Inside Cover: A Synthetic Lectin for O‐Linked β‐N‐Acetylglucosamine (Angew. Chem. Int. Ed. 10/2009)

Carbohydrates are slippery customers in water. Camouflaged by solvent‐mimicking hydroxy groups, they make challenging targets, even for natural receptors. In their Communication on page 1775 ff., A. P. Davis and co‐workers describe a synthetic receptor that is remarkably effective for the important β‐N‐acetylglucosaminyl (β‐GlcNAC) unit. The affinities of the receptor are good and its selectivities are excellent, even by the standards of natural carbohydrate‐binding proteins.

     

Delineation of G‐Quadruplex Alkylation Sites Mediated by 3,6‐Bis(1‐methyl‐4‐vinylpyridinium iodide)carbazole‐Aniline Mustard Conjugates

A new G‐quadruplex (G‐4)‐directing alkylating agent BMVC‐C3M was designed and synthesized to integrate 3,6‐bis(1‐methyl‐4‐vinylpyridinium iodide)carbazole (BMVC) with aniline mustard. Various telomeric G‐4 structures (hybrid‐2 type and antiparallel) and an oncogene promoter, c‐MYC (parallel), were constructed to react with BMVC‐C3M, yielding 35 % alkylation yield toward G‐4 DNA over other DNA categories (<6 %) and high specificity under competition conditions. Analysis of the intact alkylation adducts by electrospray ionization mass spectroscopy (ESI‐MS) revealed the stepwise DNA alkylation mechanism of aniline mustard for the first time. Furthermore, the monoalkylation sites and intrastrand cross‐linking sites were determined and found to be dependent on G‐4 topology based on the results of footprinting analysis in combination with mass spectroscopic techniques and in silico modeling. The results indicated that BMVC‐C3M preferentially alkylated at A15 (H26), G12 (H24), and G2 (c‐MYC), respectively, as monoalkylated adducts and formed A15–C3M–A21 (H26), G12–C3M–G4 (H24), and G2–C3M–G4/G17 (c‐MYC), respectively, as cross‐linked dialkylated adducts. Collectively, the stability and site‐selective cross‐linking capacity of BMVC‐C3M provides a credible tool for the structural and functional characterization of G‐4 DNAs in biological systems.     

Serine versus Threonine Glycosylation with α‐O‐GalNAc: Unexpected Selectivity in Their Molecular Recognition with Lectins

The molecular recognition of several glycopeptides bearing Tn antigen (α‐O‐GalNAc‐Ser or α‐O‐GalNAc‐Thr) in their structure by three lectins with affinity for this determinant has been analysed. The work yields remarkable results in terms of epitope recognition, showing that the underlying amino acid of Tn (serine or threonine) plays a key role in the molecular recognition. In fact, while Soybean agglutinin and Vicia villosa agglutinin lectins prefer Tn‐threonine, Helix pomatia agglutinin shows a higher affinity for the glycopeptides carrying Tn‐serine. The different conformational behaviour of the two Tn biological entities, the residues of the studied glycopeptides in the close proximity to the Tn antigen and the topology of the binding site of the lectins are at the origin of these differences.     

Highly Effective Recognition of Carbohydrates by Phenanthroline‐Based Receptors: α‐ versus β‐Anomer Binding Preference

¹H NMR spectroscopic titrations in competitive and non‐competitive media, as well as binding studies in two‐phase systems, such as phase transfer of sugars from aqueous into organic solvents and dissolution of solid carbohydrates in apolar media revealed both highly effective recognition of neutral carbohydrates and interesting binding preferences of an acyclic phenanthroline‐based receptor 1 . Compared to the previously described acyclic receptors, compound 1 displays significantly higher binding affinities, the rare capability to extract sugars from water into non‐polar organic solutions and α‐ versus β‐anomer binding preference in the recognition of glycosides, which differs from those observed for other receptor systems. X‐ray crystallographic investigations revealed the presence of water molecules in the binding pocket of 1 that are engaged in the formation of hydrogen‐bonding motifs similar to those suggested by molecular modelling for the sugar OH groups in the receptor–sugar complexes. The molecular modelling calculations, synthesis, crystal structure and binding properties of 1 are described and compared with those of the previously described receptors.     

2‐(4′‐Pyridyl‐N‐oxide)‐Substituted Hemithioindigos as Photoresponsive Guests for a Super Aryl‐Extended Calix[4]pyrrole Receptor

We report the synthesis of two 2‐(4′‐pyridyl‐N‐oxide)‐substituted hemithioindigos (HTIs). We probed their photoisomerization by using UV/Vis and ¹H NMR spectroscopy techniques. Light irradiation at λ=450 nm provoked the isomerization of the HTI Z isomer to the E counterpart to a large extent (≈80 % at the photostationary state). ¹H NMR titration experiments revealed the formation of thermodynamically and kinetically stable 1:1 inclusion complexes of the (Z)‐HTI isomers with a super aryl‐extended host (association constant>10⁴ m ^?1). Photoirradiation at λ=450 nm of the inclusion complexes induced the isomerization of the bound HTI N‐oxide to afford the (E)‐HTI?calix[4]pyrrole complex. We determined accurate association constant values for the 1:1 inclusion complexes of the (Z)‐ and (E)‐HTI isomers by using isothermal titration calorimetry experiments. The results showed that the stability constants of the (E)‐HTI complexes were 2.2–2.8‐fold lower than those of the (Z)‐HTI counterparts, which explains the lack of light‐induced release of the former to the bulk solution.     

A 5'-cap for DNA probes binding RNA target strands

Detecting short RNA strands with high fidelity at any of the bases of their sequence, including the termini, can be challenging, since fraying, wobbling, and refolding all compete with canonical base pairing. We performed a search for 5'-substituents of oligodeoxynucleotides that increase base pairing fidelity at the terminus of duplexes with RNA target strands. From a total of over 70 caps, differing in stacking moiety and linker, a phosphodiester-linked sequence of the residues of L-prolinol, glycine, and oxolinic acid, dubbed ogOA, was identified as a 5'-cap that stabilizes any of the four canonical base pairs, with ΔT(m) values of up to +13.1 °C for an octamer. At the same time, the cap increases discrimination against any of the 12 possible terminal mismatches, including mismatches that are more stable than their perfectly matched counterparts in the control duplex, such as A:A. A probe with the cap also showed increased selectivity in the detection of two closely related microRNAs, let7c and let7a, with a ΔT(m) value of 9.2 °C. Melting curves also yielded thermodynamic data that shed light on the uniformity of molecular recognition in the sequence space of DNA:DNA and DNA:RNA duplexes. Hybridization probes with fidelity-enhancing caps should find applications in the individual and parallel detection of biologically active RNA species.     

A Synthetic Lectin for O‐Linked β‐N‐Acetylglucosamine

Changing employment : Receptor 1 binds β‐N‐acetylglucosaminyl (β‐GlcNAc) up to 100 times more strongly than it does glucose. This synthetic lectin shows affinities similar to wheat germ agglutinin (WGA), a natural lectin used to bind GlcNAc. Remarkably, 1 is more selective than WGA. It favors especially the glycoside unit in glycopeptide 2 , a model of the serine‐O‐GlcNAc posttranslational protein modification.

     

NMR characterization of 1,1′‐binaphthyl‐2,2′‐diyl hydrogen phosphate binding to chiral molecular micelles

NMR spectroscopy was used to characterize the binding of the chiral compound 1,1′‐binaphthyl‐2,2′‐diyl hydrogen phosphate (BNP) to five molecular micelles with chiral dipeptide headgroups. Molecular micelles have covalent linkages between the surfactant monomers and are used as chiral mobile phase modifiers in electrokinetic chromatography. Nuclear overhauser enhancement spectroscopy (NOESY) analyses of (S)‐BNP:molecular micelle mixtures showed that in each solution the (S)‐BNP interacted predominately with the N‐terminal amino acid of the molecular micelle's dipeptide headgroup. NOESY spectra were also used to generate group binding maps for (S)‐BNP:molecular micelle mixtures. In these maps, percentages are assigned to the (S)‐BNP protons to represent the relative strengths of their interactions with a specified molecular micelle proton. All maps showed that (S)‐BNP inserted into a previously reported chiral groove formed between the molecular micelle's dipeptide headgroup and hydrocarbon chain. In the resulting intermolecular complexes, the (S)‐BNP protons nearest to the analyte phosphate group were found to point toward the N‐terminal Hα proton of the molecular micelle headgroup. Finally, pulsed field gradient NMR diffusion experiments were used to measure association constants for (R) and (S)‐BNP binding to each molecular micelle. These K values were then used to calculate the differences in the enantiomers' free energies of binding, Δ(ΔG). The NMR‐derived Δ(ΔG) values were found to scale linearly with electrokinetic chromatography (EKC) chiral selectivities from the literature. Copyright © 2010 John Wiley & Sons, Ltd.     

A nonredundant structure dataset for benchmarking protein‐RNA computational docking

Protein–RNA interactions play an important role in many biological processes. The ability to predict the molecular structures of protein–RNA complexes from docking would be valuable for understanding the underlying chemical mechanisms. We have developed a novel nonredundant benchmark dataset for protein–RNA docking and scoring. The diverse dataset of 72 targets consists of 52 unbound–unbound test complexes, and 20 unbound–bound test complexes. Here, unbound–unbound complexes refer to cases in which both binding partners of the cocrystallized complex are either in apo form or in a conformation taken from a different protein–RNA complex, whereas unbound–bound complexes are cases in which only one of the two binding partners has another experimentally determined conformation. The dataset is classified into three categories according to the interface root mean square deviation and the percentage of native contacts in the unbound structures: 49 easy, 16 medium, and 7 difficult targets. The bound and unbound cases of the benchmark dataset are expected to benefit the development and improvement of docking and scoring algorithms for the docking community. All the easy‐to‐view structures are freely available to the public at http://zoulab.dalton.missouri.edu/RNAbenchmark/ . © 2012 Wiley Periodicals, Inc.     

Pyrenylmethyldeoxyadenosine: A 3′‐Cap for Universal DNA Hybridization Probes

Effect of a PAH on base pairing : A polycyclic aromatic hydrocarbon (PAH) covalently linked to the N6‐position of a dangling deoxyadenosine residue (see scheme) of an oligonucleotide increases target affinity, but decreases base‐pairing selectivity. Melting point increases of up to 28 °C (14 °C per residue) were observed, and 20 out of 24 mismatch‐containing duplexes are stabilized more strongly by the PAH substituent than their perfectly matched counterpart.