SOLUTION STRUCTURE OF DAPI SELECTIVELY BOUND IN THE MINOR-GROOVE OF ADNA T-CENTER-DOT-T MISMATCH-CONTAINING SITE - NMR AND MOLECULAR-DYNAMICS STUDIES

The solution structure of the complex between 4',6-diamidino-2-phenyli ndole (DAPI) and DNA oligomer [d(GCGATTCGC)](2), containing a central T.T mismatch, has been characterized by combined use of proton one- an d two-dimensional NMR spectroscopy, molecular mechanics and molecular dynamics computations including relaxation matrix refinement, The resu lts show that the DAPI molecule binds in the minor groove of the centr al region 5'-A (T) under bar T-3' of the DNA oligomer, which predomina ntly adopts a duplex structure with a global right-handed B-like confo rmation. In the final models of the complex, the DAPI molecule is loca ted nearly isohelical with its NH indole proton oriented towards the D NA helix axis and forming a bifurcated hydrogen bond with the carbonyl O2 groups of a mismatched <(T5)under bar> and the T6 residue of the o pposite strand. Mismatched thymines adopt a wobble base pair conformat ion and are found stacked between the flanking base pairs, inducing on ly minor local conformational changes in global duplex structure, In a ddition, no other binding mechanisms were observed, showing that minor groove binding of DAPI to the mismatch-containing site is favoured in comparison with any other previously reported interaction with G.C se quences.