RNA modifications identification based on chemical reactions

RNA modification identification is an emerging field in epigenetics due to its indispensable regulatory role in the cell life cycle. With advancements in identification methods, an increasing number of RNA modifications has been discovered, thereby driving the development of more efficient and accurate techniques for localizing modified RNAs and elucidating their functions. High-throughput sequencing approaches for modified RNA detection can be categorized into antibody-based, enzymatic-based, and chemical-labeling-based methods. Given the intrinsic chemical reactions involved in all biochemical processes, we provide a comprehensive review of recent advancements in artificial chemical labeling and transformations of ten distinct RNA modifications and their applications in sequencing. Our aim is to contribute to a deeper understanding of the mechanisms underlying these modifications. We focus on the chemical reactions associated with RNA modifications and briefly compare the advantages and disadvantages of detection methods based on these reactions. Additionally, we introduce several approaches that identify multiple modifications through chemical labeling. As the field of RNA modification research continues to expand, we anticipate that the techniques and insights presented in this review will serve as a valuable resource for future studies aimed at further elucidating the functional roles of RNA modifications in biological processes.

Advances in the investigation of N6-isopentenyl adenosine i6A RNA modification

Prenylation (isopentenylation), a key post-transcriptional modification with a hydrophobic prenyl group onto the biomacromolecules such as RNA and proteins, influences their localization and function. Prenyltransferases mediate this process, while cytokinin oxidases degrade the prenylated adenosine in plants. This review summarizes current progress in detecting prenylation modifications in RNA across species and their effects on protein synthesis. Advanced methods have been developed to label and study these modifications in vitro and in vivo, despite challenges posed by the inert chemical properties of prenyl groups. Continued advancements in bioorthogonal chemistry promise new tools for understanding the precise biological functions of prenylated RNA modifications and other related proteins.

In situ bioorthogonal-modulation of m6A RNA methylation in macrophages for efficient eradication of intracellular bacteria

N6-Methyladenosine (m6A) methylation plays a critical role in controlling the RNA fate. Emerging evidence has demonstrated that aberrant m6A methylation in immune cells such as macrophages could alter cell homeostasis and function, which can be a promising target for disease treatment. Despite tremendous progress in regulating the level of m6A methylation, the current methods suffer from the time-consuming operation and annoying off-target effect, which hampers the in situ manipulation of m6A methylation. Here, a bioorthogonal in situ modulation strategy of m6A methylation was proposed. Well-designed covalent organic framework (COF) dots (CIDM) could deprotect the agonist prodrug of m6A methyltransferase, resulting in a considerable hypermethylation of m6A modification. Simultaneously, the bioorthogonal catalyst CIDM showed oxidase (OXD)-mimic activity that further promoted the level of m6A methylation. Ultimately, the potential therapeutic effect of bioorthogonal controllable regulation of m6A methylation was demonstrated through intracellular bacteria eradication. The remarkable antimicrobial outcomes indicate that upregulating m6A methylation in macrophages could reprogram them into the M1 phenotype with high bactericidal activity. We believe that our bioorthogonal chemistry-controlled epigenetics regulatory strategy will provide a unique insight into the development of controllable m6A methylation.

Discovery of Photoexcited 2-Chloro-3,5-Dinitrobenzoic Acid as a Chemical Deprenylase of i6A RNA

RNA modifications play crucial roles in regulating gene expression and cellular homeostasis. Modulating RNA modifications, particularly by targeting the enzymes responsible for their catalysis, has emerged as a promising therapeutic strategy. However, limitations, such as the lack of identified modifying enzymes and compensatory mechanisms, hinder targeted interventions. Chemical approaches independent of enzymatic activity offer an alternative strategy for RNA modification modulation. Here, we present the identification of 2-chloro-3,5-dinitrobenzoic acid as a highly effective photochemical deprenylase of i6A RNA. This method demonstrates exceptional selectivity towards i6A, converting its substituent into a "N-doped" ozonide, which upon hydrolysis releases natural adenine. We believe that this chemical approach will pave the way for a better understanding of RNA modification biology and the development of novel therapeutic modalities.

Photodynamic and Antibacterial Assessment of Gold Nanoparticles Mediated by Gold (III) Chloride Trihydrate and Sodium Citrate under Alkaline Conditions

Sodium citrate (SC) is sensitive to violet light illumination (VLI) and acts as a weak reductant. Conversely, gold (III) chloride trihydrate (GC) often acts as an oxidant in a redox reaction. In this study, the influences of colored light on the production of gold nanoparticles (AuNPs) in a mixture of gold (III) ions and citrate via VLI and the antibacterial photodynamic inactivation (aPDI) of Escherichia coli (E. coli) are determined under alkaline conditions. The diameter of AuNPs is within the range of 3-15 nm, i.e., their mean diameter is 9 nm; when citrate is mixed with gold (III) ions under VLI, AuNPs are formed via an electron transfer process. Additionally, GC mixed with SC (GCSC) inhibits E. coli more effectively under VLI than it does under blue, green, or red light. GCSC and SC are shown to inhibit E. coli populations by 4.67 and 1.12 logs, respectively, via VLI at 10 W/m2 for 60 min under alkaline conditions. GCSC-treated E. coli has a more significant photolytic effect on anionic superoxide radical (O2•-) formation under VLI, as more O2•- is formed within E. coli if the GCSC-treated samples are subjected to VLI. The O2•- exhibits a greater effect in a solution of GCSC than that shown by SC alone under VLI treatment. Gold (III) ions in a GCSC system appear to act as an oxidant by facilitating the electron transfer from citrate under VLI and the formation of AuNPs and O2•- via GCSC photolysis under alkaline conditions. As such, the photolysis of GCSC under VLI is a useful process that can be applied to aPDI.

Selective Methylation of Nucleosides via an In Situ Generated Methyl Oxonium

A very mild and efficient procedure has been developed for the preparation of N-methylated uridine, pseudouridine, guanosine and inosine derivatives. This process was compatible with free hydroxyls within the ribose and did not require precautions on the protection or deprotection of other functionalities. The key to this extremely mild methylation without protection relied on the in situ generated methyl oxonium from the Wittig reagent and methanol. A putative mechanism for the selective methylation was also proposed.

The effect of photolysis of sodium citrate treated with gold chloride using coloured light on the generation of gold nanoparticles and the repression of WiDr colon cancer cells

Gold nanoparticles (GNPs) are usually formed via a wet chemical method using gold (III) chloride trihydrate (GC), which is treated with stable reducing agents such as sodium citrate (SC). This study determines the effect of coloured light on the formation of GNPs by irradiation of SC after the addition of GC (SCGC) and the effect of the SCGC photolytic procedure on the suppression of WiDr colon cancer cells by forming reactive oxygen species. The absorbance of surface plasmon resonance peaks at 523 nm are 0.069 and 0.219 for SCGC when treated with blue light illumination (BLI) and violet light irradiation (VLI), respectively, whereas green and red light treatments have little or no effect. Most GNPs have diameters ranging from 3 to 15 nm, with a mean of 6 nm, when SCGC is exposed to VLI for 1.5 h. Anionic superoxide radicals (O2•-) are formed in a charge-transfer process after SCGC under VLI treatment; however, BLI treatment produces no significant reaction. Moreover, SCGC under VLI treatment proves to be considerably more effective at inhibiting WiDr cells than BLI treatment, as firstly reported in this study. The reduction rates for WiDr cells treated with SCGC under BLI and VLI at an intensity of 2.0 mW/cm2 for 1.5 h (energy dose, 10.8 J/cm2) are 4.1% and 57.7%, respectively. The suppression rates for WiDr cells treated with SCGC are inhibited in an irradiance-dependent manner, the inhibition percentages being 57.7%, 63.3%, and 80.2% achieved at VLI intensities of 2.0, 4.0, and 6.0 mW/cm2 for 1.5 h, respectively. Propidium iodide is a fluorescent dye that detects DNA changes after cell death. The number of propidium iodide-positive nuclei significantly increases in WiDr cells treated with SCGC under VLI, suggesting that SCGC photolysis under VLI is a potential treatment option for the photodynamic therapy process.

Tailoring flavin-based photosensitizers for efficient photooxidative coupling of benzylic amines

Photooxidative coupling of benzylic amines using naturally abundant O2 as an oxidant under visible light irradiation is an alternative green approach to synthesis imines and is of both fundamental and practical significance. We investigated the photophysical properties of flavin (FL) that is a naturally available sensitizer and its derivatives, i.e. 9-bromoflavin (MB-FL), 7,8-dibromoflavin (DB-FL) and 10-phenylflavin (Ph-FL), as well as the performance of these FL-based sensitizers (FLPSs) in the photooxidative coupling of benzylic amines to imines combining experimental and theoretical efforts. We showed that chemical functionalization with Br and phenyl effectively improves the photophysical properties of these FLPSs, in terms of absorption in the visible light range, singlet oxygen quantum yields, triplet lifetime, etc. Apart from nearly quantitative selectivity for the production of imines, the performance of DB-FL is superior to those of other FLPSs, and it is among the best photocatalysts for imine synthesis. Specifically, 0.5 mol% DB-FL is capable of converting 91% of 0.2 mmol benzylamine and more than 80% of 0.2 mmol fluorobenzylic amine derivatives into their corresponding imines in 5 h batch runs. Mechanistic investigation finely explained the observed photophysical properties of FLPSs and highlighted the dominant role of electron transfer in FLPS sensitized coupling of benzylic amines to imines. This work not only helps to understand the pathways for photocatalysis with FLPSs but also paves the way for the design of novel and efficient PSs to promote organic synthesis.

Kinetic isotope effect study of N-6 methyladenosine chemical demethylation in bicarbonate-activated peroxide system

N-6 methyladenosine is the most abundant nucleic acid modification in eukaryotes and plays a crucial role in gene regulation. The AlkB family of alpha-ketoglutarate-dependent dioxygenases is responsible for nucleic acid demethylation. Recent studies have discovered that a chemical demethylation system using hydrogen peroxide and ammonium bicarbonate can effectively demethylate nucleic acids. The addition of ferrous ammonium sulfate boosts the oxidation rate by forming a Fenton reagent with hydrogen peroxide. However, the specific mechanism and key steps of this process remain unclear. In this study, we investigate the influence of ferrous ammonium sulfate concentration on the kinetic isotope effect (KIE) of the chemical demethylation system using LC-MS. As the concentration of ferrous ions increases, the observed KIE decreases from 1.377 ± 0.020 to 1.120 ± 0.016, indicating a combination of the primary isotope effect and inverse α-secondary isotope effect with the ion pairing effect. We propose that the initial hydrogen extraction is the rate-limiting step and observe a tight transition state structure in the formation of the hm6A process through the analysis of KIE trends. The concentration-dependent KIE provides a novel perspective on the mechanism of chemical demethylation and offers a chemical model for enzyme-catalyzed demethylation.

Changes in m6A in Steatotic Liver Disease

Fatty liver disease is one of the major causes of morbidity and mortality worldwide. Fatty liver includes non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH), now replaced by a consensus group as metabolic dysfunction-associated steatotic liver disease (MASLD). While excess nutrition and obesity are major contributors to fatty liver, the underlying mechanisms remain largely unknown and therapeutic interventions are limited. Reversible chemical modifications in RNA are newly recognized critical regulators controlling post-transcriptional gene expression. Among these modifications, N6-methyladenosine (m6A) is the most abundant and regulates transcript abundance in fatty liver disease. Modulation of m6A by readers, writers, and erasers (RWE) impacts mRNA processing, translation, nuclear export, localization, and degradation. While many studies focus on m6A RWE expression in human liver pathologies, limitations of technology and bioinformatic methods to detect m6A present challenges in understanding the epitranscriptomic mechanisms driving fatty liver disease progression. In this review, we summarize the RWE of m6A and current methods of detecting m6A in specific genes associated with fatty liver disease.

Efficient and Selective Photogeneration of Stable N-Centered Radicals via Controllable Charge Carrier Imbalance in Cesium Lead Halide Nanocrystals

Despite the versatility of semiconductor nanocrystals (NCs) in photoinduced chemical processes, the generation of stable radicals has been more challenging due to reverse charge transfer or charge recombination even in the presence of sacrificial charge acceptors. Here, we show that cesium lead halide (CsPbX3) NCs can selectively photogenerate either aminium or aminyl radicals from amines, taking advantage of the controllable imbalance of the electron and hole populations achieved by varying the solvent composition. Using dihalomethane as the solvent, irreversible removal of the electrons from CsPbX3 NCs enabled by the photoinduced halide exchange between the NCs and the dihalomethane resulted in efficient oxidative generation of the aminium radical. In the absence of dihalomethane in solvent, the availability of both electrons and holes resulted in the production of an aminyl radical via sequential hole transfer and reductive N-H bond dissociation. The negative charge of the halide ions on the NC's lattice surface appears to facilitate the aminyl radical production, competing favorably with the reversible charge transfer reverting to the reactant.

Riboflavin mediates m6A modification targeted by miR408, promoting early somatic embryogenesis in longan

Plant somatic embryogenesis (SE) is an in vitro biological process wherein bipolar structures are induced to form somatic cells and regenerate into whole plants. MicroRNA (miRNA) is an essential player in plant SE. However, the mechanism of microRNA408 (miR408) in SE remains elusive. Here, we used stable transgenic technology in longan (Dimocarpus longan) embryogenic calli to verify the mechanism by which miR408 promotes cell division and differentiation of longan early SE. dlo-miR408-3p regulated riboflavin biosynthesis by targeting nudix hydrolase 23 (DlNUDT23), a previously unidentified gene mediating N6-methyladenosine (m6A) modification and influencing RNA homeostasis and cell cycle gene expression during longan early SE. We showed that DlMIR408 overexpression (DlMIR408-OE) promoted 21-nt miRNA biosynthesis. In DlMIR408-OE cell lines, dlo-miR408-3p targeted and downregulated DlNUDT23, promoted riboflavin biosynthesis, decreased flavin mononucleotide (FMN) accumulation, promoted m6A level, and influenced miRNA homeostasis. DNA replication, glycosylphosphatidylinositol (GPI)-anchor biosynthesis, the pentose phosphate pathway, and taurine and hypotaurine metabolism were also closely associated with riboflavin metabolism. In a riboflavin feeding assay, dlo-miR408-3p and pre-miR408 were upregulated and DlNUDT23 was downregulated, increasing the m6A level and cell division and differentiation in longan globular embryos. When riboflavin biosynthesis was inhibited, dlo-miR408-3p was downregulated and DlNUDT23 was upregulated, which decreased m6A modification and inhibited cell division but did not inhibit cell differentiation. FMN artificial demethylated m6A modification affected the homeostasis of precursor miRNA and miRNA. Our results revealed a mechanism underlying dlo-miR408-3p-activated riboflavin biosynthesis in which DlNUDT23 is targeted, m6A modification is dynamically mediated, and cell division is affected, promoting early SE in plants.

A Conformational Restriction Strategy for the Control of CRISPR/Cas Gene Editing with Photoactivatable Guide RNAs

The CRISPR/Cas system is one of the most powerful tools for gene editing. However, approaches for precise control of genome editing and regulatory events are still desirable. Here, we report the spatiotemporal and efficient control of CRISPR/Cas9- and Cas12a-mediated editing with conformationally restricted guide RNAs (gRNAs). This approach relied on only two or three pre-installed photo-labile substituents followed by an intramolecular cyclization, representing a robust synthetic method in comparison to the heavily modified linear gRNAs that often require extensive screening and time-consuming optimization. This tactic could direct the precise cleavage of the genes encoding green fluorescent protein (GFP) and the vascular endothelial growth factor A (VEGFA) protein within a predefined cutting region without notable editing leakage in live cells. We also achieved light-mediated myostatin (MSTN) gene editing in embryos, wherein a new bow-knot-type gRNA was constructed with excellent OFF/ON switch efficiency. Overall, our work provides a significant new strategy in CRISPR/Cas editing with modified circular gRNAs to precisely manipulate where and when genes are edited.

Implications of m6A methylation and microbiota interaction in non-small cell lung cancer: From basics to therapeutics

N6-methyladenine (m6A) is one of the most common RNA epigenetic modifications in all higher eukaryotes. Increasing evidence demonstrated that m6A-related proteins, acted as oncogenes or tumor suppressors, are abnormally expressed in the cell lines and tissues of non-small cell lung cancer (NSCLC). In addition, lung as the special immune organ contacts with the outer environments and thereby inevitably suffers from different types of microbial pathogen attack. Those microbial pathogens affect the development, progression, and clinical outcomes of NSCLC via altering host m6A modification to disrupt pulmonary immune homeostasis and increase the susceptibility; conversely, host cells modulate m6A modification to repress bacterial colonization. Therefore, m6A harbors the potential to be the novel biomarkers and targets for predicting poor prognosis and chemotherapy sensitivity of patients with lung cancer. In this paper, we provided an overview of the biological properties of m6A-modifying enzymes, and the mechanistic links among lung microbiota, m6A modification and NSCLC. Although the flood of novel m6A-related inhibitors represents many dramatic improvements in NSCLC therapy, their efficacy and toxicity in NSCLC are explored to address these pivotal gaps in the field.

N-Dealkylation of Amines

N-dealkylation, the removal of an N-alkyl group from an amine, is an important chemical transformation which provides routes for the synthesis of a wide range of pharmaceuticals, agrochemicals, bulk and fine chemicals. N-dealkylation of amines is also an important in vivo metabolic pathway in the metabolism of xenobiotics. Identification and synthesis of drug metabolites such as N-dealkylated metabolites are necessary throughout all phases of drug development studies. In this review, different approaches for the N-dealkylation of amines including chemical, catalytic, electrochemical, photochemical and enzymatic methods will be discussed.

A study of the effect of reactive oxygen species induced by violet and blue light from oxytetracycline on the deactivation of Escherichia coli

Oxytetracycline (OTC), a tetracycline antibiotic, is a broad-spectrum antibacterial agent. In this investigation, liquid chromatography-mass spectrometry (LC-MS) is utilized to determine the effects of blue light (λ = 448 nm) illumination (BLIA) and violet light (λ = 403 nm) illumination (VLIA) on conformational changes in OTC at pH 7.8. The photochemical effect of OTC that is exposed to BLIA and VLIA on the deactivation of Escherichia coli (E. coli) is studied. The deactivation of E. coli has an insignificant effect on treatment with OTC alone. OTC is relatively unstable under BLIA and VLIA illumination in an alkaline solution, and OTC has been shown to inactivate E. coli by generating reactive oxygen species (ROS). Less anionic superoxide radicals (O₂^•-) are generated from OTC that is treated with BLIA than that from VLIA treatment, so OTC is more efficient in inactivating E. coli under VLIA. Inactivation of reduction rates of 0.51 and 3.65 logs in E. coli are achieved using 0.1 mM OTC under BLIA for 120 min and VLIA for 30 min, respectively, under the same illumination intensity (20 W/m²). Two photolytic products of OTC (PPOs) are produced when OTC is exposed to BLIA and VLIA, with molecular ions at m/z 447 and 431, molecular formulae C₂₁H₂₂N₂O₉ and C₂₁H₂₂N₂O₈, and masses of 446.44 and 430.44 g/mol, respectively. The results show that when exposed to VLIA, OTC exhibits enhanced inactivation of E. coli, suggesting that the photochemical treatment of OTC is a potential supplement in a hygienic process.

Collateral Damage Occurs When Using Photosensitizer Probes to Detect or Modulate Nucleic Acid Modifications

Nucleic acids are chemically modified to fine-tune their properties for biological function. Chemical tools for selective tagging of base modifications enables new approaches; the photosensitizers riboflavin and anthraquinone were previously proposed to oxidize N⁶ -methyladenine (m⁶ A) or 5-methylcytosine (5mdC) selectively. Herein, riboflavin, anthraquinone, or Rose Bengal were allowed to react with the canonical nucleosides dA, dC, dG, and dT, and the modified bases 5mdC, m⁶ A, 8-oxoguanine (dOG), and 8-oxoadenine (dOA) to rank their reactivities. The nucleoside studies reveal that dOG is the most reactive and that the native nucleoside dG is higher or similar in reactivity to 5mdC or m⁶ A; competition in both single- and double-stranded DNA of dG vs. 5mdC or 6mdA for oxidant confirmed that dG is favorably oxidized. Thus, photosensitizers are promiscuous nucleic acid oxidants with poor chemoselectivity that will negatively impact attempts at targeted oxidation of modified nucleotides in cells.

Label-free and sensitive detection of RNA demethylase FTO with primer generation rolling circle amplification

We develop for the first time a label-free fluorescent method for sensitive detection of fat mass and obesity-associated protein (FTO) activity using MazF-mediated primer generation rolling circle amplification. This method is very simple with ultrahigh sensitivity and good specificity, and it can detect FTO activity at the single-cell level. Moreover, this method can be applied for the measurement of kinetic parameters and the screening of FTO inhibitors.

Effects of free radicals from doxycycline hyclate and minocycline hydrochloride under blue light irradiation on the deactivation of Staphylococcus aureus, including a methicillin-resistant strain

Doxycycline hyclate (DCH) and minocycline hydrochloride (MH) are tetracycline antibiotics and broad-spectrum antimicrobial agents. The changes in DCH and MH under blue light (λ = 462 nm) irradiation in alkaline conditions (BLIA) were investigated. Deactivation caused by superoxide anion radical (O2•-) and deactivation from DCH and MH during photolysis on Staphylococcus aureus (S. aureus), including methicillin-resistant S. aureus (MRSA), were studied. DCH is relatively unstable compared to MH under BLIA. The level of O2•- generated from the MH-treated photoreaction is lower than that from DCH photolysis, and the DCH-treated photoreaction is more efficient at inactivating S. aureus and MRSA at the same radiant intensity. DCH subjected to BLIA decreased the viability of S. aureus and MRSA by 3.84 and 5.15 log, respectively. Two photolytic products of DCH (PPDs) were generated under BLIA. The mass spectra of the PPDs featured molecular ions at m/z 460.8 and 458.8. The molecular formulas of the PPDs were C21H22N2O10 and C22H24N2O9, and their exact masses were 462.44 and 460.44 g/mol, respectively. These results bolster the photolytic oxidation that leads to DCH-enhanced deactivation of S. aureus and MRSA. Photochemical treatment of DCH could be applied as a supplement in hygienic processes.

Aqueous and Visible-Light-Promoted C-H (Hetero)arylation of Uracil Derivatives with Diazoniums

Direct C5 (hetero)arylation of uracil and uridine substrates with (hetero)aryl diazonium salts under photoredox catalysis with blue light was reported. The coupling proceeds efficiently with diazonium salts and heterocycles in good functional group tolerance at room temperature in aqueous solution without transition-metal components. A plausible radical mechanism has been proposed.

A Light-Controllable Chemical Modulation of m6 A RNA Methylation

Bioactive small molecules with photo-removable protecting groups have provided spatial and temporal control of corresponding biological effects. We present the design, synthesis, computational and experimental evaluation of the first photo-activatable small-molecule methyltransferase agonist. By blocking the functional N-H group on MPCH with a photo-removable ortho-nitrobenzyl moiety, we have developed a promising photo-caged compound that had completely concealed its biological activity. Short UV light exposure of cells treated with that caged molecule in a few minutes resulted in a considerable hypermethylation of m⁶ A modification in transcriptome RNAs, implicating a rapid release of the parent active compound. This study validates for the first time the photo-activatable small organic molecular concept in the field of RNA epigenetic research, which represents a novel tool in spatiotemporal and cellular modulation approaches.

A fast and direct iodide-catalyzed oxidative 2-selenylation of tryptophan

A metal-free 2-selenylation of tryptophan derivatives is reported, where the use of iodide as the catalyst and oxone as the oxidant is key to obtain high yields. Various functional groups within the di-seleny and the indole ring are tolerated, and no racemization is generally observed.

Regioselective synthesis and anticancer evaluation of H2O2-activable nucleosides

We describe here the design, synthesis, and biological evaluation of H2O2-activatable nucleosides via an efficient and regioselective functionalization of unprotected precursors. Biological evaluation of a H2O2-specific responsive prodrug of gemecitabin demonstrates an extremely fast activation, low toxicity and enhanced anticancer effects in two cell lines.

Selective Chemical Functionalization at N6-Methyladenosine Residues in DNA Enabled by Visible-Light-Mediated Photoredox Catalysis

Selective chemistry that modifies the structure of DNA and RNA is essential to understanding the role of epigenetic modifications. We report a visible-light-activated photocatalytic process that introduces a covalent modification at a C(sp3)-H bond in the methyl group of N6-methyl deoxyadenosine and N6-methyl adenosine, epigenetic modifications of emerging importance. A carefully orchestrated reaction combines reduction of a nitropyridine to form a nitrosopyridine spin-trapping reagent and an exquisitely selective tertiary amine-mediated hydrogen-atom abstraction at the N6-methyl group to form an α-amino radical. Cross-coupling of the putative α-amino radical with nitrosopyridine leads to a stable conjugate, installing a label at N6-methyl-adenosine. We show that N6-methyl deoxyadenosine-containing oligonucleotides can be enriched from complex mixtures, paving the way for applications to identify this modification in genomic DNA and RNA.

Chemical Deprenylation of N6 -Isopentenyladenosine (i6 A) RNA

N⁶ -isopentenyladenosine (i⁶ A) is an RNA modification found in cytokinins, which regulate plant growth/differentiation, and a subset of tRNAs, where it improves the efficiency and accuracy of translation. The installation and removal of this modification is mediated by prenyltransferases and cytokinin oxidases, and a chemical approach to selective deprenylation of i⁶ A has not been developed. We show that a selected group of oxoammonium cations function as artificial deprenylases to promote highly selective deprenylation of i⁶ A in nucleosides, oligonucleotides, and live cells. Importantly, other epigenetic modifications, amino acid residues, and natural products were not affected. Moreover, a significant phenotype difference in the Arabidopsis thaliana shoot and root development was observed with incubation of the cation. These results establish these small organic molecules as direct chemical regulators/artificial deprenylases of i⁶ A.

The Influence of the Degradation of Tetracycline by Free Radicals from Riboflavin-5'-Phosphate Photolysis on Microbial Viability

Tetracycline (TC) is a broad-spectrum antibiotic compound. Wastewater with TC may have an adverse effect on ecosystems. Riboflavin-5′-phosphate (FMN or flavin mononucleotide) is a non-toxic product of the phosphorylation of vitamin B₂ and is required for the proper functioning of the humans. FMN is sensitized to ultraviolet (UV) and blue light radiation, as evidenced by the generation of reactive oxygen species (ROS). This study inspects feasible applications of blue light on FMN so as to develop a valid way of degrading TC by FMN photolysis. We used the increased rate of bacterial survival as a practical indicator of antibiotic degradation. TC in the presence of FMN solution decomposed completely after 20 W/m² of blue light irradiation (TCF treatment), and the degradation of TC (D-TCF) occurred after the photolytic process. After TCF treatment, colony-forming units (CFUs) of Escherichia coli (E. coli) were determined for the D-TCF solution. The CFU of E. coli preservation was 93.2% of the D-TCF solution (50 μg/mL of TC in the presence of 114 μg/mL of FMN solution treated with 20 W/m² of blue light irradiation at 25 °C for 1 h) cultivation. The mass spectrum of D-TCF showed diagnostic ion signals at m/z 431.0 and 414.0 Da. The molecular formula of D-TCF was C₂₁H₂₂N₂O₈, and the exact mass was 430.44 g/mol. TC degradation by FMN photolysis can significantly decrease the antimicrobial ability of TC. The results expressed here regarding the influence of FMN photolysis on TC degradation offer an environmentally sound wastewater treatment method.

Identification of Flavin Mononucleotide as a Cell-Active Artificial N6 -Methyladenosine RNA Demethylase

N⁶ -Methyladenosine (m⁶ A) represents a common and highly dynamic modification in eukaryotic RNA that affects various cellular pathways. Natural dioxygenases such as FTO and ALKBH5 are enzymes that demethylate m⁶ A residues in mRNA. Herein, the first identification of a small-molecule modulator that functions as an artificial m⁶ A demethylase is reported. Flavin mononucleotide (FMN), the metabolite produced by riboflavin kinase, mediates substantial photochemical demethylation of m⁶ A residues of RNA in live cells. This study provides a new perspective to the understanding of demethylation of m⁶ A residues in mRNA and sheds light on the development of powerful small molecules as RNA demethylases and new probes for use in RNA biology.