Conformational dynamics in mixed alpha/beta-oligonucleotides containing polarity reversals: A molecular dynamics study using time-averaged restraints

Nucleic acid duplexes featuring a single alpha-anomeric thymidine inserted into each DNA strand via 3'-3' and 5'-5' phosphodiester linkages exhibit lo cal conformational dynamics that are not adequately depicted by conventiona l restrained molecular dynamics (rMD) methods. We have used molecular dynam ics with time-averaged NMR restraints (MDtar) to explore its applicability to describing the conformational dynamics of two alpha -containing duplexes - d(GCGAAT-3'-3'-alphaT-5'-5'-CGC)(2) and d(ATGG-3'-3'-alphaT-5'-5'-GCTC). r(gagcaccau). In contrast to rMD, enforcing NOE-based distance restraints o ver a period of time in MDtar rather than instantaneously results in better agreement with the experimental NOE and J-data. This conclusion is based o n the dramatic decreases in average distance and coupling constant violatio ns (Deltad(a)v, J(r)ms, and DeltaJ(a)v) and improvements in sixth-root R-fa ctors (R-x). In both duplexes, the deoxyribose ring puckering behavior pred icted independently by pseudorotation analysis is portrayed remarkably well using this approach compared to rMD. This indicates that the local dynamic behavior is encoded within the NOE data, although this is not obvious from the local R-x values. In both systems, the backbone torsion angles compris ing the 3'-3' linkage as well as the (high S-) sugars of the alpha -nucleot ide and preceding residue (alpha -1) are relatively static, while the confo rmations of the 5'-5' linkage and the sugar in the neighboring beta -nucleo tide (alpha +1) show enhanced flexibility. To reduce the large ensembles ge nerated by MDtar to more manageable clusters we utilized the PDQPRO program . The resulting PDQPRO clusters (in both cases, 13 structures and associate d probabilities extracted from a pool of 300 structures) adequately represe nt the structural and dynamic characteristics predicted by the experimental data.