Base pair roll

Base pair roll refers to the angle of deflection of a bp with respect to the helix axis along a line drawn between two adjacent bps relative to a line drawn perpendicular to the helix axis. 

The examination of crystallized DNA fragments of varying base composition show sequence-dependent variations in the double helix while emphasizing the A, B and Z forms as structurally distinct families. Variation occurs in the orientation of each base pair to the next by rotation about the X axis or tilt, the Y axis or roll or the Z axis or twist of the helix. Bases in a pair may also rotate in opposition producing variations in buckle, propeller and opening (Fig. 7-5). 

Fig. 18.4. a Schematic representations of selected helical parameters, characterizing the relative positions and orientations of bases within base pairs. From top Shear, buckle and propeller twist, b Schematic representations of selected helical parameters, characterizing the relative positions and orientations of base pairs. From top Displacement, roll and helical twist... 

Fig. 18.5. Correlation between observed helix-twist angles and sum function 1 (a) and correlation between observed roll angles and sum function (b) for the dodecamer [d(CGCGAATTCGCG)]2. A decrease in helical twist or an opening of the roll angle on the side of the base pair where a clash occurs will relieve the steric hindrance between adjacent purines of opposite strands. For example, the clash at the first G-C base pair step (R-Y, step 2) takes place in the major groove. To relieve the steric hindrance, the twist angle has to be decreased, and at the same time the twist at each of the two neighboring steps is increased by half that amount. Thus, the contributions to X) 1 for tbe three steps 1, 2 and 3 are +1, -2, -t-1. If the clash occurs in the minor groove (e.g. with the neighboring C-G step, step 3), each of the contributions has to be doubled. Thus, the contributions to 1 for the three steps 2, 3 and 4 are +2, -4, +2 etc. (for details, see [39, 40]). The correlation coefficients were 0.94 (a) and 0.92 (b). For the correlations, the contributions of terminal base-pair steps (1 and 11) were omitted to avoid the influence of end effects...

Figure 4.4. Schematic representations of base-pair structural deviations from the ideal coordinate frame of the upper and middle left. The most important rotations for the purposes of this chapter are propeller twist, twist, and roll. [Adapted from Figs. 7 and 8 (erroneously listed as Fig. 9 in its caption) of Ref. 13, with permission].

Fig. 13.16 Probability density distributions of inter base pair helical parameters of 6L tind 6 from molecular dynamics simulations, (a) rise distance, (b) tilt angle, (c) slide distemce, (d) twist angle, (e) shift distance and (f) roll angle for TT steps in single stranded systems 2L blue line) tmd 2 (green line) and double stianded systems 6L (red line) tmd 6 (teal line)...

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