title: Sugar-oligoamides: bound-state conformation and DNA minor-groove-binding description by TR-NOESY and differential-frequency saturation-transfer-difference experiments.
abstract: Selective-frequency saturation-transfer-difference (STD) spectra allow the description of complexes established between minor-groove binders and long tracts of calf thymus DNA (ct-DNA). Two sets of experiments with selective saturation of either the H1' or H4'/H5'/H5'' proton NMR regions of deoxyribose allow the description of the ligand residues close to the inner (H1') and outer regions (H4'/H5'/H5'') of the minor groove of double-helical DNA. A series of complexes of sugar-oligoamides (2-6) with ct-DNA have been studied by both TR-NOESY and STD experiments. The binding mode of the complexes is similar to that of netropsin (1) and allows us to define a general binding mode for this family of ligands, in which an NH rim points towards the internal area (inner region) and a CH3 rim points towards the external part (outer region) of the minor groove of DNA. Also by means of both TR-NOESY and STD experiments, a description of the asymmetric centers of the sugar residue close to the inner and outer regions of the groove has been achieved. These results confirm that the sugar is responsible for the differences previously found in binding energetics.
authors.affiliation: Departamento de Química Orgánica Biológica, Instituto de Química Orgánica general, CSIC c/Juan de la Cierva 3, 28006 Madrid, Spain.
authors.forename: Florence
authors.initials: F
authors.lastname: Souard
authors.forename: Eva
authors.initials: E
authors.lastname: Muñoz
authors.forename: Pablo
authors.initials: P
authors.lastname: Peñalver
authors.forename: Concepción
authors.initials: C
authors.lastname: Badía
authors.forename: Rafael
authors.initials: R
authors.lastname: del Villar-Guerra
authors.forename: Juan Luis
authors.initials: JL
authors.lastname: Asensio
authors.forename: Jesús
authors.initials: J
authors.lastname: Jiménez-Barbero
authors.forename: Cristina
authors.initials: C
authors.lastname: Vicent
mesh_terms: D000577:Amides / Q000737:chemistry*; D000818:Animals; D002241:Carbohydrates / Q000737:chemistry*; D002417:Cattle; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D015394:Molecular Structure
chemical_list: D000577:Amides; D002241:Carbohydrates; D004247:DNA; C427203:calf thymus DNA