Figure 3.

TAR RNA ensembles obtained by XSI-RNA. (A) The position of a helix (magenta, upper) with respect to a second helix (grey, lower) is defined by a set of rotations (Euler angles) followed by a translation. From a straight position, the set of rotations are defined as follows: i. twist: rotating the upper helix around the z-axis by an amount α + γ; ii. bend: rotating the upper helix by an amount β in the direction defined by the bend direction (γ); subsequently, the helix is translated in the Cartesian coordinate (the xyz space) (see (12) for a more detailed description). (B) The spatial representation of the inter-helical orientation of XSI-resolved TAR ensemble under low (left) and high (right) salt. (Low salt: as in Figure 2C; high salt: 70 mM Tris-HCl, pH 7.4, 150 mM NaCl and 10 mM sodium ascorbate.) The helix 5΄ to the TAR bulge (grey) is fixed along the z-axis as in part A and the probability distribution of the angular orientation of the top helix (without translation) is displayed on the surface of a unit sphere. The (C) inter-helical orientation and (D) translational probability distributions of TAR RNA under the low (green) and high (red) salt solution conditions. Twist, bend and bend direction are as defined in part A and correspond to α + γ, β and γ, respectively, for Euler angle (α, β, γ) of the zyz convention (12).