Figure 3.

Sequence-dependent motions along the longest principal axes of P⋅DNA dimer steps: pyrimidine–purine (YR), purine–purine (RR), and purine–pyrimidine (RY) steps. Nonequilibrium forms, corresponding to the parametric changes in Table 2, are superimposed on the average dimer structures (thickened bonds). Perturbed conformations correspond to states deformed along the longest principal axes of the derived energy functions, with increments equal to changes of 〈λ₁²〉^−1/2 (Table 2) and energies ranging from 0 to 12.5 k_BT for ±5〈λ₁²〉^−1/2 deviations. Opposing directions of fluctuations are distinguished by color-coded (Y, light blue; R, red) and gray images. Motions illustrated with respect to a reference frame in the 5′ base pair (i.e., the M in MpN dimers). Views from the leading strand. Base pairs represented as ideal Watson–Crick pairs with C1′ atoms of rest structures noted by circles. Note the decreasing range of motions from left to right.