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The interaction of nucleic acids with their molecular targets often involves structural reorganization that may traverse a complex folding landscape. With the more recent recognition that many RNAs, both coding and noncoding, may regulate cellular activities by interacting with target molecules, it becomes increasingly important to understand how nucleic acids interact with their targets and how drugs might be developed that can influence critical folding transitions. We have extensively investigated the interaction of the Spinach2 and Broccoli aptamers with a library of small molecule ligands modified by various extensions from the imido nitrogen of DFHBI [(Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one] that reach out from the Spinach2 ligand binding pocket. Studies of the interaction of these compounds with the aptamers revealed that polyfluorophenyl-modified ligands initiate a slow change in aptamer affinity that takes an extended time (half-life of ∼40 min) to achieve. The change in affinity appears to involve an initial disruption of the entrance to the ligand binding pocket followed by a gradual transition to a more defined structure for which the most likely driving force is an interaction of the gateway adenine with a nearby 2′OH group. These results suggest that polyfluorophenyl modifications might increase the ability of small molecule drugs to disrupt local structure and promote RNA remodeling.

The regulation of RNA transcription is central to cellular function. Changes in gene expression drive differentiation and cellular responses to events such as injury. RNA trafficking can also have a large impact on protein expression and its localization. Thus, the ability to image RNA transcription and trafficking in real time and in living cells is a worthwhile goal that has been difficult to achieve. The availability of "light-up" aptamers that cause an increase in fluorescence of their ligands when bound by the aptamer have shown promise for reporting on RNA production and localization in vivo. Here we have investigated two light-up aptamers (the malachite green aptamer and the Spinach aptamers) for their suitabilities as reporters of RNA expression in vivo using two eukaryotic cell types, yeast and mammalian. Our analysis focused on the aptamer ligands, their contributions to background noise, and the impact of tandem aptamer strings on signal strength and ligand affinity. Whereas the background fluorescence is very low in vitro, this is not always true for cell imaging. Our results suggest the need for caution in using light up aptamers as reporters for imaging RNA. In particular, images should be collected and analyzed by operators blinded to the sample identities. The appropriate control condition of ligand with the cells in the absence of aptamer expression must be included in each experiment. This control condition establishes that the specific interaction of ligand with aptamer, rather than nonspecific interactions with unknown cell elements, is responsible for the observed fluorescent signals. High background signals due to nonspecific interactions of aptamer ligands with cell components can be minimized by using IMAGEtags (Intracellular Multiaptamer GEnetic tags), which signal by FRET and are promising RNA reporters for imaging transcription.

Arylpropynals and two equivalents of phloroglucinol react to produce pentacyclic ketals. In addition, 4-methoxydibromocinnamaldehyde also reacted to form procyanidin A-skeleton.

( Z)-5-(3,5-Difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4 H-imidazol-4-one (DFHBI) and its analogues are fluorogenic molecules that bind the Spinach aptamer (a small RNA molecule), which was selected for imaging RNA. They are extremely weakly fluorescent in liquid solvents. It had been hypothesized that photoisomerization is a very efficient nonradiative process of deactivation. We show, consistent with the results of other studies, that if the isomerization is impeded, the fluorescence signal is enhanced significantly. In addition, we provide a thorough characterization of the photophysical behavior of DFHBI and its derivatives, notably that of ( Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-((perfluorophenyl)methyl)-3,5-dihydro-4 H-imidazol-4-one (PFP-DFHBI) in various solvent environments. Solvent-dependent studies were performed with various mixtures of solvents. The results suggest that hydrogen bonding or strong interactions of the solvents with the phenolic-OH group change the absorption band near 420-460 nm and the nature of emission near 430 and 500 nm through various degrees of stabilization and the transformation between the neutral and the anionic species at both ground and excited states. These observations are confirmed by using a methoxy-substituted molecule (( Z)-5-(4-methoxybenzylidene)-2,3-dimethyl-3,5-dihydro-4 H-imidazol-4-one), where the 420-460 nm band is absent in the presence of methanol and the spectra are similar to those of PFP-DFHBI in noninteracting solvents, such as acetonitrile and dichloromethane. Thus, in addition to the major role of photoisomerization as a nonradiative process of deactivation of the excited state, the fluorescence of DFHBI-type molecules is very sensitively dependent upon the pH of the medium as well as upon solvent-specific interactions, such as hydrogen-bonding ability and polarity.

A hydride abstraction strategy can be used to make anthocyanidins and isoflavylium salts from benzopyrans in good yields.

New tosyl derivatives of 2-iodylaniline and 2-iodylphenol were prepared by the dimethyldioxirane oxidation of the corresponding 2-iodophenyltosylamides or 2-iodophenyl tosylate and isolated as stable, microcrystalline products. Single-crystal X-ray diffraction analysis of N-(2-iodylphenyl)-N,4-dimethylbenzenesulfonamide revealed pseudocyclic structure formed by intramolecular I...O interactions between the hypervalent iodine center and the sulfonyl oxygens in the tosyl group. This tosylamide has an excellent solubility in organic solvents and is a potentially useful hypervalent iodine oxidant.

A comparative study of the reactivity of 2-iodylbenzoic acid isopropyl ester (IBX-ester), oligomeric iodosylbenzene sulfate [(PhIO) 3 ·SO 3 ] n , and iodosylbenzene in the oxygenation of anthracene in the presence of metal porphyrin or phthalocyanine complexes is reported. Results of this study demonstrate that oligomeric iodosylbenzene sulfate and the IBX-ester are the most reactive oxygenating reagents that can be used as a safe and convenient alternative to the thermally unstable and potentially explosive iodosylbenzene.

2-Iodylphenol ethers were prepared by the dimethyldioxirane oxidation of the corresponding 2-iodophenol ethers and isolated as chemically stable, microcrystalline products. Single-crystal X-ray diffraction analysis of 1-iodyl-2-isopropoxybenzene 8c and 1-iodyl-2-butoxybenzene 8d revealed pseudopolymeric arrangements in the solid state formed by intermolecular interactions between IO2 groups of different molecules. 2-Iodylphenol ethers can selectively oxidize sulfides to sulfoxides and alcohols to the respective aldehydes or ketones.

The pseudocyclic iodine(V) oxidants, such as esters of iodoxybenzoic acid (IBX-esters) and 2-iodylphenol ethers, can serve as stable and efficient sources of oxygen in catalytic oxidations, and their reactivity is similar to the commonly used thermally unstable and potentially explosive iodosylbenzene. In a specific example, primary or secondary benzylic alcohols are selectively oxidized by isopropyl IBX-ester in the presence of μ-oxo-(tetra-tert-butylphthalocyaninato)iron(III) (0.1 mol equiv) in dichloromethane at room temperature in 0.5–2 h to afford the respective carbonyl compounds in 100% conversion and preparative yields 91–95% after column chromatography.

A hydride abstraction strategy can be used to make anthocyanidins and isoflavylium salts from benzopyrans in good yields.

The pseudocyclic iodine(V) oxidants, such as esters of iodoxybenzoic acid (IBX-esters) and 2-iodylphenol ethers, can serve as stable and efficient sources of oxygen in catalytic oxidations, and their reactivity is similar to the commonly used thermally unstable and potentially explosive iodosylbenzene. In a specific example, primary or secondary benzylic alcohols are selectively oxidized by isopropyl IBX-ester in the presence of μ-oxo-(tetra-tert-butylphthalocyaninato)iron(III) (0.1 mol equiv) in dichloromethane at room temperature in 0.5–2 h to afford the respective carbonyl compounds in 100% conversion and preparative yields 91–95% after column chromatography.