Israel Journal of Chemistry最新文献

{"title":"Cover Picture: Isr. J. Chem. 3/2024)","authors":"","doi":"10.1002/ijch.202480301","DOIUrl":"https://doi.org/10.1002/ijch.202480301","url":null,"abstract":"<p>Chemical Biology of Nucleic Acid Modifications Issue editor: Chun-Xiao Song, Guifang Jia, Seraphine Wegner, and Chengqi Yi. The cover picture highlights Chuan He's wide-ranging research contributions across chemical biology, nucleic acid chemistry, biology, and epigenetics. His work focused on understanding DNA and RNA modifications in gene regulation. His groundbreaking discovery of reversible RNA modification revealed a new mode of gene regulation by RNA alongside DNA — and protein-based epigenetic mechanisms, leading to the emergence of the epitranscriptomics field.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure>\u0000 </p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 3-4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202480301","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140648114","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":"Chemical Biology of Nucleic Acid Modifications – Celebrating the Groundbreaking Contributions of Chuan He","authors":"Chun-Xiao Song,&nbsp;Guifang Jia,&nbsp;Seraphine Wegner,&nbsp;Chengqi Yi","doi":"10.1002/ijch.202400036","DOIUrl":"https://doi.org/10.1002/ijch.202400036","url":null,"abstract":"&lt;p&gt;We are excited to present this special issue of the Israel Journal of Chemistry, which is dedicated to the prestigious Wolf Prize in Chemistry 2023 awarded to Chuan He for his &lt;i&gt;“pioneering work elucidating the chemistry and functional consequences of RNA modification”&lt;/i&gt;. In honor of Chuan's remarkable achievements, this special issue features contributions from a number of his past trainees, collaborators, and colleagues. Focusing on “Chemical Biology of nucleic acid modifications,” this collection underscores Chuan's pioneering work in epigenetics and epitranscriptomics, which has transformed our understanding of DNA and RNA modifications, unlocking new paths for diagnostics and treatments.&lt;span&gt;&lt;sup&gt;1, 2&lt;/sup&gt;&lt;/span&gt; We present a collection of 15 Research and Review Articles that demonstrate the wide-ranging impact of Chuan's work across chemical biology, nucleic acid chemistry, biology, epigenetics, biochemistry, and genomics.&lt;/p&gt;&lt;p&gt;The diverse chemical modifications in cellular DNA and RNA, as Chuan has shown, add new dimensions to gene regulation that are crucial throughout development and disease progression. Chuan has been a trailblazer in applying chemical biology tools to mapping and understanding these modifications. This special issue opens with a research article from Chuan's lab, which presents a quantitative sequencing method for 5-formylcytosine (f&lt;sup&gt;5&lt;/sup&gt;C) in RNA (R. Lyu &lt;i&gt;et al&lt;/i&gt;. https://doi.org/10.1002/ijch.202300111). f&lt;sup&gt;5&lt;/sup&gt;C is found in human tRNA and yeast mRNA, however, its transcriptome-wide distribution in mammals remained unexplored. Chuan's lab developed f&lt;sup&gt;5&lt;/sup&gt;C-seq based on pic-borane reduction to map f&lt;sup&gt;5&lt;/sup&gt;C transcriptome-wide and advanced our understanding of f&lt;sup&gt;5&lt;/sup&gt;C in human and mouse cells. The research paper on f&lt;sup&gt;5&lt;/sup&gt;C sequencing is complemented by a review from Cheng and coworkers, summarizing recent advances in f&lt;sup&gt;5&lt;/sup&gt;C detection methods through selective chemical labeling, enrichment, and sequencing (X. Wang &lt;i&gt;et al&lt;/i&gt;. https://doi.org/10.1002/ijch.202300178).&lt;/p&gt;&lt;p&gt;&lt;i&gt;N&lt;/i&gt;&lt;sup&gt;6&lt;/sup&gt;-methyladenosine (m&lt;sup&gt;6&lt;/sup&gt;A) is the most common mRNA modification in eukaryotes. Chuan's lab made a landmark discovery in 2011 by identifying the first RNA demethylase, FTO, which removes the methyl group from m&lt;sup&gt;6&lt;/sup&gt;A.&lt;span&gt;&lt;sup&gt;3&lt;/sup&gt;&lt;/span&gt; This discovery unveiled the concept of reversible RNA methylation and led to the birth of the epitranscriptomics field. Today, m&lt;sup&gt;6&lt;/sup&gt;A has become the most extensively studied RNA modification. Reflecting its prevalence, five articles in this issue are dedicated to m&lt;sup&gt;6&lt;/sup&gt;A, including two complementary review papers offer a comprehensive look at m&lt;sup&gt;6&lt;/sup&gt;A research. The review by Tang and coworkers is centered on m&lt;sup&gt;6&lt;/sup&gt;A detection methods (R. Ge &lt;i&gt;et al&lt;/i&gt;. ijch.202300181R1, accepted), while the review by Zhao and coworkers focuses on the biological functions of m&lt;sup&gt;6&lt;/sup&gt;A in gene regulation a","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 3-4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400036","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140648117","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":"Advanced Sequencing Techniques to Map RNA Methylation","authors":"Ge-Ge Song,&nbsp;Xiu Fan,&nbsp;Chun-Chun Gao,&nbsp;Yong-Liang Zhao,&nbsp;Yun-Gui Yang","doi":"10.1002/ijch.202400003","DOIUrl":"https://doi.org/10.1002/ijch.202400003","url":null,"abstract":"<p>RNA methylation is a crucial epigenetic modification widely present in RNA molecules, and has been demonstrated to play significant roles in diverse biological processes. Advances in detection and sequencing technologies have facilitated the identification of RNA modification-related regulatory proteins and their corresponding biological functions. In this paper, we provide a brief overview of several RNA methylation, including <i>N</i>⁶-methyladenosine(m⁶A), 5-methylcytidine(m⁵C), <i>N</i>¹-methyladenosine(m¹A), <i>N</i>⁷-methylguanosine(m⁷G) and <i>N</i>⁶, 2’-O-dimethyladenosine(m⁶Am), about their regulatory proteins, distribution patterns and biological functions, and mainly outline the advantages and limitations of the representative sequencing techniques. Finally, we discuss the technological challenges and future perspectives in RNA transcriptomic field.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 3-4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140648116","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":"25 Years of Quasiperiodic Crystallography in Physical Space using the Average Unit Cell Approach","authors":"J. Wolny,&nbsp;I. Bugański,&nbsp;R. Strzałka,&nbsp;J. Śmietańska-Nowak,&nbsp;A. Wnęk","doi":"10.1002/ijch.202300141","DOIUrl":"10.1002/ijch.202300141","url":null,"abstract":"<p>Since the discovery of quasicrystals 40 years ago, many new paradigms and methods have been introduced to crystallography. 25 years ago, a statistical method of structure and diffraction analysis of aperiodic materials was proposed and, over these years, developed to describe model and real systems. This short review paper briefly invokes the basic concepts of the method: a reference lattice and an average unit cell, but also gives an overview of its application to atomic structure and diffraction analysis of various systems. Results are briefly discussed for mathematical sequences (Fibonacci and Thue-Morse), model quasilattices in 2D and 3D (Penrose and Ammann tiling), refinements of real decagonal and icosahedral quasicrystals, analysis of structure disorder in quasicrystals, description of modulated systems, including macromolecular biological systems, and beyond usual application in crystallography.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 10-11","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140636753","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":"N6-Methyladenosine in Mammalian Messenger RNA: Function, Location, and Quantitation","authors":"Ruiqi Ge,&nbsp;Mengshu Emily He,&nbsp;Weixin Tang","doi":"10.1002/ijch.202300181","DOIUrl":"10.1002/ijch.202300181","url":null,"abstract":"<p><i>N</i>⁶-methyladenosine (m⁶A) is the most abundant internal modification in mammalian messenger RNA (mRNA), constituting 0.1 %–0.4 % of total adenosine residues in the transcriptome. m⁶A regulates mRNA stability and translation, pre-mRNA splicing, miRNA biogenesis, lncRNA binding, and many other physiological and pathological processes. While the majority of m⁶As occur in a consensus motif of DRm⁶ACH (D=A/G/U, R=A/G, H=U/A/C), the presence of such a motif does not guarantee methylation. Different RNA copies transcribed from the same gene may be methylated to varying levels. Within a single transcript, m⁶As are not evenly distributed, showing an enrichment in long internal and terminal exons. These characteristics of m⁶A deposition call for sequencing methods that not only pinpoint m⁶A sites at base resolution, but also quantitate the abundance of methylation across different RNA copies. In this review, we summarize existing m⁶A profiling methods, with an emphasis on next generation sequencing-(NGS−)based, site-specific, and quantitative methods, as well as several emerging single-cell methods.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 3-4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202300181","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140600915","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":"On the Fibonacci Tiling and its Modern Ramifications","authors":"Michael Baake,&nbsp;Franz Gähler,&nbsp;Jan Mazáč","doi":"10.1002/ijch.202300155","DOIUrl":"10.1002/ijch.202300155","url":null,"abstract":"<p>In the last 30 years, the mathematical theory of aperiodic order has developed enormously. Many new tilings and properties have been discovered, few of which are covered or anticipated by the early papers and books. Here, we start from the well-known Fibonacci chain to explain some of them, with pointers to various generalisations as well as to higher-dimensional phenomena and results. This should give some entry points to the modern literature on the subject.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 10-11","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202300155","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140600712","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":"Canonical-Cell Tilings and their Atomic Decorations","authors":"Nobuhisa Fujita,&nbsp;Marek Mihalkovič,&nbsp;Christopher L. Henley","doi":"10.1002/ijch.202300130","DOIUrl":"10.1002/ijch.202300130","url":null,"abstract":"<p>The canonical cell tiling is a geometrical framework that uses four kinds of basic polyhedra, called the canonical cells, to model the packing of atoms and clusters in icosahedral quasicrystals and related periodic approximants. Over the past three decades, it has become increasingly clear that this framework is the most sensible approach to describe related structures, albeit technically much less tractable than the Ammann-Kramer-Neri tiling, which is the simplest icosahedral tiling geometry based on the two Ammann rhombohedra. Geometrical arrangements of cells pose a number of combinatorial problems that cannot be handled using simple linear algebra, making it infeasible to determine structures using the standard six-dimensional scheme. This up-to-date review begins with the motivation, definition, and mathematical facts about the canonical cell tiling. Then the reader is taken through the zoo of concrete structures, from smaller periodic approximants to larger ones, along with an overview of the techniques and heuristics used to study them. The recent discovery of a quasiperiodic canonical cell tiling is also briefly illustrated. The latter half of this review surveys the atomistic modeling of real atomic structures in all the three existing structural families based on the decoration concept of the canonical cell tiling.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 10-11","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202300130","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140310882","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":"The Tsai vs. Bergman Cluster Stability in ZnMgSc 1/1 Periodic Approximant Crystal","authors":"Ireneusz Buganski,&nbsp;Radoslaw Strzalka,&nbsp;Janusz Wolny","doi":"10.1002/ijch.202300139","DOIUrl":"10.1002/ijch.202300139","url":null,"abstract":"<p>Quasicrystals with icosahedral symmetry can be classified into two main groups: Bergman-type and Tsai-type. While these are considered as distinct phases, they share a common feature of being constructed from atomic clusters, either Tsai or Bergman. In this study, we employ Density Functional Theory to perform electronic structure calculations on the Zn_84.79Mg_0.86Sc_14.35 periodic approximant crystal phase. Our investigation involves systematically displacing atoms from Tsai cluster sites to Bergman cluster sites, allowing us to explore modifications in the electronic structure. Our findings reveal that the stability of the phase is influenced by the interaction between Zn-4p and Sc-3d orbitals. We observe that the sp-d hybridization effect may play a more crucial role rather than Hume-Rothery stabilization, as this observation holds true regardless of the presence or absence of periodic boundary conditions. Notably, the additional atom present in the Tsai structure serves as a significant electron acceptor in low-energy orbitals. Its absence in Bergman structures results in a composition with fewer atoms possessing high-energy d orbitals. This discovery provides a rationale for the frequent occurrence of Bergman phases with transition metals or rare earth elements, which occupy less than 10 % of the sites in the structure.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 10-11","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140311064","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":"Approximations of Symbolic Substitution Systems in One Dimension","authors":"Lior Tenenbaum","doi":"10.1002/ijch.202300121","DOIUrl":"10.1002/ijch.202300121","url":null,"abstract":"<p>Periodic approximations of quasicrystals are a powerful tool in analyzing spectra of Schrödinger operators arising from quasicrystals, given the known theory for periodic crystals. Namely, we seek periodic operators whose spectra approximate the spectrum of the limiting operator (of the quasicrystal). This naturally leads to study the convergence of the underlying dynamical systems.</p><p>We treat dynamical systems which are based on one-dimensional substitutions. We first find natural candidates of dynamical subsystems to approximate the substitution dynamical system. Subsequently, we offer a characterization of their convergence and provide estimates for the rate of convergence. We apply the proposed theory to some guiding examples.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 10-11","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202300121","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140203997","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":"Non-Canonical Amino Acids for Engineering Peptides and Proteins with new Functions","authors":"Kelly Zhi Qi Zhou,&nbsp;Richard Obexer","doi":"10.1002/ijch.202400006","DOIUrl":"10.1002/ijch.202400006","url":null,"abstract":"<p>The universal genetic code, which specifies the 20 standard amino acids (AAs), forms the basis for all natural proteins. Researchers have developed efficient and robust <i>in vivo</i> and <i>in vitro</i> strategies to overcome the constraints of the genetic code to expand the repertoire of AA building blocks that can be ribosomally incorporated into proteins. This review summarizes the development of these <i>in vivo</i> and <i>in vitro</i> systems and their subsequent use for engineering of peptides and proteins with new functions. <i>In vivo</i> genetic code expansion employing engineered othogonal tRNA/aaRS pairs has led to the development of proteins that selectively bind small molecules, cleave nucleic acids and catalyze non-natural chemical transformations. <i>In vitro</i> genetic code reprogramming using Flexizymes coupled with mRNA display has resulted in potent macrocyclic peptides that selectively bind to therapeutically important proteins. Through these examples, we hope to illustrate how genetic code expansion and reprogramming, especially when coupled with directed evolution or <i>in vitro</i> selection techniques, have emerged as powerful tools for expanding the functional capabilities of peptides and proteins.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140204339","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}