Mannose glyco‐oligoamide β‐D‐Man‐Py‐γ‐Py‐Ind (β‐D‐Man, 1) and two new glyco‐oligoamides, β‐L‐Man‐Py‐γ‐Py‐Ind (β‐L‐Man, 2) and 6‐deoxy‐β‐D‐Man‐Py‐γ‐Py‐Ind (6‐deoxy‐β‐D‐Man, 3), have been designed and synthesized to investigate the role of hydrogen‐bonding cooperative donor centres of carbohydrates in their recognition by DNA. The free‐ and bound‐state geometries were studied, as were the affinities of the D and L enantiomers of the mannose glyco‐oligoamides (1 and 2) for DNA polymers [ct‐DNA and poly(dA‐dT)2]. TR‐NOESY and DF‐STD experiments for the diastereomeric complexes formed with DNA allow the asymmetric centres of the sugar residue that are close to the inner and outer regions of the DNA minor grooves to be distinguished. A C→N hairpin folding in β‐L‐Man derivative 2 was observed, with the α face of the sugar close to the indole ring. The C‐2 and C‐3 centres are orientated towards the inner region of the DNA minor groove. The affinity data for poly(dA‐dT)2 indicate that there is a chiral discrimination process, with β‐L‐Man derivative 2 being the best ligand. 6‐Deoxy‐β‐D‐Man derivative 3 forms the least stable complexes with DNA. Molecular dynamics simulations of β‐L‐Man derivative 2 in complex with a double‐strand dodecamer d(AT)12 are in agreement with the experimental NMR spectroscopic data. Thus, the cooperative donor centre 2‐OH in the L‐mannose enantiomer is a key contributor to the stability of the 2·poly(dA‐dT)2 complex.

A strategy to create cooperative hydrogen‐bonding centers by using strong and directional intramolecular hydrogen‐bonding motifs that can survive in aqueous media is presented. In particular, glyco–oligoamides, a family of DNA minor groove binders, with cooperative and non‐cooperative hydrogen‐bonding donor centers in the carbohydrate residues have been designed, synthesized, and studied by means of NMR spectroscopy and molecular modeling methods. Indeed, two different sugar moieties, namely, β‐D‐Man‐Py‐γ‐Py‐Ind (1; Ind=indole, Man=mannose, Py=pyrrole) and β‐D‐Tal‐Py‐γ‐Py‐Ind (2; Tal=talose), were chosen according to our design. These sugar molecules should present one‐ or two‐directional intramolecular hydrogen bonds. The challenge has been to study the conformation of the glyco–oligoamides at low temperature in physiological media by detecting the exchangeable protons (amide NH and OH resonances) by means of NMR spectroscopic analysis. In addition, two more glyco–oligoamides with non‐cooperative hydrogen‐bonding centers, that is, β‐D‐Glc‐Py‐γ‐Py‐Ind (3; Glc=glucose), β‐D‐Gal‐Py‐γ‐Py‐Ind (4; Gal=galactose), and the model compounds β‐D‐Man‐Py‐NHAc (5) and β‐D‐Tal‐Py‐NHAc (6) were synthesized and studied for comparison. We have demonstrated the existence of directional intramolecular hydrogen bonds in 1 and 2 in aqueous media. The unexpected differences in terms of stabilization of the intramolecular hydrogen bonds in 1 and 2 relative to 5 and 6 promoted us to evaluate the influence of CH—π interactions on the establishment of intramolecular hydrogen bonds by using computational methods. Initial binding studies of 1 and 2 with calf‐thymus DNA and poly(dA‐dT)2 by NMR spectroscopic analysis and molecular dynamics simulations were also carried out. Both new sugar–oligoamides are bound in the minor groove of DNA, thus keeping a stable hairpin structure, as in the free state, in which both intramolecular hydrogen‐bonding and CH—π interactions are present.