Invariant and variable base stacking geometries in B-DNA and A-DNA

We calculated the interatomic distances between all couples of non-hydrogen atoms belonging to the neighboring Watson-Crick base pairs in the availabl e crystal structures of DNA. Their standard deviations revealed remarkably large differences in the variability of the base stacking geometries of the particular steps. In line with experimental studies in solution, (CpA).(Tp G) and (TpA).(TpA) were identified as the most variable or flexible steps i n the crystal structures of B-DNA. On the other hand, base stacking geometr ies of the (ApT).(ApT) steps were the most invariant, which was very surpri sing because all three steps composed only of C and G were much more flexib le. This finding suggests that conformational stability of DNA and the rigi dity have different origins. Furthermore, the nucleotide sequence dependenc e of the flexibility was almost reversed in A-DNA because the most flexible steps in B-DNA were the least flexible in A DNA. The most invariant steps of B-DNA were variable in A-DNA. The (ApT)(ApT) step was a notable exceptio n to this rule because it belonged to the most rigid steps in both B-DNA an d A-DNA. The present results are fully consistent with the properties that poly(dA-dT)poly(dA-dT), poly(dA) poly(dT), poly(dA-dC)poly(dG-dT) and poly( dA-dc) poly(dC-dT) exhibit in solution.