Excited-State Proton Transfer in 8-Azapurines I: A Kinetic Analysis of 8-Azaxanthine Fluorescence

Chemo-Enzymatic Generation of Highly Fluorescent Nucleoside Analogs Using Purine-Nucleoside Phosphorylase

Chemo-enzymatic syntheses of strongly fluorescent nucleoside analogs, potentially applicable in analytical biochemistry and cell biology are reviewed. The syntheses and properties of fluorescent ribofuranosides of several purine, 8-azapurine, and etheno-purine derivatives, obtained using various types of purine nucleoside phosphorylase (PNP) as catalysts, as well as α-ribose-1-phosphate (r1P) as a second substrate, are described. In several instances, the ribosylation sites are different to the canonical purine N9. Some of the obtained ribosides show fluorescence yields close to 100%. Possible applications of the new analogs include assays of PNP, nucleoside hydrolases, and other enzyme activities both in vitro and within living cells using fluorescence microscopy.

Mechanism of Ligand Discrimination by the NMT1 Riboswitch

Riboswitches are conserved functional domains in mRNA that almost exclusively exist in bacteria. They regulate the biosynthesis and transport of amino acids and essential metabolites such as coenzymes, nucleobases, and their derivatives by specifically binding small molecules. Due to their ability to precisely discriminate between different cognate molecules as well as their common existence in bacteria, riboswitches have become potential antibacterial drug targets that could deliver urgently needed antibiotics with novel mechanisms of action. In this work, we report the recognition mechanisms of four oxidization products (XAN, AZA, UAC, and HPA) generated during purine degradation by an RNA motif termed the NMT1 riboswitch. Specifically, we investigated the physical interactions between the riboswitch and the oxidized metabolites by computing the changes in the free energy on mutating key nucleobases in the ligand binding pocket of the riboswitch. We discovered that the electrostatic interactions are central to ligand discrimination by this riboswitch. The relative binding free energies of the mutations further indicated that some of the mutations can also strengthen the binding affinities of the ligands (AZA, UAC, and HPA). These mechanistic details are also potentially relevant in the design of novel compounds targeting riboswitches.

Embedding Photoacids into Polymer Opal Structures: Synergistic Effects on Optical and Stimuli-Responsive Features

Opal films with their vivid structural colors represent a field of tremendous interest and obtained materials offer the possibility for many applications, such as optical sensors or anti-counterfeiting materials. A convenient method for the generation of opal structures relies on the tailored design of core-interlayer-shell (CIS) particles. Within the present study, elastomeric opal films were combined with stimuli-responsive photoacids to further influence the optical properties of structurally colored materials. Starting from cross-linked polystyrene (PS) core particles featuring a hydroxy-rich and polar soft shell, opal films were prepared by application of the melt-shear organization technique. The photoacid tris(2,2,2-trifluoroethyl) 8-hydroxypyrene-1,3,6-trisulfonate (TFEHTS) could be conveniently incorporated during freeze-drying the particle dispersion and prior to the melt-shear organization. Furthermore, the polar opal matrix featuring hydroxylic moieties enabled excited-state proton transfer (ESPT), which is proved by spectroscopic evaluation. Finally, the influence of the photoacid on the optical properties of the 3-dimensional colloidal crystals were investigated within different experimental conditions. The angle dependence of the emission spectra unambiguously shows the selective suppression of the photoacid's fluorescence in its deprotonated state.

Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition

Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation. Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson–Crick base pair to junction J2. Xanthine inserts between a G–U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg²⁺ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg²⁺ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding analysis to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic analysis of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch.

Benzimidazoazapurines: Design, Synthesis, and Photophysical Study

A highly efficient approach to a new class of polycyclic 8-azapurines, benzo[4,5]imidazo[1,2-a][1,2,3]triazolo[4,5-e]pyrimidines (BITPs), with good photophysical characteristics is proposed. The approach comprises condensation of aminobenzimidazoles with 3-oxo-2-phenylazopropionitrile to form 3-(arylazo)benzo[4,5]imidazo[1,2-a]pyrimidine-4-amines, which undergo oxidative cyclization by the catalytic action of copper(II) acetate, resulting in BITPs with 73-84% yield. Spectral investigations demonstrated the fluorescent properties of BITPs, exhibiting good quantum yields (up to 60%) with maxima absorption at 379-399 and emission at 471-505 nm.