Efficient Osmium/Rhenium‐Catalyzed Dihydroxylation of Olefins with Hydrogen Peroxide under Acidic Conditions

Simple addition of citric acid confers great stability to the catalytically active osmium and rhenium species involved in a triple catalytic system utilizing aqueous hydrogen peroxide as the terminal oxidant. The resulting system is capable of dihydroxylating traditionally resistant olefins in high yields.     

Anticancer Organometallic Osmium(II)‐p‐cymene Complexes

Osmium compounds are attracting increasing attention as potential anticancer drugs. In this context, a series of bifunctional organometallic osmium(II)‐p‐cymene complexes functionalized with alkyl or perfluoroalkyl groups were prepared and screened for their antiproliferative activity. Three compounds from the series display selectivity toward cancer cells, with moderate cytotoxicity observed against human ovarian carcinoma (A2780) cells, whereas no cytotoxicity was observed on non‐cancerous human embryonic kidney (HEK‐293) cells and human endothelial (ECRF24) cells. Two of these three cancer‐cell‐selective compounds induce cell death largely via apoptosis and were also found to disrupt vascularization in the chicken embryo chorioallantoic membrane (CAM) model. Based on these promising properties, these compounds have potential clinical applications.     

Formation of RNA Phosphodiester Bond by Histidine‐Containing Dipeptides

A new scenario for prebiotic formation of nucleic acid oligomers is presented. Peptide catalysis is applied to achieve condensation of activated RNA monomers into short RNA chains. As catalysts, L ‐dipeptides containing a histidine residue, primarily Ser‐His, were used. Reactions were carried out in selforganised environment, a water‐ice eutectic phase, with low concentrations of reactants. Incubation periods up to 30 days resulted in the formation of short oligomers of RNA. During the oligomerisation, an active intermediate (dipeptide–mononucleotide) is produced, which is the reactive species. Details of the mechanism and kinetics, which were elucidated with a set of control experiments, further establish that the imidazole side chain of a histidine at the carboxyl end of the dipeptide plays a crucial role in the catalysis. These results suggest that this oligomerisation catalysis occurs by a transamination mechanism. Because peptides are much more likely products of spontaneous condensation than nucleotide chains, their potential as catalysts for the formation of RNA is interesting from the origin‐of‐life perspective. Finally, the formation of the dipeptide–mononucleotide intermediate and its significance for catalysis might also be viewed as the tell‐tale signs of a new example of organocatalysis.     

Dry Polymerization of 3′,5′‐Cyclic GMP to Long Strands of RNA

Recent progress in the synthesis of nucleotides from prebiotically plausible precursors has opened up new ways to explain the origin of genetic matter. Mechanisms for the polymerization of nucleotides without the help of catalysts are, however, rare. Complementary to the experiments done by Costanzo et al., we found that drying 3′,5′‐cyclic GMP leads to poly‐G RNA strands with lengths of up to 40 nucleotides. We also show that the polymerization to long RNA strands is considerably more efficient under dry conditions than for cGMP polymerization in water. The length depends on the incubation time of dry nucleotides at temperatures of 40–80 °C. No enzymes or other catalysts are needed for successful polymerization.     

Microencapsulated Osmium Tetroxide‐Catalyzed Asymmetric Dihydroxylation of Olefins in Water without Using Organic Cosolvents

The asymmetric dihydroxylation of olefin using phenoxyethoxymethyl‐polystyrene (PEM)‐based microencapsulated osmium tetroxide (PEM‐MC OsO₄) proceeded smoothly in water as the sole solvent. The catalyst was recovered quantitatively by simple filtration and reused several times without loss of activity.     

Catalytic Asymmetric Dihydroxylation of Aliphatic Olefins with Reusable Resin‐Osmium Tetroxide

Asymmetric dihydroxylation of aliphatic olefins to chiral diols with good yields and ees by a heterogeneous Resin‐OsO₄ catalyst using ferricyanide as cooxidant is disclosed for the first time. The catalyst was recovered quantitatively by simple filtration and reused for several times without significant loss of activity.     

A Novel Microencapsulated Osmium Catalyst Using Cross‐Linked Polystyrene as an Efficient Catalyst for Asymmetric Dihydroxylation of Olefins in Water

A novel microencapsulated osmium catalyst (PSresin‐MC Os) was developed using cross‐linked polystyrene. The concept of this method may go beyond that of microencapsulation. The catalyst was successfully used in asymmetric dihydroxylation in water, and it was recovered quantitatively by simple filtration and reused several times without loss of activity. The shape of the catalyst was maintained even after several uses. Moreover, no leaching of the Os component was detected.     

Silica Gel‐Supported Cinchona Alkaloid‐OsO4 Complex for Catalytic Heterogeneous Asymmetric Dihydroxylation of Olefins by H2O2 using a Titanium Silicalite‐Based Coupled Catalytic System

A triple catalytic system designed for asymmetric dihydroxylation of olefins, composed of NMM and two divergent heterogeneous catalysts, titanium silicalite and silica gel‐supported 1,4‐bis(9‐O‐dihydroquinidinyl)phthalazine [SGS‐(DHQD)₂PHAL)]‐OsO₄ complex relays the transport of two electrons from olefin to H₂O₂ used as a terminal oxidant to provide chiral diols with good yields and high enantiomeric excesses in a single pot.     

2′‐Bispyrene‐Modified 2′‐O‐Methyl RNA Probes as Useful Tools for the Detection of RNA: Synthesis,Fluorescent Properties,and Duplex Stability

The synthesis and properties two series of new 2′‐O‐methyl RNA probes, each containing a single insertion of a 2′‐bispyrenylmethylphosphorodiamidate derivative of a nucleotide (U, C, A, and G), are described. As demonstrated by UV melting studies, the probes form stable complexes with model RNAs and DNAs. Significant increases (up to 21‐fold) in pyrene excimer fluorescence intensity were observed upon binding of most of the probes with complementary RNAs, but not with DNAs. The fluorescence spectra are independent of the nature of the modified nucleotides. The nucleotides on the 5′‐side of the modified nucleotide have no effect on the fluorescence spectra, whereas the natures of the two nucleotides on the 3′‐side are important: CC, CG, and UC dinucleotide units on the 3′‐side of the modified nucleotide provide the maximum increases in excimer fluorescence intensity. This study suggests that these 2′‐bispyrene‐labeled 2′‐O‐methyl RNA probes might be useful tools for detection of RNAs.     

Development and Applications of Coarse-Grained Models for RNA

In contrast to proteins, much less attention has been focused on the development of computational models for describing RNA molecules, which are being recognized as playing key roles in many cellular functions. Current atomically detailed force fields are not accurate enough to capture the properties of even simple nucleic acid constructs. In this article, we review our efforts to develop coarse-grained (CG) models that capture the underlying physics for the particular length scale of interest. Two models are discussed. One of them is the three interaction site (TIS) model, in which each nucleotide is represented by three beads corresponding to sugar, phosphate, and base. The other is the self-organized polymer (SOP) model, in which each nucleotide is represented as a single interaction center. Applications of the TIS model to study the complexity of hairpin formation and the effects of crowding in a shifting equilibrium between two conformations in human telomerase pseudoknot are described. The work on crowding illustrates a direct link to the activity of telomerase. We use the SOP model to describe the response of the Tetrahymena ribozyme to force. The simulated unfolding pathways agree well with single molecule pulling experiments. We also review predictions for the unfolding pathways for the Azoarcus ribozyme. The success of the CG applications to describe dynamics in RNA gives hope that more complex processes involving RNA-protein interactions can be tackled using variants of the proposed models.     

Long Non-Coding RNA Epigenetics

Long noncoding RNAs exceeding a length of 200 nucleotides play an important role in ensuring cell functions and proper organism development by interacting with cellular compounds such as miRNA, mRNA, DNA and proteins. However, there is an additional level of lncRNA regulation, called lncRNA epigenetics, in gene expression control. In this review, we describe the most common modified nucleosides found in lncRNA, 6-methyladenosine, 5-methylcytidine, pseudouridine and inosine. The biosynthetic pathways of these nucleosides modified by the writer, eraser and reader enzymes are important to understanding these processes. The characteristics of the individual methylases, pseudouridine synthases and adenine–inosine editing enzymes and the methods of lncRNA epigenetics for the detection of modified nucleosides, as well as the advantages and disadvantages of these methods, are discussed in detail. The final sections are devoted to the role of modifications in the most abundant lncRNAs and their functions in pathogenic processes.     

Nonenzymatic Oligomerization of 3′,5′‐Cyclic CMP Induced by Proton and UV Irradiation Hints at a Nonfastidious Origin of RNA

We report that 3′,5′‐cyclic CMP undergoes nonenzymatic di‐ and trimerization at 20 °C under dry conditions upon proton or UV irradiation. The reaction involves stacking of the cyclic monomers and subsequent polymerization through serial transphosphorylations between the stacked monomers. Proton‐ and UV‐induced oligomerization of 3′,5′‐cyclic CMP demonstrates that pyrimidines—similar to purines—might also have taken part in the spontaneous generation of RNA under plausible prebiotic conditions as well as in an extraterrestrial context. The observed polymerization of naturally occurring 3′,5′‐cyclic nucleotides supports the possibility that the extant genetic nucleic acids might have originated by way of a straight Occamian path, starting from simple reactions between plausibly preactivated monomers.     

Molar mass distributions of polymers from size exclusion chromatography and matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry: Methods for comparison

Equations are presented for calculating molar mass averages and molar mass distributions from matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) data and from size exclusion chromatography (SEC) data. The utility of polydispersity is examined as an indicator of the expectation of MALDI‐TOF MS mass discrimination effects. Cumulative distributions are found to be rich in information for comparing the two techniques and are easily obtained from both SEC and MALDI‐TOF MS data. Analyses of a series of narrow molar mass distribution poly(methyl methacrylate) (PMMA) standards and one polydisperse sample have been performed with both methods. MALDI‐TOF MS did not detect dimer and trimer in the PMMA samples, and it often indicated lower amounts of high‐molar‐mass polymers than did SEC. The results showed that the distribution breadth, as evidenced by the standard deviation of the distribution (calculated from the polydispersity and number‐average molar mass), correlated well with the molar mass range observed in the MALDI‐TOF MS spectra, whereas the polydispersity alone did not. Ratioing the extremes in the molar mass concentrations measured with the SEC differential refractometer, which were necessary to adequately define molar mass distributions, showed that detector dynamic range values as high as approximately 370,000 were required for the polydisperse samples. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 97: 627–639, 2005     

Vicinal Diol-Tethered Nucleobases as Targets for DNA Redox Labeling with Osmate Complexes

Six-valent osmium (osmate) complexes with nitrogenous ligands have previously been used for the modification and redox labeling of biomolecules involving vicinal diol moieties (typically, saccharides or RNA). In this work, aliphatic (3,4-dihydroxybutyl and 3,4-dihydroxybut-1-ynyl) or cyclic (6-oxo-6-(cis-3,4-dihydroxypyrrolidin-1-yl)hex-2-yn-1-yl, PDI) vicinal diols are attached to nucleobases to functionalize DNA for subsequent redox labeling with osmium(VI) complexes. The diol-linked 2′-deoxyribonucleoside triphosphates were used for the polymerase synthesis of diol-linked DNA, which, upon treatment with K₂OsO₃ and bidentate nitrogen ligands, gave the desired Os-labeled DNA, which were characterized by means of the gel-shift assay and ESI-MS. Through ex situ square-wave voltammetry at a basal plane pyrolytic graphite electrode, the efficiency of modification/labeling of individual diols was evaluated. The results show that the cyclic cis-diol (PDI) was a better target for osmylation than that of the flexible aliphatic ones (alkyl- or alkynyl-linked). The osmate adduct-specific voltammetric signal obtained for Os^VI-treated DNA decorated with PDI showed good proportionality to the number of PDI per DNA molecule. The Os^VI reagents (unlike OsO₄) do not attack nucleobases; thus offering specificity of modification on the introduced glycol targets.