We have used quantitative DNase I footprinting to examine the ability of @entity38140 and @entity2455 to discriminate between different arrangements of @entity1129 residues, using synthetic DNA fragments containing multiple blocks of (A/T)6or (A/T)10in identical sequence environments. Previous studies have shown that these ligands bind less well to (A/T)4sites containing TpA steps. We find that in (A/T)6tracts distamycin shows little discrimination between the various sites, binding approximately 2-fold stronger to TAATTA than (TA)3, T3A3and GAATTC. In contrast, @entity2455 binds approximately 20-fold more tightly to GAATTC and TAATTA than T3A3and (TA)3. @entity3787 radical footprinting reveals that both ligands bind in similar locations at the centre of each @entity1129 tract. At (A/T)10sites distamycin binds with similar affinity to T5A5, (TA)5and AATT, though bands in the centre of (TA)5are protected at approximately 50-fold lower concentration than those towards the edges. @entity2455 shows a similar pattern of preference, with strong binding to AATT, T5A5and the centre of (TA)5. @entity3787 radical footprinting reveals that at low concentrations both ligands bind at the centre of (TA)5and A5T5, while at higher concentrations ligand molecules bind to each end of the (A/T)10tracts. At T5A5two ligand molecules bind at either end of the site, even at the lowest ligand concentration, consistent with the suggestion that these compounds avoid the TpA step. Similar DNase I footprinting experiments with a DNA fragment containing T n (n = 3-6) tracts reveals that both ligands bind in the order T3< T4 < T5 = T6.

Interaction of minor groove binding ligands with long XXXX tracts.

@entity2455 :: ('MESH:D006690', 'Chemical') :: ['Hoechst 33258'] @entity38140 :: ('MESH:C030000', 'Chemical') :: ['distamycin'] @entity1129 :: ('MESH:D001260', 'Disease') :: ['AT'] @entity3787 :: ('MESH:D017665', 'Chemical') :: ['Hydroxyl']
@entity1129 :: (MESH:D001260,Disease) :: ['AT']
