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Sugar–Oligoamides: Bound‐State Conformation and DNA Minor‐Groove‐Binding Description by TR‐NOESY and Differential‐Frequency Saturation‐Transfer‐Difference Experiments
Author(s) -
Souard Florence,
Muñoz Eva,
Peñalver Pablo,
Badía Concepción,
del VillarGuerra Rafael,
Asensio Juan Luis,
JiménezBarbero Jesús,
Vicent Cristina
Publication year - 2008
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.200701103
Subject(s) - two dimensional nuclear magnetic resonance spectroscopy , crystallography , dna , deoxyribose , chemistry , groove (engineering) , stereochemistry , materials science , biochemistry , metallurgy
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 CH 3 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.