Figure 1.
Representation of the three contributions to the IDI illustrated using non-isosteric base pairs. To calculate the IDI for two base pairs, the bases designated ‘first base’ in each base pair are superposed (bases on the left in each panel) and then the following three quantities are evaluated, normalized and summed: (1) The difference, Δc, in the intra-base pair C1′–C1′ distances, illustrated for two non-isosteric cWW base pairs, AG and AU. (2) The inter-base pair C1′–C1′ distance, t1, between the C1′ atoms of the second bases of the base pairs, illustrated for the near isosteric cWW AU and AC base pairs. We also calculate the corresponding distance t2 after first superposing the second bases of the base pairs. (3) The angle, θ, about an axis perpendicular to the base pair plane, required to superpose the second bases, illustrated using non-isosteric cWW AU and cWS AU base pairs. For some pairs of base pairs, a 180° rotation (flip) about an axis in the base pair plane is required to superpose the second bases (case not shown).