Homooligomeric dA.dU and dA.dT sequences in parallel and antiparallel strand orientation: consequence of the 5-methyl groups on stability, structure and interaction with the minor groove binding drug Hoechst 33258.

Oligodeoxyribonucleotides containing dA.dU base combinations were shown to form parallel stranded DNA. CD spectra and hyperchromicity profiles provide evidence that the structure is very similar to that of a related parallel stranded dA.dT oligomer. Thermal denaturation studies show that these parallel dA.dU sequences are significantly less stable than their dA.dT analogues in either antiparallel or parallel stranded orientations. The stabilizing effect of the 5-methyl group is similar for parallel and antiparallel sequences. The minor groove binding drug Hoechst 33258 binds with similar affinity to APS dA.dT and APS dA.dU sequences. However, binding to the PS dA.dT hairpin is significantly impaired as a consequence of the different groove dimensions and the presence of thymine methyl groups at the binding site. This results in an 8.6 kJmol-1 reduced free energy of binding for the PS dA.dT sequence. Replacement of the bulky methyl group with a hydrogen (ie. T-->U) results in significantly stronger Hoechst 33258 binding to the parallel dA.dU sequences with a penalty of only 4.1 kJmol-1. Our data demonstrate that although Hoechst 33258 detects the altered groove, it is still able to bind a PS duplex containing dA.dU base pairs with high affinity, despite the large structural differences from its regular binding site in APS DNA.