribution at least ball park numbers. In general propeller and opening are unequal and A opens more than Thy, and Cyt propeller twist more than Gua. 1.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Relative Positions of Bases with respect to Neighboring Basepairs Basepair-1 Basepair+1 #Ch #Ch #Ch #Ch Base Base Base Base #Ch Base Buckle Prop Open Angle Shear Stretch Stagger Dist Dev ---------------------------------------------------------------------------------------------------------------------- 1a: 24a 3a: 22a 2a G -0.015 -0.165 0.885 0.166 -0.146 -0.076 0.013 0.165 G: C A: T 23a C 0.207 -5.326 3.531 5.329 0.105 0.163 -0.061 0.203 TOTAL 0.192 -5.490 4.416 5.494 -0.041 0.086 -0.048 0.368 ACTUAL 0.156 -5.493 4.414 5.494 -0.080 0.080 -0.053 0.125 0.267 2a: 23a 4a: 21a 3a A 2.581 -0.863 4.596 2.721 0.319 0.142 -0.070 0.356 G: C G: C 22a T -0.639 -5.279 2.215 5.317 -0.271 -0.162 0.105 0.332 TOTAL 1.942 -6.142 6.811 8.038 0.048 -0.020 0.035 0.688 ACTUAL 1.746 -6.064 6.932 6.307 0.081 -0.003 0.002 0.081 0.384 3a: 22a 5a: 20a 4a G -1.312 1.104 1.364 1.714 -0.010 0.000 -0.099 0.099 A: T G: C 21a C 3.469 2.532 3.312 4.294 -0.049 0.085 0.033 0.104 TOTAL 2.157 3.636 4.675 6.009 -0.059 0.085 -0.066 0.203 ACTUAL 2.156 3.556 4.737 4.158 -0.091 0.086 0.011 0.126 0.046 4a: 21a 6a: 19a 5a G 1.112 -1.435 2.089 1.815 -0.096 -0.165 0.072 0.204 G: C A: T 20a C -2.166 -0.643 3.339 2.259 -0.004 0.250 -0.144 0.289 TOTAL -1.054 -2.078 5.428 4.074 -0.100 0.085 -0.072 0.493 ACTUAL -1.024 -2.006 5.461 2.251 -0.112 0.081 -0.124 0.186 0.263 5a: 20a 7a: 18a 6a A 2.420 -0.959 3.914 2.602 0.149 0.158 -0.007 0.217 G: C G: C 19a T 0.166 -4.127 1.998 4.131 -0.079 -0.183 0.101 0.223 TOTAL 2.585 -5.087 5.913 6.733 0.070 -0.024 0.094 0.441 ACTUAL 2.460 -5.049 5.997 5.614 0.092 -0.019 0.067 0.115 0.253 6a: 19a 8a: 17a 7a G 1.026 4.036 2.053 4.164 0.028 0.073 -0.210 0.224 A: T G: C 18a C 7.760 0.890 3.606 7.810 -0.030 0.015 0.284 0.286 TOTAL 8.786 4.926 5.660 11.974 -0.002 0.088 0.074 0.509 ACTUAL 8.673 4.813 5.922 9.915 -0.039 0.101 0.185 0.214 0.021 7a: 18a 9a: 16a 8a G 2.180 -0.132 1.452 2.184 -0.145 -0.108 0.162 0.243 G: C A: T 17a C -3.253 -5.851 3.272 6.694 0.157 0.213 -0.106 0.285 TOTAL -1.073 -5.983 4.724 8.878 0.012 0.105 0.056 0.528 ACTUAL -1.146 -5.878 4.836 5.987 -0.017 0.100 -0.039 0.109 0.337 8a: 17a 10a: 15a 9a A 2.567 -0.232 7.360 2.575 0.461 0.272 -0.055 0.538 G: C G: C 16a T 3.704 -2.828 2.626 4.660 -0.319 -0.244 0.346 0.530 TOTAL 6.271 -3.060 9.986 7.235 0.142 0.028 0.291 1.068 ACTUAL 6.092 -3.237 10.040 6.889 0.197 0.063 0.334 0.393 0.424 9a: 16a 11a: 14a 10a G -1.675 -2.768 2.117 3.235 -0.086 0.079 -0.054 0.129 A: T G: C 15a C 4.633 6.712 4.683 8.153 -0.052 0.029 0.003 0.060 TOTAL 2.957 3.945 6.800 11.388 -0.138 0.108 -0.051 0.188 ACTUAL 3.195 3.793 6.777 4.956 -0.181 0.104 0.060 0.217 0.079 10a: 15a 12a: 13a 11a G -2.635 -5.177 1.879 5.809 0.023 -0.192 0.221 0.294 G: C A: T 14a C -9.230 -3.404 3.362 9.836 -0.044 0.256 -0.356 0.441 TOTAL -11.865 -8.581 5.241 15.645 -0.021 0.063 -0.135 0.735 ACTUAL -11.767 -8.500 5.578 14.510 -0.053 0.084 -0.217 0.238 0.133 The general trends are maintained in this structure.