{"title":"Discovery and Accurate Detection of Rare Nucleic Acid Modifications","authors":"Ru-Jia Luo, Hong-Xuan Chen, Jin-Wen Kong, Zhang Zhang, Nabieh Ayoub, Guan-Zheng Luo","doi":"10.1002/ijch.202400024","DOIUrl":"https://doi.org/10.1002/ijch.202400024","url":null,"abstract":"<p>Nucleic acid modifications play essential roles in diverse biological processes, ranging from gene expression regulation to stress response. While traditional research focused on common modifications like methylation, recent discoveries are unveiling a wide range of rare modifications with potentially crucial functions. However, accurately detecting and mapping these modifications pose significant challenges due to their low abundance and diverse chemical properties. This article summarizes the recent discoveries of rare DNA and RNA modifications across various organisms, highlighting their potential biological significance. Furthermore, it critically evaluates the limitations of current mapping techniques, including potential sources of false positives and negatives. Finally, the article discusses emerging strategies for overcoming these challenges and future opportunities in the field of rare nucleic acid modification detection.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 5","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141488673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Namjin Cho, Haneul Jin, Hyewon Jeon, Kanghun Lee, Joongoo Lee
{"title":"Expanding the Scope of Ribosome-Mediated Biosynthesis in vitro using tRNA-Aminoacylating Ribozyme","authors":"Namjin Cho, Haneul Jin, Hyewon Jeon, Kanghun Lee, Joongoo Lee","doi":"10.1002/ijch.202300174","DOIUrl":"https://doi.org/10.1002/ijch.202300174","url":null,"abstract":"<p>Proteins are synthesized within ribosomes through the polymerization of amino acids (AAs). This process requires prior activation of AAs through aminoacylation that attaches them to their corresponding transfer RNAs (tRNAs). Within cells, this attachment is facilitated by aminoacyl-tRNA synthetase, resulting in a tRNA:AA conjugate. A set of ribozymes developed to acylate tRNA with non-canonical substrates enables this process outside the confines of living cells, thereby facilitating the synthesis of novel bio-based products. In modern biotechnology, aminoacylating ribozymes contribute to the production of innovative bio-based materials bearing functional non-canonical chemical substrates (NCSs) and fill the gaps in synthesizing unique polymeric backbones, extending the scope beyond traditional peptide bonds. This review summarizes current understanding of flexizymes at the molecular level and their application in generating exceptional polymeric backbones through ribosome-mediated synthesis <i>in vitro</i>.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202300174","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142328506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Anionic Calixarenes in Biomembrane Transport of Peptides","authors":"Justin Neumann, Andreas Hennig","doi":"10.1002/ijch.202400023","DOIUrl":"https://doi.org/10.1002/ijch.202400023","url":null,"abstract":"<p>Biomembranes function as hydrophobic barriers for hydrophilic substances enabling compartmentalization in biological systems. This poses, however, a problem for the targeted introduction of cargo into cells. The result is a high demand for delivery pathways into cells with the goal to investigate biological processes or to treat diseases by improved delivery. Polycationic cell-penetrating peptides (CPPs) are interesting as they can cross cell membranes and transport attached cargos directly into the cytosol. Their efficiency can be improved by anionic amphiphilic counterion activators, which bind to the CPPs to form charge-neutralized counterion-CPP complexes with sufficient hydrophobicity to cross the lipid bilayer membrane. This review summarizes recent results, which establish amphiphilic calixarenes as a new class of biocompatible and non-cytotoxic counterion activators with very high transport activities at nanomolar concentrations. We also include a brief summary of fluorescence-based assays with large unilamellar vesicles (LUVs) to investigate counterion-activated transport. Current methods use liposome-encapsulated, supramolecular host-dye reporter pairs including calixarenes, which provide new mechanistic insights and enable rapid in vitro identification of suitable activators. Taken together, amphiphilic calixarenes are currently emerging as prime candidates for counterion activation of membrane transport, which are highly modifiable and can be specifically tailored towards different cargoes and membrane types.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 6-7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400023","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141967954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Practical Applications of Supramolecular Macrocyclic Hosts in the Field of Herbal Medicines","authors":"Huijuan Yu, Kejing Niu, Yuting Zhao, Yuefei Wang","doi":"10.1002/ijch.202300179","DOIUrl":"10.1002/ijch.202300179","url":null,"abstract":"<p>Herbal medicines (HMs) are gaining increasing popularity and recognition worldwide due to their eco-friendliness and efficacy. With their multi-compounds, multi-targets, and multi-pathways characteristics, HMs have been used in treatment of various diseases. However, the clinical applications of preparations containing HMs have been limited due to their inherent physicochemical properties, including low water solubility, poor stability, and unsatisfactory bioavailability of bioactive compounds. Supramolecular macrocyclic hosts, like cyclodextrins, calixarenes, cucurbiturils, and pillararenes, are important objects of researches in supramolecular chemistry. These hosts have been utilized to encapsulate the ingredients, improve the solubility of poorly water-soluble components, enhance the stability of the tested compounds, increase the bioavailability of bioactive compounds, and ensure the safety of HMs. Herein, we provide a brief introduction to the theories of supramolecular chemistry and summarize the extensive applications of supramolecular macrocyclic hosts in the field of HMs. These applications encompass the screening of bioactive compounds in HMs and the enhancement of druggability for HMs. We hope this review can provide a strategy for dealing with the challenges of HMs, thereby enabling their better applications and development.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 6-7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141343353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Antonius J. P. Hopstaken, Enno Große Wichtrup, Dr. Seino A. K. Jongkees
{"title":"The Great Codon Escape: Vacating Codons for Genetic Code Expansion and Ribosome Stalling","authors":"Antonius J. P. Hopstaken, Enno Große Wichtrup, Dr. Seino A. K. Jongkees","doi":"10.1002/ijch.202400012","DOIUrl":"10.1002/ijch.202400012","url":null,"abstract":"<p>In ribosomal synthesis of peptides and proteins, genetic information is translated into an amino acid polymer according to the genetic code, which describes the translational command encoded by each codon. However, parts of the genetic code can be adjusted to customize translations. One option is to remove decoding for a specific codon, resulting in a vacant codon. Such vacant codons can be used to stall the ribosome for mechanistic studies and display techniques. Alternatively, the liberated codon can be assigned to encode for incorporation of a noncanonical building block for expansion of the genetic code. In this review we provide an overview of the methods currently available for vacating codons in prokaryotic translation (agnostic of how these are later applied), targeting factors such as amino-acyl tRNA synthetases, tRNA, release factors, and the initiation machinery. Moreover, we assess applicability and compatibility of the currently available techniques and discuss which have the potential to develop into even more powerful approaches in the future.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141352039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Supramolecular Approaches to the Detoxification of Nerve Agents","authors":"Prof. Dr. Stefan Kubik","doi":"10.1002/ijch.202400019","DOIUrl":"10.1002/ijch.202400019","url":null,"abstract":"<p>A promising, but not yet practiced, approach to the treatment of neurotoxic organophosphate poisoning is the administration of a scavenger that rapidly deactivates the nerve agent before it can exert its toxic effects. The detoxification rates required for successful use of this therapy can currently only be achieved with enzymes, but synthetic scavengers, whose mode of action is based on key concepts of supramolecular chemistry, are an attractive alternative. Considerable progress has recently been made in the development of such scavengers, and compounds from several receptor classes are now available that not only bind nerve agents but also degrade them at promising rates. This review provides an overview of the field and highlights recent developments.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 6-7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400019","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141357892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Spatially and Single-Cell Resolved Profiling of RNA Life Cycle and Epitranscriptomics","authors":"Qiyang Zhou, Jianting Guo, Xiao Wang","doi":"10.1002/ijch.202400028","DOIUrl":"10.1002/ijch.202400028","url":null,"abstract":"<p>The intricate network of cell functions relies on gene expression programs, where the whole RNA life cycle from DNA to protein is subjected to extensive transcriptional and post-transcriptional gene regulation events. Established bulk RNA sequencing methods provide an averaged, transcriptome-wide quantification of the RNA life cycle, including transcription, processing, translation, transport, and degradation through RNA-protein interactions. Furthermore, numerous studies using bulk epitranscriptomic profiling unveiled that dynamic RNA modifications (e. g., <i>N</i><sup>6</sup>-Methyladenosine), add another layer of gene regulations. However, many regulatory events are cell-type specific, subcellularly localized, and subjected to cell-cell communications within the native tissue environment. Thanks to the advances in single-cell sequencing, spatial sequencing, and highly multiplexed imaging methods, we can routinely measure single-cell and spatial transcriptomics. Yet more comprehensive methods to profile every step of the RNA life cycle with single-cell and spatial information are still lacking. In this review, we will summarize and compare early explorations in developing state-of-the-art methods for spatially and single-cell resolved mapping of RNA kinetics, translation, RNA-protein interactions, and epitranscriptomics. It is promising that these new techniques will greatly facilitate our understanding of the RNA-centered regulation landscapes in different cell types and how the post-transcriptional regulations are interconnected within cellular and tissue architecture.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 5","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400028","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141270198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Direct, Quantitative, and Base-Resolution Sequencing of DNA and RNA Modifications","authors":"Haiqi Xu, Chun-Xiao Song","doi":"10.1002/ijch.202400007","DOIUrl":"10.1002/ijch.202400007","url":null,"abstract":"<p>Cellular DNA and RNA are decorated with diverse chemical modifications, which add new layers to gene regulation and play crucial roles across development and disease progression. Interest in understanding the functions of DNA and RNA modifications, as well as the related molecular mechanisms, has been growing, driving progress in developing chemical and biochemical tools to detect specific modifications. New technologies are important not only for uncovering biological functions, but also for driving conceptual revolutions. In this review, we highlighted our recent advances in developing new chemical tools to detect DNA and RNA modifications in a direct, quantitative, and base-resolution manner. These includes a novel borane reduction chemistry for DNA methylation sequencing; new cytosine modificaiton oxdation chemistry for enhanced DNA hydroxymethylation sequencing; and a novel bromoacrylamide cyclization chemistry for RNA pseudouridylation sequencing. We present a mechanistic overview of these tools and their applications in epigenetic and epitranscriptomic research.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 5","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141197612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Goonho Park, Angela Galdamez, Keon‐Hyoung Song, Masako Le, Kyle Kim, Jonathan H. Lin
{"title":"Ethnic Variation and Structure‐Function Analysis of Tauopathy‐Associated PERK Alleles","authors":"Goonho Park, Angela Galdamez, Keon‐Hyoung Song, Masako Le, Kyle Kim, Jonathan H. Lin","doi":"10.1002/ijch.202300173","DOIUrl":"https://doi.org/10.1002/ijch.202300173","url":null,"abstract":"EIF2AK3, also known as PERK, plays a pivotal role in cellular proteostasis, orchestrating the Unfolded Protein Response (UPR) and Integrated Stress Response (ISR) pathways. In addition to its central position in intracellular stress regulation, human GWAS identify EIF2AK3 as a risk factor in tauopathies, neurodegenerative diseases caused by aberrant tau protein accumulation. Guided by these genomic indicators, our investigation systematically analyzed human PERK variants, focusing on those with potential tauopathy linkages. We assembled a comprehensive data set of human PERK variants associated with Wolcott Rallison Syndrome (WRS), tauopathies, and bioinformatically predicted loss‐of‐function, referencing the gnomAD, Ensembl, and NCBI databases. We found extensive racial/ethnic variation in the prevalence of common <jats:italic>PERK</jats:italic> polymorphisms linked to tauopathies. Using SWISS‐MODEL, we identified structural perturbations in the ER stress‐sensing luminal domain dimers/oligomers of tauopathy‐associated PERK variants, Haplotypes A and B, in combination with another tauopathy‐linked R240H mutation. Recombinant expression of disease‐associated variants <jats:italic>in vitro</jats:italic> revealed altered PERK signal transduction kinetics in response to ER stress compared to the predominant non‐disease variant. In summary, our data further substantiates that human PERK variants identified in tauopathy genetic studies negatively impact PERK structure, function, and downstream signaling with significant variations in prevalence among different racial and ethnic groups.","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"35 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141152436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Porous Crystalline Organic Cages Made by Design","authors":"Dr. Svetlana Ivanova, Prof. Dr. Florian Beuerle","doi":"10.1002/ijch.202400025","DOIUrl":"10.1002/ijch.202400025","url":null,"abstract":"<p>Shape-persistent organic cages are an intriguing class of molecular porous materials. Through hierarchical molecular design, size and shape of the intrinsic molecular voids are controlled by dynamic covalent chemistry, while pore structure and topology are governed by noncovalent alignment in the solid state. However, the predictable and reliable crystallization of organic cages is still challenging since long-range superstructures are solely based on weak and rather unidirectional supramolecular interactions. In this tutorial review, we provide a general classification of porous solid-state materials and discuss specific design principles regarding the dynamic covalent reactions, the small-molecule building blocks and solid-state engineering. Furthermore, we introduce the most important analytical techniques for porous materials with a special focus on organic cages.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 6-7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400025","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140973743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}