Studies of RNA cleavage by photolysis of N-hydroxypyridine-2(1H)-thione. A new photochemical footprinting method

Photochemical Hydroxyl Group Abstraction from N-Hydroxypyridine-2(1H)-thione Isolated in a Solid Hydrogen Matrix: Photogeneration of 2-Mercaptopyridine

Monomers of N-hydroxypyridine-2(1H)-thione were isolated in low-temperature matrices of solid normal hydrogen (n-H2). The matrix-isolated compound was irradiated with UV-B (λ = 305 nm) or UV-A (λ > 360 nm) light. Upon such irradiation, the initial form of N-hydroxypyridine-2(1H)-thione was completely consumed and converted into photoproducts. 2-Mercaptopyridine and water were identified as the main products of these photochemical transformations. Identification of photoproduced 2-mercaptopyridine is unquestionable. It is based on the identity of two sets of IR bands: (i) the bands observed in the IR spectrum recorded (in a separate experiment) for monomers of 2-mercaptopyridine trapped in an n-H2 matrix and (ii) a set of IR bands observed in the spectrum recorded after UV irradiation of N-hydroxypyridine-2(1H)-thione. It should be emphasized that the UV-induced processes, occurring for N-hydroxypyridine-2(1H)-thione isolated in an n-H2 matrix, lead to products that are significantly different from those generated from the compound trapped in solid Ar or in solid N2.

Metal Complexes of Omadine (N-Hydroxypyridine-2-thione): Differences of Antioxidant and Pro-Oxidant Behavior in Light and Dark Conditions with Possible Toxicity Implications

Omadine or N-hydroxypyridine-2-thione and its metal complexes are widely used in medicine and show bactericidal, fungicidal, anticancer, and photochemical activity. The redox activity of omadine complexes with iron, copper, and zinc on lipid peroxidation under light and dark conditions has been investigated. The monitoring of the oxidation of linoleic acid micelles, resembling a model of lipid membrane, was carried out using nuclear magnetic resonance (¹H-NMR). It has been shown that the omadine-zinc complex can induce the oxidation of linoleic acid under light irradiation, whereas the complexes with iron and copper are photochemically stable. All the chelating complexes of omadine appear to be redox-inactive in the presence of hydrogen peroxide under dark conditions. These findings suggest that omadine can demonstrate antioxidant behavior in processes involving reactive oxygen species generation induced by transition metals (Fenton and photo-Fenton reactions). However, the omadine complex with zinc, which is widely used in shampoos and ointments, is photochemically active and may cause oxidative cell membrane damage when exposed to light, with possible implications to health.

Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications

Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.

DNA methylation and transcriptomic changes in response to different lights and stresses in 7B-1 male-sterile tomato

We reported earlier that 7B-1 mutant in tomato (Solanum lycopersicum L., cv. Rutgers), an ABA overproducer, is defective in blue light (B) signaling leading to B-specific resistance to abiotic and biotic stresses. Using a methylation-sensitive amplified polymorphism (MSAP) assay, a number of genes were identified, which were differentially methylated between 7B-1 and its wild type (WT) seedlings in white (W), blue (B), red (R) lights and dark (D) or in response to exogenous ABA and mannitol-induced stresses. The genomic methylation level was almost similar in different lights between 7B-1 and WT seedlings, while significant differences were observed in response to stresses in D, but not B. Using a cDNA-AFLP assay, several transcripts were identified, which were differentially regulated between 7B-1 and WT by B or D or in response to stresses. Blue light receptors cryptochrome 1 and 2 (CRY1 and CRY2) and phototropin 1 and 2 (PHOT1 and PHOT2) were not affected by the 7B-1 mutation at the transcriptional level, instead the mutation had likely affected downstream components of the light signaling pathway. 5-azacytidine (5-azaC) induced DNA hypomethylation, inhibited stem elongation and differentially regulated the expression of a number of genes in 7B-1. In addition, it was shown that mir167 and mir390 were tightly linked to auxin signaling pathway in 5-azaC-treated 7B-1 seedlings via the regulation of auxin-response factor (ARF) transcripts. Our data showed that DNA methylation remodeling is an active epigenetic response to different lights and stresses in 7B-1 and WT, and highlighted the differences in epigenetic and transcriptional regulation of light and stress responses between 7B-1 and WT. Furthermore, it shed lights on the crosstalk between DNA hypomethylation and miRNA regulation of ARFs expression. This information could also be used as a benchmark for future studies of male-sterility in other crops.

Tertiary structure mapping of the pri-miRNA miR-17~92

The understanding of RNA in regulating gene expression has exploded over the past 15 years. MicroRNAs (miRNAs) have vastly expanded the role of RNA in gene regulation beyond spliceosomal, ribosomal, and messenger RNAs. Approximately one half of miRNAs are polycistronic, where two or more miRNAs are encoded on a single pri-miRNA transcript, termed a miRNA cluster. The six miRNAs of the miR-17~92 cluster are contained within a ~800 nucleotide region within intron 3 of the cl13orf25 ~7 kb pri-miRNA transcript. We recently reported on the tertiary structured domain of miR-17~92 and its role in modulating miRNA biogenesis. The key finding was that the cluster structure explained the differential processing of the miRNA hairpins by Drosha. This work demonstrated the need to consider pri-miRNA tertiary structure in miRNA biogenesis. Since biochemical structure probing is typically performed on relatively short RNAs (≤200 nucleotides), we had to adapt these methodologies for application on large RNAs (~800 nucleotide miR-17~92 pri-miRNA). We present here our adaptation of a protection footprinting method using ribonucleases to probe the structure of the ~800 nucleotide miR-17~92 pri-miRNA. We outline the technical difficulties involved in probing large RNAs and data visualization using denaturing polyacrylamide gel electrophoresis and how we adapted the existing approaches to probe large RNAs. The methodology outlined here is generally applicable to large RNAs including long noncoding RNAs (lncRNA).

Precursors and formation of pyrithione and other pyridyl-containing sulfur compounds in drumstick onion, Allium stipitatum

Two novel, structurally unusual cysteine derivatives were isolated from the bulbs of Allium stipitatum (Allium subg. Melanocrommyum) and shown to be S-(2-pyridyl)cysteine N-oxide and S-(2-pyridyl)glutathione N-oxide. The former compound is the first example of a naturally occurring alliinase substrate that contains an N-oxide functionality instead of the S-oxide group. In addition, S-methylcysteine S-oxide (methiin) and S-(methylthiomethyl)cysteine 4-oxide (marasmin) were found in the bulbs. Presented data suggest that the previously reported identification of S-(2-pyridyl)cysteine S-oxide was most likely erroneous. The alliinase-mediated formation of pyridyl-containing compounds following disruption of A. stipitatum bulbs was studied by a combination of HPLC-MS, HPLC-PDA, DART-MS, and NMR techniques. It was found that no pyridyl-containing thiosulfinates are present in homogenized bulbs in detectable quantities. Instead, various pyridine N-oxide derivatives are formed, including N-hydroxypyridine-2(1H)-thione (pyrithione), 2-(methyldithio)pyridine N-oxide, 2-[(methylthio)methyldithio]pyridine N-oxide, di(2-pyridyl) disulfide N-oxide, and di(2-pyridyl) disulfide N,N'-dioxide. This represents the first report of pyrithione formation as a natural product.

Chemical probing of RNA and RNA/protein complexes

Chemical probing is widely used as a rapid approach for assessing RNA structure, folding, and function. In this chapter, we outline procedures for handling and using chemicals commonly used to probe nucleic acids. Detailed experimental conditions and design for footprinting and modification interference are presented herein. Protocols for RNA extraction, normalization, primer extension, and data evaluation are also provided. The methods described are designed to aid in the study of large RNAs, but with slight modifications are applicable to smaller RNAs.

Thioperoxy derivative generated by UV-induced transformation of N-hydroxypyridine-2(1H)-thione isolated in low-temperature matrixes

Photochemical transformations of N-hydroxypyridine-2(1H)-thione and its deuterated isotopologue were studied using the matrix-isolation technique. Low-temperature Ar and N2 matrixes containing monomers of this compound were irradiated with continuous-wave near-UV light. Photogeneration of two products was observed in these experiments. The relative population of these photogenerated species was found to be dependent on the wavelength of the UV light used for irradiation. By comparison of the IR spectra of the photoproducts with the spectra simulated theoretically at the DFT(B3LYP)/6-311++G(d, p) level, the final and the intermediate products were identified as rotameric forms of 2-hydroxysulfanyl-pyridine. This is the first report on generation of this thioperoxy derivative of pyridine. The mechanism of photogeneration of 2-hydroxysulfanyl-pyridine involves a photoinduced cleavage of the N-O bond in N-hydroxypyridine-2(1H)-thione, generation of the .OH radical weakly bound with the remaining pyridylthiyl radical, and recombination of these two radicals by formation of the new -S-O- bond. A theoretical model supporting this interpretation was constructed on the basis of approximate coupled cluster (CC2) calculations of the potential energy surfaces of the ground and first excited singlet electronic states of the system. After electronic excitation of the monomeric N-hydroxypyridine-2(1H)-thione, the molecule evolves to the conical intersection with the potential energy surface of the ground state and then to the global minimum corresponding to 2-hydroxysulfanyl-pyridine.

Efficient visible light induced nuclease activity of a ternary mono-1,10-phenanthroline copper(II) complex containing 2-(methylthio)ethylsalicylaldimine

Ternary Schiff base copper(II) complex [CuL(phen)](ClO(4)), where HL is 2-(methylthio)ethylsalicylaldimine and phen is 1,10-phenanthroline, has been prepared and structurally characterized by X-ray crystallography. The complex shows a CuN(3)OS coordination in a square-pyramidal (4 + 1) geometry with the sulfur as an equatorial ligand. The complex is an avid binder to double-stranded DNA in the minor groove and exhibits both photonuclease and chemical nuclease activity. When exposed to UV light of 312 nm (96 W) or visible light of 532 nm (125 W) under aerobic conditions, the complex causes significant cleavage of supercoiled pUC19 DNA in the absence of any externally added reducing agent or H(2)O(2).

Studies on cytotoxic and genotoxic effects of N-hydroxypyridine-2-thione (Omadine) in L5178Y mouse lymphoma cells

The cytotoxicity and genotoxicity of the antifungal and antimicrobial agent Omadine, i.e. N-hydroxypyridine-2-thione (HOPT), has been investigated in L5178Y mouse lymphoma cells in the dark and under UVA irradiation. Omadine inhibits cell growth and induces micronuclei at concentrations >0.5 microM in the absence of light. At a 0.5-microM concentration, an UVA-dose-dependent induction of micronuclei is observed, conditions at which the cytotoxicity and genotoxicity in the dark is negligible. The photogenotoxicity is not accompanied by cytotoxicity. Control experiments with the radical scavengers GSH and GSHOEt implicate the involvement of hydroxyl radicals in the photogenotoxicity of Omadine.

Beyond kinetic traps in RNA folding

Large RNAs often have rugged folding energy landscapes that result in severe misfolding and slow folding kinetics. Several interdependent parameters that contribute to misfolding are now well understood and examples of large RNAs and ribonucleoproteins that avoid kinetic traps have been reported. These advances have facilitated the exploration of fundamental RNA folding processes that were previously inaccessible.