Bridgehead-Substituted Triptycenes for Discovery of Nucleic Acid Junction Binders

Blue-Shift Hydrogen Bonds in Silyltriptycene Derivatives: Antibonding σ* Orbitals of the Si-C Bond as Effective Acceptors of Electron Density

Triptycene derivatives are widely utilized in different fields of chemistry and materials sciences. Their physicochemical properties, often of pivotal importance for the rational design of triptycene-based functional materials, are influenced by noncovalent interactions between substituents mounted on the triptycene skeleton. Herein, a unique interaction between electron-rich substituents in the peri position and the silyl group located on the bridgehead sp³ -carbon is discussed on the example of 1,4-dichloro-9-(p-methoxyphenyl)-silyltriptycene (TRPCl) which exists in solution in the form of two rotamers differing by dispositions, syn or anti, of the Si-C_Ph (the C_Ph atom is from the p-methoxyphenyl group) bond against the peri-Cl atom. For the first time, substantial differences between the Si-C_Ph bonds in these two dispositions are identified, based on indirect experimental and direct theoretical evidence. For these two orientations, the experimental ¹ J(Si,C_Ph ) values differ by as much as 10 percent. The differences are explained in terms of effective electron density transfer from the peri-Cl atom to the antibonding σ* orbitals of the Si-X bonds (X=H, C_Ph ) oriented anti to that atom. The electronic effects are revealed by an NBO analysis. Connections of these observations with the notion of blue-shifting hydrogen bonds are discussed.

Increased Flexibility between Stems of Intramolecular Three-Way Junctions by the Insertion of Bulges

Intramolecular junctions are a ubiquitous structure within DNA and RNA; three-way junctions in particular have high strain around the junction because of the lack of flexibility, preventing the junctions from adopting conformations that would allow for optimal folding. In this work, we used a combination of calorimetric and spectroscopic techniques to study the unfolding of four intramolecular three-way junctions. The control three-way junction, 3H, has the sequence d(GAAATTGCGCT5GCGCGTGCT5GCACAATTTC), which has three arms of different sequences. We studied three other three-way junctions in which one (2HS1H), two (HS12HS1), and three (HS1HS1HS1) cytosine bulges were placed at the junction to allow the arms to adopt a wider range of conformations that may potentially relieve strain. Through calorimetric studies, it was concluded that bulges produce only minor effects on the enthalpic and thermal stability at physiological salt concentrations for 2HS1H and HS1HS1HS1. HS12HS1 displays the strongest effect, with the GTGC stem lacking a defined transition. In addition to unfolding thermodynamics, the differential binding of counterions, water, and protons was determined. It was found that with each bulge, there was a large increase in the binding of counterions; this correlated with a decrease in the immobilization of structural water molecules. The increase in counterion uptake upon folding likely displaces binding of structural water, which is measured by the osmotic stress method, in favor of electrostricted waters. The cytosine bulges do not affect the binding of protons; this finding indicates that the bulges are not forming base-triplet stacks. These results indicate that bulges in junctions do not affect the unfolding profile or the enthalpy of oligonucleotides but do affect the number and amount of molecules immobilized by the junction.

Synthesis of fused benzimidazoles via successive nucleophilic additions of benzimidazole derivatives to arynes under transition metal-free conditions

An expedient and efficient strategy was developed for the synthesis of benzimidazole derivatives from aryne precursors under transition metal-free conditions.

The Emerging Role of RNA as a Therapeutic Target for Small Molecules

Recent advances in understanding different RNAs and unique features of their biology have revealed a wealth of information. However, approaches to identify small molecules that target these newly discovered regulatory elements have been lacking. The application of new biochemical screening and design-based technologies, coupled with a resurgence of interest in phenotypic screening, has resulted in several compelling successes in targeting RNA. A number of recent advances suggest that achieving the long-standing goal of developing drug-like, biologically active small molecules that target RNA is possible. This review highlights advances and successes in approaches to targeting RNA with diverse small molecules, and the potential for these technologies to pave the way to new types of RNA-targeted therapeutics.

Aryne Compatible Solvents are not Always Innocent

Arynes are important and versatile intermediates in a variety of transformations. Commonly used solvents for aryne chemistry include acetonitrile and dichloromethane. Although rarely reported, the reactive nature of aryne intermediates makes them prone to side reactions, which sometimes involve solvent participation. Acetonitrile and dichloromethane are not always innocent solvents and can participate in aryne-based reactions. These results are presented in the context of ongoing mechanistic investigations of the triple aryne-tetrazine reaction.