Structure–Activity Studies on the Fluorescent Indicator in a Displacement Assay for the Screening of Small Molecules Binding to RNA

A series of xanthone and thioxanthone derivatives with aminoalkoxy substituents were synthesized as fluorescent indicators for a displacement assay in the study of small‐molecule–RNA interactions. The RNA‐binding properties of these molecules were investigated in terms of the improved binding selectivity to the loop region in the RNA secondary structure relative to 2,7‐bis(2‐aminoethoxy)xanthone (X2S) by fluorimetric titration and displacement assay. An 11‐mer double‐stranded RNA and a hairpin RNA mimicking the stem loop IIB of Rev response element (RRE) RNA of HIV‐1 mRNA were used. The X2S derivatives with longer aminoalkyl substituents showed a higher affinity to the double‐stranded RNA than the parent molecule. Introduction of a methyl group on the aminoethoxy moiety of X2S effectively modulated the selectivity to the RNA secondary structure. Methyl group substitution at the C1′ position suppressed the binding to the loop regions. Substitution with two methyl groups on the amino nitrogen atom resulted in reducing the affinity to the double‐stranded region by a factor of 40 %. The effect of methyl substitution on the amino nitrogen atom was also observed for a thioxanthone derivative. Titration experiments, however, suggested that thioxanthone derivatives showed a more prominent tendency of multiple binding to RNA than xanthone derivatives. The selectivity index calculated from the affinity to the double‐stranded and loop regions suggested that the N,N‐dimethyl derivative of X2S would be suitable for the screening of small molecules binding to RRE.     

Membrane properties of archaeal macrocyclic diether phospholipids

Several biophysical properties of four synthetic archaeal phospholipids [one polyprenyl macrocyclic lipid A and three polyprenyl double-chain lipids (B, C, D) bearing zero, one or four double bonds in each chain] were studied using differential scanning calorimetry, electron and optical microscopies, stopped-flow/light scattering and solid-state 2H-NMR techniques. These phospholipids gave a variety of self-organized structures in water, in particular vesicles and tubules. These assemblies change in response to simple thermal convection. Some specific membrane properties of these archaeal phospholipids were observed: They are in a liquid-crystalline state over a wide temperature range; the dynamics of their polyprenyl chains is higher than that of n-acyl chains; the water permeability of the membranes is lower than that of n-acyl phospholipid membranes. It was also found that macrocyclization remarkably improves the barrier properties to water and the membrane stability. This may be related to the adaptation of Methanococcus jannaschii to the extreme conditions of the deep-sea hydrothermal vents.     

Single-Microparticle Injection and Microabsorptiometry: Direct Analysis of Sorption Processes

Sorption processes of methylene blue in a single silica gel microparticle in an aqueous solution was kinetically analyzed by a new technique combined with the microcapillary injection/manipulation and microabsorptiometry of the single particle. The observed sorption rates were analyzed in terms of the solute concentration in water and the particle size. The sorption processes were governed by diffusion of the solute in the particle. Copyright 2000 Academic Press.     

Site-specific binding of chelerythrine and sanguinarine to single pyrimidine bulges in hairpin DNA

Spectrofluorometric titration, electrospray ionization time-of-flight mass spectrometric and UV melting methods were employed to study the binding of chelerythrine and sanguinarine to bulged DNA. The results showed that both alkaloids bind specifically to single pyrimidine (C, T) bulge sites. The ability of sanguinarine to bind to both regular and bulged hairpins was found to be stronger than that of chelerythrine, but the binding selectivity of chelerythrine toward single-base bulges was much larger than that of sanguinarine. Figure Association constants for chelerythrine and sanguinarine toward regular and single-base bulged hairpins obtained from fluorometric analysis     

Formation of a Ligand‐Assisted Complex of Two RNA Hairpin Loops

The hairpin structure is one of the most common secondary structures in RNA and holds a central position in the stream of RNA folding from a non‐structured RNA to structurally complex and functional ribonucleoproteins. Since the RNA secondary structure is strongly correlated to the function and can be modulated by the binding of small molecules, we have investigated the modulation of RNA folding by a ligand‐assisted formation of loop–loop complexes of two RNA hairpin loops. With a ligand (NCT6), designed based on the ligand binding to the G–G mismatches in double‐stranded DNA, we successfully demonstrated the formation of both inter‐ and intra‐molecular NCT6‐assisted complex of two RNA hairpin loops. NCT6 selectively bound to the two hairpin loops containing (CGG)₃ in the loop region. Native polyacrylamide gel electrophoresis analysis of two doubly‐labeled RNA hairpin loops clearly showed the formation of intermolecular NCT6‐assisted loop–loop complex. Förster resonance energy‐transfer studies of RNA constructs containing two hairpin loops, in which each hairpin was labeled with Alexa488 and Cy3 fluorophores, showed the conformational change of the RNA constructs upon binding of NCT6. These experimental data showed that NCT6 simultaneously bound to two hairpin RNAs at the loop region, and can induce the conformational change of the RNA molecule. These data strongly support that NCT6 functions as molecular glue for two hairpin RNAs.     

RNA Aptamers That Reversibly Bind Photoresponsive Azobenzene‐Containing Peptides

Modulation of biological networks assembled by diverse interactions among biologically active molecules has provided a platform for innovative biotechnologies. Here, we report RNA aptamers that bind to a photoresponsive peptide (KRAzR; Lys‐Arg‐azobenzene‐Arg) containing azobenzene chromophore, which can change its structure by photoirradiation. Aptamers were identified after 10 cycles of an in vitro selection procedure starting with a DNA library containing a 70 nt random region. Surface plasmon resonance (SPR) analysis demonstrated that interactions between aptamers and KRAzR were fully controlled by appropriate photoirradiation to the SPR sensor chip. Upon irradiation of 360 nm on the KRAzR‐immobilized surface, the binding of each aptamer to the surface was significantly decreased. Subsequent photoirradiation of the same surface with 430 nm restored the aptamer binding to the surface. We also observed that direct photoirradiation of the aptamer–peptide complex on a gold surface actively promoted dissociation of the complex. Furthermore, a doped reselection method was applied to acquire structural and sequence information of aptamer 66. From a data analysis of the conserved region and the mutation frequency, we were able to select a plausible secondary structure among three candidates predicted by computational folding simulation.     

Synthesis of hyperolactones A and C

Hyperolactones A ( 1 ) and C ( 3 ) have been synthesized starting from (S)‐malic acid by a straightforward route. The unique spirolactone skeleton was efficiently constructed by one‐pot reaction as a key step. The absolute stereochemistry of hyperolactones was unambiguously established by this synthesis.     

Quantum yield for hydrogen atom formation from H2O2 photolysis in the range 193–240 nm

Photodissociation processes of H₂O₂ in the range 193–240 nm have been studied by pulsed laser photolysis and laser‐induced fluorescence detection of H atom fragments at 121.56 nm. The quantum yield values for H atom formation at 295 ± 2 K have been determined to be 0.20 ± 0.03, 0.038 ± 0.008, 0.029 ± 0.003, 0.015 ± 0.006, 0.007 ± 0.002 at 193, 207, 210, 220, and 230 nm, respectively. At 240 nm, only the upper limit value of <0.002 has been obtained. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 751–754, 2005     

Conjugated Polymer Nanoparticle‐Triplet Emitter Hybrids in Aqueous Dispersion: Fabrication and Fluorescence Quenching Behavior

Conjugated polymer nanoparticles based on poly[9,9‐bis(2‐ethylhexyl)fluorene] and poly[N‐(2,4,6‐trimethylphenyl)‐N,N‐diphenylamine)‐4,4′‐diyl] are fabricated using anionic surfactant sodium dodecylsulphate in water by miniemulsion technique. Average diameters of polyfluorene and polytriarylamine nanoparticles range from 70 to 100 and 100 to 140 nm, respectively. The surface of the nanoparticles is decorated with triplet emitting dye, tris(2,2′‐bipyridyl)ruthenium(II) chloride. Intriguing photophysics of aqueous dispersions of these hybrid nanoparticles is investigated. Nearly 50% quenching of fluorescence is observed in the case of dye‐coated polyfluorene nanoparticles; excitation energy transfer is found to be the dominant quenching mechanism. On the other hand, nearly complete quenching of emission is noticed in polytriarylamine nanoparticle‐dye hybrids. It is proposed that the excited state electron transfer from the electron‐rich polytriarylamine donor polymer to Ru complex leads to the complete quenching of emission of polytriarylamine nanoparticles. The current study offers promising avenues for developing aqueous solution processed‐electroluminescent devices involving a conjugated polymer nanoparticle host and Ru or Ir‐based triplet emitting dye as the guest.