Cooperative hydrogen bonding in glyco-oligoamides: DNA minor groove binders in aqueous media

An overview of recent advances in duplex DNA recognition by small molecules

As the carrier of genetic information, the DNA double helix interacts with many natural ligands during the cell cycle, and is amenable to such intervention in diseases such as cancer biogenesis. Proteins bind DNA in a site-specific manner, not only distinguishing between the geometry of the major and minor grooves, but also by making close contacts with individual bases within the local helix architecture. Over the last four decades, much research has been reported on the development of small non-natural ligands as therapeutics to either block, or in some cases, mimic a DNA–protein interaction of interest. This review presents the latest findings in the pursuit of novel synthetic DNA binders. This article provides recent coverage of major strategies (such as groove recognition, intercalation and cross-linking) adopted in the duplex DNA recognition by small molecules, with an emphasis on major works of the past few years.

Glycan OH Exchange Rate Determination in Aqueous Solution: Seeking Evidence for Transient Hydrogen Bonds

Hydrogen bonds (Hbonds) are important stabilizing forces in biomolecules. However, for glycans in aqueous solution, direct NMR detection of Hbonds is elusive because of their transient nature. Here, we present Isotope-based Natural-abundance TOtal correlation eXchange SpectroscopY (INTOXSY), a new ¹H-¹³C heteronuclear single quantum coherence-total correlation spectroscopy based method, to extract OH groups' exchange rate constants (k_ex) for molecules in natural ¹³C abundance and show that OH Hbonds can be inferred from "slower" H/D k_ex. We evaluate k_ex measured with INTOXSY in light of those extracted with line-shape analysis. Subsequently, we use a set of common glycans to establish a k_ex reference basis set and to infer the existence of transient Hbonds involving OH donor groups. Then, we report k_ex values for a series of mono- and disaccharides, as well as for oligosaccharides sialyl Lewis X and β-cyclodextrin, and compare the results with those from the reference set to extract Hbond information. Finally, we utilize NMR experimental data in conjunction with molecular dynamics simulations to establish donor and acceptor Hbond pairs. Our exchange rate measurements indicate that OH/OD exchange rates, k_HD, values <10 s^-1 are consistent with transient Hbond OH groups and potential acceptor groups can be uncovered through MD simulations.

Association of symmetrical alkane diols with pyridine: DFT/GIAO calculation of 1 H NMR chemical shifts

Proton nuclear magnetic resonance (NMR) shifts of the free diol and of its 1 : 1 and 1 : 2 hydrogen-bonded complexes with pyridine have been computed for five symmetrical alkane diols on the basis of density functional theory, by applying the gauge-including atomic orbital method to geometry-optimized conformers. For certain conformers, intramolecular OH···OH interactions, evidenced by high NMR OH proton shifts, are further enhanced on going from the free diol to the corresponding 1 : 1 diol/pyridine complex. This is confirmed by atoms-in-molecules and non-covalent interaction plots. The computed OH and CH proton shifts for the diol and the two complexes correlate well with values obtained by analysing data from the NMR titration of the diols in benzene against pyridine. Shift values for the diols in neat pyridine are calculated by weighting the shifts of the various protons in the three forms (free diol, 1 : 1 and 1 : 2 diol/pyridine complexes) according to the experimentally determined association constants. The results are in good agreement with those observed, and after empirical scaling, the root mean square difference is 0.18 ppm. Copyright © 2016 John Wiley & Sons, Ltd.