The ATT strand of AAT center dot ATT trinucleotide repeats adopts stable hairpin structures induced by minor groove binding ligands

AAT.ATT is the most abundant and also the most frequently polymorphic class of trinucleotide repeats in the human genome, To characterize its structur al properties and conformational changes induced by minor groove ligands, ( AAT)(6) and (ATT)(6) oligomers as well as their complexes with DAPI were in vestigated by electrophoretic mobility and UV thermal stability as well as fluorescence and NMR spectroscopy. The results show that individual (AAT)(6 ) and (ATT)(6) strands exist principally as monomeric non-hydrogen-bonded s tructures. Their individual interaction with DAPI induces the formation of base-paired structures with different thermal stabilities by quite spectros copically distinct binding mechanisms. In the presence of DAPI, (ATT)(6) fo rms a monomeric hairpin structure stabilized by two ligands located in the minor groove with a strong apparent binding constant of 3.4 x 10(6) M-1. Th e DAPI-induced (ATT)(6) hairpin is characterized by well-stacked A.T Watson -Crick and T.T wobble base pairs, a high electrophoretic mobility, and a me lting temperature of 41 degrees C. Interaction of DAPI with the complementa ry (AAT)(6) strand favors less stable base-paired structures, and the resul ts are consistent with electrostatic and hydrogen-bond interactions of the ligand with the phosphodiester backbone of (AAT)(6) by minor involvement of DNA bases.