DNAzymes are catalytic DNA molecules that can perform a variety of reactions. Although advances have been made in obtaining DNAzymes via in vitro selection and many of them have been developed into sensors and imaging agents for metal ions, bacteria, and other molecules, the structural features responsible for these enzymatic reactions are still not well understood. Previous studies of the 8-17 DNAzyme have suggested conserved guanines close to the phosphodiester transfer site may play a role in the catalytic reaction. To identify the specific guanine and functional group of the guanine responsible for the reaction, we herein report the effects of replacing G1.1 and G14 (G; p K = 9.4) with analogues with a different p K at the N1 position, such as inosine (G14I; p K = 8.7), 2,6-diaminopurine (G14diAP; p K = 5.6), and 2-aminopurine (G14AP; p K = 3.8) on pH-dependent reaction rates. A comparison of the pH dependence of the reaction rates of these DNAzymes demonstrated that G14 in the bulge loop next to the cleavage site, is involved in proton transfer at the catalytic site. In contrast, we did not find any evidence of G1.1 being involved in acid-base catalysis. These results support general acid-base catalysis as a feasible strategy used in DNA catalysis, as in RNA and protein enzymes.
The review examines functional knowledge gathered over two decades of research on the 8-17 DNAzyme, focusing on three aspects: the structural requirements for catalysis, the role of metal ions and the participation of general acid-base catalysis.
Artículo de publicación ISIRhenium complexes are versatile molecular building blocks whose tunable photophysical properties are useful in diverse opto-related applications. Herein we report the synthesis and characterization of a novel ReI tricarbonyldiimine complex, [(phen)Re(CO)3Br] (phen: 1,10-phenanthroline), which was found to be an efficient singlet oxygen [O2(1Δg)] photosensitizer in homogeneous solution [ΦO2(1Δg) = 0.55 (dichloromethane) and 0.16 (dimethylformamide)]. The photophysical properties of [(phen)Re(CO)3Br] were thoroughly characterized in solution and modeled by means of density functional theory (DFT) and time-dependent (TD)-DFT quantum mechanical calculations. The Re complex was incorporated into a flexible polymeric silsesquioxane (SSO) film, which has excellent dopant compatibility, chemical resistance, and mechanical properties. When [(phen)Re(CO)3Br] is embedded in the SSO film, it is found to retain most of the photophysical characteristics observed for the complex in solution. In particular, the [(phen)Re(CO)3Br]-doped SSO films were able to photosensitize O2(1Δg) when illuminated with blue light (∼405 nm). The O2(1Δg) sensitization by films in acetonitrile was followed by the photooxidation of the well-known O2(1Δg) chemical trap 9,10-dimethylanthracene (DMA) and confirmed by the direct observation of the O2(1Δg) luminescence spectrum (centered at 1270 nm) and the measurement of its kinetic profile. These results highlight the potential application of this type of polymeric material in the production of biological- or microbial-photoinactivating flexible surfaces or in the implementation of interfacial solid/liquid strategies for the photoinduced oxidation of organic compounds in solution.CONICYT 7913003
DNAzymes are known to bind metal ions specifically to carry out catalytic functions. Despite many studies since DNAzymes were discovered nearly two decades ago, the metal-binding sites in DNAzymes are not fully understood. Herein, we adopt uranyl photocleavage to probe specific uranyl-binding sites in the 39E DNAzyme with catalytically relevant concentrations of uranyl. The results indicate that uranyl binds between T23 and C25 in the bulge loop, G11 and T12 in the stem loop of the enzyme strand, as well as between T2.4 and G3 close to the cleavage site in the substrate strand. Control experiments using two 39E DNAzyme mutants revealed a different cleavage pattern of the mutated region. Another DNAzyme, the 8–17 DNAzyme, which has a similar secondary structure but shows no activity in the presence of uranyl, indicated a different uranyl-dependent photocleavage as well. In addition, a close correlation between the concentration-dependent photocleavage and enzymatic activities is also demonstrated. Together, these experiments suggest that uranyl photocleavage has been successfully used to probe catalytically relevant uranyl-binding sites in the 39E DNAzyme. As uranyl is the cofactor of the 39E DNAzyme as well as the probe, specific uranyl binding has now been identified without disruption of the structure.
The spectroscopic, electrochemical, and photophysical properties of the new complex [P,N-{(C6H5)2(C5H4N)P}Re(CO)3Br] are reported. The UV-vis spectrum in dichloromethane shows an absorption maximum centered at 315 nm and a shoulder at 350 nm. These absorption bands have been characterized to have MLCT character. Excitation at both wavelengths (maximum and shoulder) leads to an emission band centered at 550 nm. Cyclic voltammetry experiments show two ill-defined irreversible oxidation waves around +1.50 and 1.80 V that are assigned to Re(I)/Re(II) and Re(II)/Re(III) couples whereas an irreversible reduction signal centered at -1.80 V is likewise assigned to a ligand reduction process. These results support the proposal of the MLCT nature of the states implied by the emission of the complex. The luminescent decay fits to a biexponential function, where the lifetimes and emission quantum yields are dependent on the solvent polarity. DFT calculations suggest that dπ → π*pyridine and dπ → π*phenyl excited states may account for the existence of two decay lifetimes.
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