Pulling and pushing the DNA double helix

DNA stretching and compression: large-scale simulations of double helical structures 1 1Edited by I. Tinoco

“…The variations in local base-pair step and global helical parameters with longitudinal deformations also follow the conformational patterns exhibited by dimer steps in high resolution A and B-DNA crystal structures (Olson et al, 1998(Olson et al, , 1999. Speci®cally, the local Twist and Rise are positively correlated in nine out of ten dimeric steps, a ®nding which is in agreement with the present simulations and which serves as further indication of the sequence independence of this important correlation.…”

“…The B 1 3 B t transition involves the correlated switching of a and g torsions (Table 1) and little, if any, reorientation of neighboring basepairs (Figure 2(b), (d), and (f)). The B t 3 B 2 step, by contrast, entails relatively minor changes in backbone torsions (e, z, b), but large (anti to high anti) variations in the glycosyl rotation w and accompanying sharp jumps in base-pair Roll and Slide ($40 and $4-5 A Ê , respectively), which are expected to introduce an extremely high energy barrier at the borders between the two equi-potential forms (Olson et al, 1999; see Figure 7). We therefore hypothesize that the``energetically expensive'' switch into the B 2 conformation may account for the sharp phase transition observed at 60-70 % DNA extension (Cluzel et al, 1996;Smith et al, 1996).…”

“…Third, the two classes of structures are energetically equivalent at``intermediate'' stretching ( Figure 1). The substantial differences in basepair inclination between these equipotential forms introduce a steric barrier at the boundaries between the different conformations (Olson et al, 1999). The considerable magnitude of this barrier compared to the energy of base stacking is consist-ent with the sharp cooperative transition observed at this level of DNA extension.…”