A GTP-synthesizing ribozyme selected by metabolic coupling to an RNA polymerase ribozyme.

Synthesis of RNA in early life forms required chemically activated nucleotides, perhaps in the same form of nucleoside 5'-triphosphates (NTPs) as in the contemporary biosphere. We show the development of a catalytic RNA (ribozyme) that generates the nucleoside triphosphate guanosine 5'-triphosphate (GTP) from the nucleoside guanosine and the prebiotically plausible cyclic trimetaphosphate. Ribozymes were selected from 1.6 × 1014 different randomized sequences by metabolically coupling 6-thio GTP synthesis to primer extension by an RNA polymerase ribozyme within 1016 emulsion droplets. Several functional RNAs were identified, one of which was characterized in more detail. Under optimized reaction conditions, this ribozyme produced GTP at a rate 18,000-fold higher than the uncatalyzed rate, with a turnover of 1.7-fold, and supported the incorporation of GTP into RNA oligomers in tandem with an RNA polymerase ribozyme. These results are discussed in the context of early life forms.

Water/Oil Emulsions with Controlled Droplet Sizes for In Vitro Selection Experiments.

In the early history of life, RNA might have had many catalytic functions as ribozymes that do not exist today. To explore this possibility, catalytically active RNAs can be identified by in vitro selection experiments. Some of these experiments are best performed in nanodroplets to prevent diffusion between individual RNA sequences. In order to explore the suitability for the large-scale in emulsio selection of water-in-oil emulsions made by passing a mixture of mineral oil, the emulsifier ABIL-EM90, and a few percent of an aqueous phase through a microfluidizer, we used dynamic light scattering to characterize the size of aqueous droplets dispersed throughout the oil. We found that seven or more passes through the microfluidizer at 8000 psi with close to half molar inorganic salts and 10% polyethylene glycol produced droplets with sizes below 100 nm that were ideal for our purposes. We also identified conditions that would produce larger or smaller droplets, and we demonstrate that the emulsions are stable over weeks and months, which is desirable for different types of in vitro selection experiments.

Optical and electrochemical properties of shell-core dendrimers: ruthenium coordination complexes capped with sized phenothiazine-substituted bipyridines.

A family of ruthenium coordination compounds capped by 4,4'-dimethylbipyridine ligands bearing 0, 1, 2, and 3 generations of dendritic phenothiazine moieties exhibit size-dependent electrochemical properties and structure-dependent absorption and luminescence spectra. Emission quantum yields, photoluminescence decay kinetics, and transient absorption spectra varied roughly with dendrimeric size and complexity on timescales from subnanoseconds to milliseconds. All complexes exhibit microsecond-lived lowest lying metal-to-ligand charge transfer excited states. Luminescence spectra were broadened compared with the unsubstituted parent, and quantum yields of emission for the large dendritic clusters were reduced by factors of two to five. Although the observed decay kinetics were complex, one transient decayed rapidly on a nanosecond scale, and a second intermediate showed no decay over a time scale of several tens of nanoseconds. Transient absorption measurements showed ground-state bleaching in regions of high ground-state absorptivity by the metal-to-ligand charge-transfer transient, as well as transient absorption shifts characteristic of isolated phenothiazine and ruthenium bipyridyl moieties.

The effect of dye density on the efficiency of photosensitization of TiO2 films: light-harvesting by phenothiazine-labelled dendritic ruthenium complexes.

A family of dendritic tris-bipyridyl ruthenium coordination complexes incorporating two or four carboxylate groups for binding to a TiO(2) surface site and another dendritic linker between the metal complex and highly absorptive dyes were formulated as thin films on TiO(2) coated glass. The family included phenothiazine-substituted dendrons of increasing structural complexity and higher optical density. The dye-loaded films were characterized by steady-state emission and absorption measurements and by kinetic studies of luminescence and transient absorption. Upon photoexcitation of the bound dyes, rapid electron injection into the metal oxide film was the dominant observed process, producing oxidized dye that persisted for hundreds of milliseconds. Complex decay profiles for emission, transient absorption, and optical bleaching of the dendritic dyes point to highly heterogeneous behavior for the films, with observed persistence lifetimes related directly to structurally enhance electronic coupling between the metal oxide support and the dendritic dyes.

Luminescent oligo(tetraphenyl)silole nanoparticles as chemical sensors for aqueous TNT.

Colloidal oligo(tetraphenyl)silole nanoparticles in THF/H2O suspensions show increased luminescence and offer a method to detect TNT in an aqueous environment.

Fluorescence quantum yields and their relation to lifetimes of rhodamine 6G and fluorescein in nine solvents: improved absolute standards for quantum yields.

Absolute fluorescence quantum yields are reported for the rhodamine 6G cation and the fluorescein dianion dyes in nine solvents. This information is combined with previously reported fluorescence lifetimes to deduce radiative and nonradiative decay rates. Along the alcohol series from methanol to octanol, rhodamine 6G displays an increasing radiative rate, in parallel with the square of the refractive index increase, and a slightly decreasing nonradiative rate. Fluorescein is different: the apparent radiative rate actually decreases, suggesting that the emissive species is perturbed in some fashion. For both dyes, fluorescence yields are enhanced in D2O, rising to 0.98, in parallel with a corresponding increase in lifetimes. Protonated solvents invariably give shorter lifetimes and lower quantum yields, contrary to some previous speculation. From this work and an analysis of existing literature values, more precise values have been obtained for two previously proposed absolute quantum yield standards. The yield of fluorescein in 0.1 N NaOH(aq) is 0.925+/-0.015, and for rhodamine 6G in ethanol, it is 0.950+/-0.015. In both cases, the solutions are assumed to be in the limit of low concentration, excited close to their long-wave absorption band and at room temperature but may be either air-saturated or free of oxygen.

Hydrogen-bond rigidified BODIPY dyes.

Boron difluoride adducts of diamidodipyrromethenes have been synthesized and characterized. The compounds represent a new group of the BODIPY family of fluorescent dyes. X-ray crystallography and solution (19)F NMR experiments show that a persistent hydrogen bond is formed between the boron-bound fluoride groups and the peripheral amide substituents. The modular synthesis of these compounds and their robust photophysical properties suggest that they may be useful compounds for materials and biological photochemical applications.

Ruthenium complexes that break the rules: structural features controlling dual emission.

A family of heteroleptic RuII coordination complexes containing substituted 1,10-phenanthroline (phen) ligands with extended conjugation was found to exhibit two simultaneously emissive excited states at room temperature in fluid solution. These systems demonstrate a breakdown of the standard nonradiative decay pathways that normally lead to a single, dominant, lowest energy emissive excited state in RuII complexes and most other chromophores. The structural requirements for dual emission were explored through the synthesis and characterization of isomeric systems. Two features were found to be primarily responsible for resolvable dual emission. Extended conjugation at the 4-position of the 1,10-phenanthroline ligand was identified as an essential feature, and asymmetry in the phenanthroline ligand substitutions appears to greatly facilitate the production of these two nonequilibrated emissive states. Additional complexes were studied which displayed "tunable" emissive characteristics for the two excited states as a function of covalent and noncovalent modification.

Luminescent dipyrrinato complexes of trivalent group 13 metal ions.

Although free dipyrrins (dipyrromethenes) do not strongly luminesce, certain dipyrrinato complexes of BF2 and zinc(II) are known to be intensely luminescent species. Two new dipyrrinato fluorophores, based on complexes with gallium(III) and indium(III), are described. Using a previously described meso-mesityl-substituted dipyrrin, namely 5-mesityldipyrrin (mesdpm), the complexes [Ga(mesdpm)3] and [In(mesdpm)3] were prepared and structurally characterized. The complexes display the expected octahedral geometry about the metal ions. In some solvents, such as hexanes, the complexes emit green light upon excitation with UV light at room temperature, with quantum yields of 2.4% ([Ga(mesdpm)3]) and 7.4% ([In(mesdpm)3]) and lifetimes in the low nanosecond range. Observations are consistent with assignment to ligand-localized transitions, and this interpretation is further confirmed by density functional calculations described herein. The new complexes are important additions to the widely used family of dipyrrin-based fluorescent species and show that dipyrrinato complexes containing metals other than BF2 and zinc(II) may be useful fluorophores.

Dual emission from a family of conjugated dinuclear Ru(II) complexes.

Dual emission is observed from a family of simple acetylene-linked dinuclear RuII complexes, where two MLCT excited states coexist at room temperature and in fluid solution. This unique behavior is attributed to a specific substitution pattern on the bridging ligand and provides the opportunity to investigate the structural and electronic features that result in decoupling of standard nonradiative decay pathways.

Conformational control of excited-state dynamics in highly distorted Ru(II) polypyridyl complexes.

Tris(bipyridyl)ruthenium(II) complexes modified such that one of the bipyridines is appended with a crown ether display luminescence that is responsive to complexation with metal ions. The parent species, Ru(bpy)3(2+), is moderately luminescent, with an emission lifetime of about 1 micros in fluid solution at room temperature. The modified complexes are much less emissive, with lifetimes near 1 ns. Conformational flexibility and distortion in the crown-ether complexes enhance nonradiative decay. Noncovalent binding of metal ions, however, restores luminescence intensity by reducing nonradiative decay and increasing the lifetime 10- to 100-fold. Reported here are the syntheses and steady-state and time-resolved luminescence measurements in addition to other supporting spectroscopic characterization. Seven metals were investigated; significant luminescence enhancements occur in the presence of Mg2+, Ca2+, and Pb2+. Effective concentrations of metal ions range from tens of microM to hundreds of mM. The steady-state enhancements are readily measured, but they are less than would be expected from the lifetime changes, partly because only a portion (not more than 50%) of the fast (1 ns) decay in Ru(bpy)2(bpy-crown) is capable of converting to the conformation possessing the longer lifetime. A photophysical model is proposed to explain these and other observations.

Luminescent silole nanoparticles as chemoselective sensors for Cr(VI).

Colloidal suspensions of 3-aminopropylmethyl(tetraphenyl)silole nanoparticles can be used as selective chemosensors for carcinogenic chromium(VI) analyte. Methylhydrosilole is functionalized by hydrosilation of allylamine, and the colloid is prepared by the rapid addition of water to a THF solution of the silole. The method of detection is through electron-transfer quenching of the fluorescence of the silole colloid (lambda(em) = 485 nm at 360 nm excitation) by the analytes, with hundred parts per billion detection limits. Stern-Volmer plots are linear up to 10 ppm in the case of chromium, but exhibit saturation behavior near 5-10 ppm for arsenic. Dynamic light scattering experiments and AFM measurements show the particle sizes to be around 100 nm in diameter and dependent on solvent composition, with a particle size dispersity of +/-25%. The fluorescence lifetimes of the silole in solution and colloid are approximately 31 ps and approximately 4.3 ns, respectively, while the silole has a lifetime of 6 ns in the bulk solid. A minimum volume fraction of 80% water is necessary to precipitate the colloid from THF, and the luminescence continues to rise with higher water fractions. Colloids in a pH 7 phosphate-buffered suspension show both higher sensitivity and greater selectivity (100-fold) for CrO4(2-) detection than for other oxoanion interferents, NO3-, NO2-, SO4(2-), and ClO4-.

Reactions of nitric oxide with vitamin B12 and its precursor, cobinamide.

Despite early claims that nitric oxide does not react with cobalamin under any circumstances, it is now accepted that NO has a high affinity for cobalamin in the 2+ oxidation state [Cbl(II)]. However, it is still the consensus that NO does not react with Cbl(III). We confirmed that NO coordinates to Cbl(II) at all pH values and that Cbl(III) does not react with NO at neutral pH. At low pH, however, Cbl(III) does react with NO by way of a two-step process that also reduces Cbl(III) to Cbl(II). To account for the pH dependence, and because of its intrinsic interest, we also studied reactions of NO with cobinamide [Cbi] in the 2+ and 3+ oxidation states. Both Cbi(II) and Cbi(III) react readily with NO at all pH values. Again, Cbi(III) is reduced during the process of coordinating NO. Compared to cobalamin, cobinamide lacks the tethered 5,6-dimethylbenzamidazolyl moiety bound to the cobalt ion. It may, therefore, be considered a "base-off" form of Cbl. To explain the reaction of Cbl(III) at low pH, we infer that the base-off form of Cbl(III) exists in trace amounts that are rapidly reduced to Cbl(II), which then binds NO efficiently. Base dissociation, we postulate, is the rate-limiting step. Interestingly, Cbi(II) has 100 times greater affinity for NO than does Cbl(II), proving that there is a strong trans effect due to the tethered base in nitrosyl derivatives of both Cbl(II) and Cbl(III). The affinity of Cbi(II) for NO is so high that it is a very efficient NO trap and, consequently, may have important biomedical uses.

Detection of nitroaromatic explosives based on photoluminescent polymers containing metalloles.

The synthesis, spectroscopic characterization, and fluorescence quenching efficiency of polymers and copolymers containing tetraphenylsilole or tetraphenylgermole with Si-Si, Ge-Ge, and Si-Ge backbones are reported. Poly(tetraphenyl)germole, 2, was synthesized from the reduction of dichloro(tetraphenyl)germole with 2 equivs of Li. Silole-germole alternating copolymer 3 was synthesized by coupling dilithium salts of tetraphenylsilole dianion with dichloro(tetraphenyl)germole. Other tetraphenylmetallole-silane copolymers, 4-12, were synthesized through the Wurtz-type coupling of the dilithium salts of the tetraphenylmetallole dianion and corresponding dichloro(dialkyl)silanes. The molecular weights (M(w)) of these metallole-silane copolymers are in the range of 4000 approximately 6000. Detection of nitroaromatic molecules, such as nitrobenzene (NB), 2,4-dinitrotoluene (DNT), 2,4,6-trinitrotoluene (TNT), and picric acid (PA), has been explored. A linear Stern-Volmer relationship was observed for the first three analytes, but not for picric acid. Fluorescence spectra of polymetalloles or metallole-silane copolymers obtained in either toluene solutions or thin polymer films displayed no shift in the maximum of the emission wavelength. This suggests that the polymetalloles or metallole-silanes exhibit neither pi-stacking of polymer chains nor excimer formation. Fluorescence lifetimes of polymetalloles and metallole-silanes were measured both in the presence and absence of TNT, and tau(o)/tau is invariant. This requires that photoluminescence quenching occurs by a static mechanism.

Synthesis and photochemical properties of a novel iron-sulfur-nitrosyl cluster derivatized with the pendant chromophore protoporphyrin IX.

The novel Roussin red-salt ester (PPIX-RSE) with a pendant porphyrin chromophore was prepared and investigated as a precursor for the photochemical generation of nitric oxide. PPIX-RSE has the general formula Fe(2)(NO)(4)[(mu-S,mu-S')P] (where (S,S')P is the bis(2-thiolatoethyl) diester of protoporphyrin IX. The photoexcitation of PPIX-RSE with 436- or 546-nm light in an aerated chloroform solution led to the photodecomposition of the cluster with the respective quantum yields (5.2 +/- 0.7) x 10(-4) and (2.5 +/- 0.5 x 10(-4)) and the concomitant release of NO. PPIX-RSE is a significantly more effective NO generator at longer wavelength excitation than are other Fe(2)(mu-SR)(2)(NO)(4) esters for which R is a simple alkyl group such as CH(3)CH(2)- because of the much higher absorptivity of the pendant PPIX chromophore at these wavelengths and a modestly higher quantum yield. Fluorescence intensity and lifetime data indicate that the photoexcited porphyrin of PPIX-RSE is largely quenched by the energy transfer to the Fe(2)S(2)(NO)(4) cluster's core. However, a small fraction of this emission is not quenched, and it is proposed that PPIX-RSE may exist in solution as two conformers.

Role of the interdomain linker probed by kinetics of CO ligation to an endothelial nitric oxide synthase mutant lacking the calmodulin binding peptide (residues 503-517 in bovine).

Oxygenase and reductase domains in nitric oxide synthase are linked by a peptide region that binds calmodulin. Here we study the effects of modifying the length of the interdomain linker in a deletion mutant lacking 15 amino acids (residues 503-517) in bovine eNOS. The kinetics of CO ligation with the mutant were determined in the presence and absence of tetrahydrobiopterin and arginine and compared with the CO binding kinetics of wild-type eNOS and the eNOS oxygenase domain. In the mutant, electron flow is interrupted. The association kinetics of CO with both mutant and wild-type eNOS can be approximated with two kinetic phases, but the relative proportions change in the mutant. Both the abrogation of electron flow in the mutant and the differences in CO binding may be explained by an alteration in the docking of the FMN domain to the heme domain. We propose that the calmodulin binding residues form a helix that is critical for the proper alignment of the adjacent reductase and oxygenase domains within the active eNOS dimer in achieving proper electron transfer between them.