Journal of the American Chemical Society, Vol.126, No.36, 11338-11349, 2004
Short lexitropsin that recognizes the DNA minor groove at 5'-ACTAGT-3': Understanding the role of isopropyl-thiazole
lsopropyl-thiazole (Th-ipr) represents a new addition to the building blocks of nucleic acid minor groove-binding molecules. The DNA decamer duplex d(CGACTAGTCG)(2) is bound by a short lexitropsin of sequence formyl-(PyPyTh)-Th-ipr-Dp (where Py represents N-methyl pyrrole, Th-ipr represents thiazole with an isopropyl group attached, and Dp represents dimethylaminopropyl). NMR data indicate ligand binding in the minor groove of DNA to the sequence 5'-ACT(5)AG(7)T-3' at a 2:1 ratio of ligand to DNA duplex. Ligand binding, assisted by the enhanced hydrophobicity of the Th-ipr group, occurs in a head-to-tail fashion, the formyl headgroups being located toward the 5'-ends of the DNA sequence. Sequence reading is augmented through hydrogen bond formation between the exocyclic amine protons of G(7) and the Th-iPr nitrogen, which lies on the minor groove floor. The B-I/B-II DNA backbone equilibrium is altered at the T-5 3'-phosphate position to accommodate a B-II configuration. The ligands bind in a staggered mode with respect to one another creating a six base pair DNA reading frame. The introduction of a new DNA sequence-reading element into the recognition jigsaw, combined with an extended reading frame for a small lexitropsin with enhanced hydrophobicity, holds great promise in the development of new, potentially commercially viable drug lead candidates for gene targeting.