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Journal articles on the topic 'Molecular Modifications'

Author: Grafiati

Published: 6 September 2023

Last updated: 31 July 2025

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1

Abbas, Sk Jahir, Sabina Yesmin, Sandeepa K. Vittala, et al. "Target Bioconjugation of Protein Through Chemical, Molecular Dynamics, and Artificial Intelligence Approaches." Metabolites 14, no. 12 (2024): 668. https://doi.org/10.3390/metabo14120668.

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Covalent modification of proteins at specific, predetermined sites is essential for advancing biological and biopharmaceutical applications. Site-selective labeling techniques for protein modification allow us to effectively track biological function, intracellular dynamics, and localization. Despite numerous reports on modifying target proteins with functional chemical probes, unique organic reactions that achieve site-selective integration without compromising native functional properties remain a significant challenge. In this review, we delve into site-selective protein modification using

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Rehpenn, Andreas, Alexandra Walter, and Golo Storch. "Molecular Editing of Flavins for Catalysis." Synthesis 53, no. 15 (2021): 2583–93. http://dx.doi.org/10.1055/a-1458-2419.

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AbstractThe diverse activity of flavoenzymes in organic transformations has fascinated researchers for a long time. However, when applied outside an enzyme environment, the isolated flavin cofactor only shows largely reduced activity. This highlights the importance of embedding the reactive isoalloxazine core of flavins in defined surroundings. The latter include crucial non-covalent interactions with amino acid side chains or backbone as well as controlled access to reactants such as molecular oxygen. Nevertheless, molecular flavins are increasingly applied in the organic laboratory as valuab

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Li, Yinglu, Zhiming Li, and Wei-Guo Zhu. "Molecular Mechanisms of Epigenetic Regulators as Activatable Targets in Cancer Theranostics." Current Medicinal Chemistry 26, no. 8 (2019): 1328–50. http://dx.doi.org/10.2174/0929867324666170921101947.

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Epigenetics is defined as somatically inheritable changes that are not accompanied by alterations in DNA sequence. Epigenetics encompasses DNA methylation, covalent histone modifications, non-coding RNA as well as nucleosome remodeling. Notably, abnormal epigenetic changes play a critical role in cancer development including malignant transformation, metastasis, prognosis, drug resistance and tumor recurrence, which can provide effective targets for cancer prognosis, diagnosis and therapy. Understanding these changes provide effective means for cancer diagnosis and druggable targets for better

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4

Eichler, Jerry, and Michael W. W. Adams. "Posttranslational Protein Modification in Archaea." Microbiology and Molecular Biology Reviews 69, no. 3 (2005): 393–425. http://dx.doi.org/10.1128/mmbr.69.3.393-425.2005.

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SUMMARY One of the first hurdles to be negotiated in the postgenomic era involves the description of the entire protein content of the cell, the proteome. Such efforts are presently complicated by the various posttranslational modifications that proteins can experience, including glycosylation, lipid attachment, phosphorylation, methylation, disulfide bond formation, and proteolytic cleavage. Whereas these and other posttranslational protein modifications have been well characterized in Eucarya and Bacteria, posttranslational modification in Archaea has received far less attention. Although ar

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5

Winter, Stefan, and Wolfgang Fischle. "Epigenetic markers and their cross-talk." Essays in Biochemistry 48 (September 20, 2010): 45–61. http://dx.doi.org/10.1042/bse0480045.

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Post-translational modifications of histone proteins in conjunction with DNA methylation represent important events in the regulation of local and global genome functions. Advances in the study of these chromatin modifications established temporal and spatial co-localization of several distinct ‘marks’ on the same histone and/or the same nucleosome. Such complex modification patterns suggest the possibility of combinatorial effects. This idea was originally proposed to establish a code of histone modifications that regulates the interpretation of the genetic code of DNA. Indeed, interdependenc

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Miki, Keishu, Takeshi Watanabe, and Shinji Koh. "Electrochemical Characterization of CVD-Grown Graphene for Designing Electrode/Biomolecule Interfaces." Crystals 10, no. 4 (2020): 241. http://dx.doi.org/10.3390/cryst10040241.

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In research on enzyme-based biofuel cells, covalent or noncovalent molecular modifications of carbon-based electrode materials are generally used as a method for immobilizing enzymes and/or mediators. However, the influence of these molecular modifications on the electrochemical properties of electrode materials has not been clarified. In this study, we present the electrochemical properties of chemical vapor deposition (CVD)-grown monolayer graphene electrodes before and after molecular modification. The electrochemical properties of graphene electrodes were evaluated by cyclic voltammetry an

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Wang, Ya-Nan, Chen-Yang Yu, and Hong-Zhong Jin. "RNA N6-Methyladenosine Modifications and the Immune Response." Journal of Immunology Research 2020 (January 21, 2020): 1–6. http://dx.doi.org/10.1155/2020/6327614.

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N6-methyladenosine (m6A) is the most important modification of messenger RNAs (mRNAs) and long noncoding RNAs (lncRNAs) in higher eukaryotes. Modulation of m6A modifications relies on methyltransferases and demethylases. The discovery of binding proteins confirms that the m6A modification has a wide range of biological effects and significance at the molecular, cellular, and physiological levels. In recent years, techniques for investigating m6A modifications of RNA have developed rapidly. This article reviews the biological significance of RNA m6A modifications in the innate immune response,

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8

Han, Dali, and Meng Michelle Xu. "RNA Modification in the Immune System." Annual Review of Immunology 41, no. 1 (2023): 73–98. http://dx.doi.org/10.1146/annurev-immunol-101921-045401.

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Characterization of RNA modifications has identified their distribution features and molecular functions. Dynamic changes in RNA modification on various forms of RNA are essential for the development and function of the immune system. In this review, we discuss the value of innovative RNA modification profiling technologies to uncover the function of these diverse, dynamic RNA modifications in various immune cells within healthy and diseased contexts. Further, we explore our current understanding of the mechanisms whereby aberrant RNA modifications modulate the immune milieu of the tumor micro

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9

Chukwuma Sr, Chrysanthus. "Characterization of the Clinical and Molecular Perspectives of Epigenetics." Archives of Clinical Investigation 1, no. 1 (2022): 01–07. http://dx.doi.org/10.31579/2834-8087/003.

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This review provides the latitude to examine the extant information in the univeral characterizations of epigenetic formulations. Epigenetics encompasses the interaction of behaviours and environment culminating in changes which influence gene activity. In contrast to genetic modifications, epigenetic modifications are reversible; and do not alter the DNA sequence but are capable of interferring in the way the DNA sequence is read. Epigenetic alterations involve genetic changes which effect gene functionality without modifying the underlying DNA sequence. DNA methylation depicts the covalent s

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10

Carson, Spencer, James Wilson, Aleksei Aksimentiev, Peter R. Weigele, and Meni Wanunu. "Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA." Nucleic Acids Research 44, no. 5 (2015): 2085–92. http://dx.doi.org/10.1093/nar/gkv1199.

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Abstract Oxidation of a DNA thymine to 5-hydroxymethyluracil is one of several recently discovered epigenetic modifications. Here, we report the results of nanopore translocation experiments and molecular dynamics simulations that provide insight into the impact of this modification on the structure and dynamics of DNA. When transported through ultrathin solid-state nanopores, short DNA fragments containing thymine modifications were found to exhibit distinct, reproducible features in their transport characteristics that differentiate them from unmodified molecules. Molecular dynamics simulati

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Wölk, Michele, Theres Schröter, Ralf Hoffmann, and Sanja Milkovska-Stamenova. "Profiling of Low-Molecular-Weight Carbonyls and Protein Modifications in Flavored Milk." Antioxidants 9, no. 11 (2020): 1169. http://dx.doi.org/10.3390/antiox9111169.

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Thermal treatments of dairy products favor oxidations, Maillard reactions, and the formation of sugar or lipid oxidation products. Additives including flavorings might enhance these reactions or even induce further reactions. Here we aimed to characterize protein modifications in four flavored milk drinks using samples along the production chain—raw milk, pasteurization, mixing with flavorings, heat treatment, and the commercial product. Therefore, milk samples were analyzed using a bottom up proteomics approach and a combination of data-independent (MSE) and data-dependent acquisition methods

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Ogihara, Takuo, Kenta Mizoi, and Akiko Ishii-Watabe. "Pharmacokinetics of Biopharmaceuticals: Their Critical Role in Molecular Design." Biomedicines 11, no. 5 (2023): 1456. http://dx.doi.org/10.3390/biomedicines11051456.

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Biopharmaceuticals have developed rapidly in recent years due to the remarkable progress in gene recombination and cell culture technologies. Since the basic structure of biopharmaceuticals can be designed and modified, it is possible to control the duration of action and target specific tissues and cells by kinetic modification. Amino acid sequence modifications, albumin fusion proteins, polyethylene glycol (PEG) modifications, and fatty acid modifications have been utilized to modify the duration of action control and targeting. This review first describes the position of biopharmaceuticals,

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Zou, Yingying, Zhoule Guo, Xing-Yi Ge, and Ye Qiu. "RNA Modifications in Pathogenic Viruses: Existence, Mechanism, and Impacts." Microorganisms 12, no. 11 (2024): 2373. http://dx.doi.org/10.3390/microorganisms12112373.

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RNA modification is a key posttranscriptional process playing various biological roles, and one which has been reported to exist extensively in cellular RNAs. Interestingly, recent studies have shown that viral RNAs also contain a variety of RNA modifications, which are regulated dynamically by host modification machinery and play critical roles in different stages of the viral life cycle. In this review, we summarize the reports of four typical modifications reported on viral RNAs, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N4-acetylcytosine (ac4C), and N1-methyladenosine (m1

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Estevez, Mariana, Rui Li, Biplab Paul, et al. "Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcript Ast in human cells." RNA 28, no. 5 (2022): 697–710. http://dx.doi.org/10.1261/rna.079043.121.

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The human immunodeficiency virus type 1 (HIV-1) encodes multiple RNA molecules. Transcripts that originate from the proviral 5′ long terminal repeat (LTR) function as messenger RNAs for the expression of 16 different mature viral proteins. In addition, HIV-1 expresses an antisense transcript (Ast) from the 3′LTR, which has both protein-coding and noncoding properties. While the mechanisms that regulate the coding and noncoding activities of Ast remain unknown, post-transcriptional modifications are known to influence RNA stability, interaction with protein partners, and translation capacity. H

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He, Ruidi, Songnan Li, Gongqi Zhao, Ligong Zhai, Peng Qin, and Liping Yang. "Starch Modification with Molecular Transformation, Physicochemical Characteristics, and Industrial Usability: A State-of-the-Art Review." Polymers 15, no. 13 (2023): 2935. http://dx.doi.org/10.3390/polym15132935.

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Starch is a readily available and abundant source of biological raw materials and is widely used in the food, medical, and textile industries. However, native starch with insufficient functionality limits its utilization in the above applications; therefore, it is modified through various physical, chemical, enzymatic, genetic and multiple modifications. This review summarized the relationship between structural changes and functional properties of starch subjected to different modified methods, including hydrothermal treatment, microwave, pre-gelatinization, ball milling, ultrasonication, rad

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Luo, Danzhi, Xiaohong Li, Simin Tang, et al. "Epigenetic modifications in neuropathic pain." Molecular Pain 17 (January 2021): 174480692110567. http://dx.doi.org/10.1177/17448069211056767.

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Neuropathic pain (NP) is a common symptom in many diseases of the somatosensory nervous system, which severely affects the patient’s quality of life. Epigenetics are heritable alterations in gene expression that do not cause permanent changes in the DNA sequence. Epigenetic modifications can affect gene expression and function and can also mediate crosstalk between genes and the environment. Increasing evidence shows that epigenetic modifications, including DNA methylation, histone modification, non-coding RNA, and RNA modification, are involved in the development and maintenance of NP. In thi

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Kao, Robert M., Yan Liu, and Jihong Bai. "Doing the Molecular Splits: Hands-On Demonstration Tips to Promote Student Engagement Using Split Inteins in Molecular Biology." American Biology Teacher 82, no. 7 (2020): 499–502. http://dx.doi.org/10.1525/abt.2020.82.7.499.

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Engaging undergraduates in the mechanisms of post-translational modifications lies at the heart of molecular and cell biology education. An important challenge for science educators is developing inclusive and equitable approaches and hands-on demonstrations to clarify post-translational modification mechanisms, such as the protein-splicing mechanism called split inteins. Here, we describe step-by-step assembly of recycled materials to help clarify the molecular action of split inteins in inclusive classroom teaching settings.

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Valadon, Charlène, and Olivier Namy. "The Importance of the Epi-Transcriptome in Translation Fidelity." Non-Coding RNA 7, no. 3 (2021): 51. http://dx.doi.org/10.3390/ncrna7030051.

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RNA modifications play an essential role in determining RNA fate. Recent studies have revealed the effects of such modifications on all steps of RNA metabolism. These modifications range from the addition of simple groups, such as methyl groups, to the addition of highly complex structures, such as sugars. Their consequences for translation fidelity are not always well documented. Unlike the well-known m6A modification, they are thought to have direct effects on either the folding of the molecule or the ability of tRNAs to bind their codons. Here we describe how modifications found in tRNAs an

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Hawer, Harmen, Alexander Hammermeister, Keerthiraju Ravichandran, Sebastian Glatt, Raffael Schaffrath, and Roland Klassen. "Roles of Elongator Dependent tRNA Modification Pathways in Neurodegeneration and Cancer." Genes 10, no. 1 (2018): 19. http://dx.doi.org/10.3390/genes10010019.

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Transfer RNA (tRNA) is subject to a multitude of posttranscriptional modifications which can profoundly impact its functionality as the essential adaptor molecule in messenger RNA (mRNA) translation. Therefore, dynamic regulation of tRNA modification in response to environmental changes can tune the efficiency of gene expression in concert with the emerging epitranscriptomic mRNA regulators. Several of the tRNA modifications are required to prevent human diseases and are particularly important for proper development and generation of neurons. In addition to the positive role of different tRNA

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Xie, Gloria S., and Hope T. Richard. "m6A mRNA Modifications in Glioblastoma: Emerging Prognostic Biomarkers and Therapeutic Targets." Cancers 16, no. 4 (2024): 727. http://dx.doi.org/10.3390/cancers16040727.

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Glioblastoma, the most common and aggressive primary brain tumor, is highly invasive and neurologically destructive. The mean survival for glioblastoma patients is approximately 15 months and there is no effective therapy to significantly increase survival times to date. The development of effective therapy including mechanism-based therapies is urgently needed. At a molecular biology level, N6-methyladenine (m6A) mRNA modification is the most abundant posttranscriptional RNA modification in mammals. Recent studies have shown that m6A mRNA modifications affect cell survival, cell proliferation

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Mori, Kota, Yuki Kurokawa, and Shyam S. Pandey. "Synthesis and Characterization of Multifunctional Symmetrical Squaraine Dyes for Molecular Photovoltaics by Terminal Alkyl Chain Modifications." Colorants 3, no. 3 (2024): 198–213. http://dx.doi.org/10.3390/colorants3030014.

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Novel far-red sensitive symmetric squaraine (SQ) dyes with terminal alkyl chain modifications were designed, synthesized, and characterized, aiming towards imparting multifunctionalities such as photosensitization, dye aggregation prevention, and source of electrolyte components. The dye sensitizer SQ-80 with alkyl chain terminal modifications consisting of 1-methylimidazolium iodide was designed and synthesized as a new dye sensitizer for DSSCs based on symmetric SQ-4 without any terminal modification used as reference. Upon adsorption on the mesoporous TiO2 surface, SQ-80 demonstrated reduce

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22

Jeltsch, Albert, Julian Broche, and Pavel Bashtrykov. "Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes." Genes 9, no. 11 (2018): 566. http://dx.doi.org/10.3390/genes9110566.

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DNA methylation is an essential part of the epigenome chromatin modification network, which also comprises several covalent histone protein post-translational modifications. All these modifications are highly interconnected, because the writers and erasers of one mark, DNA methyltransferases (DNMTs) and ten eleven translocation enzymes (TETs) in the case of DNA methylation, are directly or indirectly targeted and regulated by other marks. Here, we have collected information about the genomic distribution and variability of DNA methylation in human and mouse DNA in different genomic elements. A

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Leseva, Milena N., Brigitta Buttari, Luciano Saso, and Petya A. Dimitrova. "Infection Meets Inflammation: N6-Methyladenosine, an Internal Messenger RNA Modification as a Tool for Pharmacological Regulation of Host–Pathogen Interactions." Biomolecules 13, no. 7 (2023): 1060. http://dx.doi.org/10.3390/biom13071060.

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The significance of internal mRNA modifications for the modulation of transcript stability, for regulation of nuclear export and translation efficiency, and their role in suppressing innate immunity is well documented. Over the years, the molecular complexes involved in the dynamic regulation of the most prevalent modifications have been characterized—we have a growing understanding of how each modification is set and erased, where it is placed, and in response to what cues. Remarkably, internal mRNA modifications, such as methylation, are emerging as an additional layer of regulation of immun

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Rabany, Ofri, and Daphna Nachmani. "Small Nucleolar (Sno)RNA: Therapy Lays in Translation." Non-Coding RNA 9, no. 3 (2023): 35. http://dx.doi.org/10.3390/ncrna9030035.

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The ribosome is one of the largest complexes in the cell. Adding to its complexity are more than 200 RNA modification sites present on ribosomal RNAs (rRNAs) in a single human ribosome. These modifications occur in functionally important regions of the rRNA molecule, and they are vital for ribosome function and proper gene expression. Until recent technological advancements, the study of rRNA modifications and their profiles has been extremely laborious, leaving many questions unanswered. Small nucleolar RNAs (snoRNAs) are non-coding RNAs that facilitate and dictate the specificity of rRNA mod

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Li, Xu, Pingdong Cai, Xinyuan Tang, Yingzi Wu, Yue Zhang, and Xianglu Rong. "Lactylation Modification in Cardiometabolic Disorders: Function and Mechanism." Metabolites 14, no. 4 (2024): 217. http://dx.doi.org/10.3390/metabo14040217.

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Cardiovascular disease (CVD) is recognized as the primary cause of mortality and morbidity on a global scale, and developing a clear treatment is an important tool for improving it. Cardiometabolic disorder (CMD) is a syndrome resulting from the combination of cardiovascular, endocrine, pro-thrombotic, and inflammatory health hazards. Due to their complex pathological mechanisms, there is a lack of effective diagnostic and treatment methods for cardiac metabolic disorders. Lactylation is a type of post-translational modification (PTM) that plays a regulatory role in various cellular physiologi

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Vasileva-Slaveva, Mariela, Angel Yordanov, Gergana Metodieva, and Metodi V. Metodiev. "Exploring Protein Post-Translational Modifications of Breast Cancer Cells Using a Novel Combinatorial Search Algorithm." International Journal of Molecular Sciences 25, no. 18 (2024): 9902. http://dx.doi.org/10.3390/ijms25189902.

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Post-translational modification of proteins plays an important role in cancer cell biology. Proteins encoded by oncogenes may be activated by phosphorylation, products of tumour suppressors might be inactivated by phosphorylation or ubiquitinylation, which marks them for degradation; chromatin-binding proteins are often methylated and/or acetylated. These are just a few of the many hundreds of post-translational modifications discovered by years of painstaking experimentation and the chemical analysis of purified proteins. In recent years, mass spectrometry-based proteomics emerged as the prin

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Ontiveros, R. Jordan, Julian Stoute, and Kathy Fange Liu. "The chemical diversity of RNA modifications." Biochemical Journal 476, no. 8 (2019): 1227–45. http://dx.doi.org/10.1042/bcj20180445.

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AbstractNucleic acid modifications in DNA and RNA ubiquitously exist among all the three kingdoms of life. This trait significantly broadens the genome diversity and works as an important means of gene transcription regulation. Although mammalian systems have limited types of DNA modifications, over 150 different RNA modification types have been identified, with a wide variety of chemical diversities. Most modifications occur on transfer RNA and ribosomal RNA, however many of the modifications also occur on other types of RNA species including mammalian mRNA and small nuclear RNA, where they a

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Chen, Xiaoqian, Yuanyuan Li, Youfang Gan, Yuyang Guo, Hongling Zhou, and Rui Wang. "Sequencing, Physiological Regulation, and Representative Disease Research Progress of RNA m6A Modification." Pharmaceutical Fronts 06, no. 01 (2024): e29-e46. http://dx.doi.org/10.1055/s-0044-1780506.

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AbstractTo date, more than 150 chemical modifications have been disclosed in different RNA species, which are employed to diversify the structure and function of RNA in living organisms. The N 6-methyladenosine (m6A) modification, which is found in the adenosine N 6 site of RNA, has been demonstrated to be the most heavy modification in the mRNA in cells. Moreover, the m6A modification in mRNAs of mammalian and other eukaryotic cells is highly conserved and mandatorily encoded. Increasing evidence indicates that the m6A modification plays a pivotal role in gene-expression regulation and cell-f

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Noon, Kathleen R., Rebecca Guymon, Pamela F. Crain, et al. "Influence of Temperature on tRNA Modification in Archaea: Methanococcoides burtonii (Optimum Growth Temperature [Topt], 23°C) and Stetteria hydrogenophila (Topt, 95°C)." Journal of Bacteriology 185, no. 18 (2003): 5483–90. http://dx.doi.org/10.1128/jb.185.18.5483-5490.2003.

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ABSTRACT We report the first study of tRNA modification in psychrotolerant archaea, specifically in the archaeon Methanococcoides burtonii grown at 4 and 23°C. For comparison, unfractionated tRNA from the archaeal hyperthermophile Stetteria hydrogenophila cultured at 93°C was examined. Analysis of modified nucleosides using liquid chromatography-electrospray ionization mass spectrometry revealed striking differences in levels and identities of tRNA modifications between the two organisms. Although the modification levels in M. burtonii tRNA are the lowest in any organism of which we are aware,

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AL-Abedi, Yasameen Waleed, Alaa Abdalhadi Halboti, and Ali Abdulhussein Saleh. "UNRAVELING THE ROLE OF EPIGENETIC MODIFICATIONS IN GENE REGULATION A MOLECULAR GENETICS PERSPECTIVE." European Journal of Medical Genetics and Clinical Biology 1, no. 9 (2024): 44–59. https://doi.org/10.61796/jmgcb.v1i9.928.

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Epigenetic modifications is very crucial in managing on/off switch of the genes, and the kind of cell that is being built. The specific goals of this study are to identify the role of histone modifications, DNA methylation, and their interaction with each other on gene expression according to the ChIP-Seq, RNA-Seq, and bisulfite sequencing results. Therefore, in order to offer wide and profound analysis we went to specify the strains for regulatory components, to describe the molecular events, and to contemplate concerning potential clinical utility. Typically, for ChIP-Seq analysis, the numbe

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Jo, Chanhee, Seokjae Park, Sungjoon Oh, et al. "Histone acylation marks respond to metabolic perturbations and enable cellular adaptation." Experimental & Molecular Medicine 52, no. 12 (2020): 2005–19. http://dx.doi.org/10.1038/s12276-020-00539-x.

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AbstractAcetylation is the most studied histone acyl modification and has been recognized as a fundamental player in metabolic gene regulation, whereas other short-chain acyl modifications have only been recently identified, and little is known about their dynamics or molecular functions at the intersection of metabolism and epigenetic gene regulation. In this study, we aimed to understand the link between nonacetyl histone acyl modification, metabolic transcriptional regulation, and cellular adaptation. Using antibodies specific for butyrylated, propionylated, and crotonylated H3K23, we analy

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Chiu, Norman H., Jennifer H. Simpson, Renata L. Fleming, Jian Teng, and Bakhos A. Tannous. "Abstract LB507: Towards elucidating the role of RNA modifications in cancer by improving the quantitative accuracy of mass spectrometric profiling of RNA modifications." Cancer Research 82, no. 12_Supplement (2022): LB507. http://dx.doi.org/10.1158/1538-7445.am2022-lb507.

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Abstract The molecular structure of both coding and non-coding RNA is frequently altered by the enzymatic activity of either writer or eraser of RNA modifications. Since the RNA functions are dependent on its molecular structure, cellular activities that involve specific RNA molecule(s) can potentially be regulated by the reversible nature of RNA modifications. There are more than 140 known RNA modifications. Mass spectrometry is a proven technique for the identification of RNA modifications. However, due to the lack of ribonucleoside standards and biases in normalizing the level of RNA modifi

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Pan, Shengyu, Tianhui Yuan, Yuqi Xia, Weimin Yu, Xiangjun Zhou, and Fan Cheng. "Role of Histone Modifications in Kidney Fibrosis." Medicina 60, no. 6 (2024): 888. http://dx.doi.org/10.3390/medicina60060888.

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Chronic kidney disease (CKD) is characterized by persistent kidney dysfunction, ultimately resulting in end-stage renal disease (ESRD). Renal fibrosis is a crucial pathological feature of CKD and ESRD. However, there is no effective treatment for this condition. Despite the complex molecular mechanisms involved in renal fibrosis, increasing evidence highlights the crucial role of histone modification in its regulation. The reversibility of histone modifications offers promising avenues for therapeutic strategies to block or reverse renal fibrosis. Therefore, a comprehensive understanding of th

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Bohnsack, Markus T., and Katherine E. Sloan. "Modifications in small nuclear RNAs and their roles in spliceosome assembly and function." Biological Chemistry 399, no. 11 (2018): 1265–76. http://dx.doi.org/10.1515/hsz-2018-0205.

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Abstract Modifications in cellular RNAs have emerged as key regulators of all aspects of gene expression, including pre-mRNA splicing. During spliceosome assembly and function, the small nuclear RNAs (snRNAs) form numerous dynamic RNA-RNA and RNA-protein interactions, which are required for spliceosome assembly, correct positioning of the spliceosome on substrate pre-mRNAs and catalysis. The human snRNAs contain several base methylations as well as a myriad of pseudouridines and 2′-O-methylated nucleotides, which are largely introduced by small Cajal body-specific ribonucleoproteins (scaRNPs).

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Hili, Ryan, Chun Guo, Dehui Kong, and Yi Lei. "Expanding the Chemical Diversity of DNA." Synlett 29, no. 11 (2018): 1405–14. http://dx.doi.org/10.1055/s-0036-1591959.

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Nucleic acid polymers can be evolved to exhibit desired properties, including molecular recognition of a molecular target and catalysis of a specific reaction. These properties can be readily evolved despite the dearth of chemical diversity available to nucleic acid polymers, especially when compared to the rich chemical complexity of proteins. Expansion of nucleic acid chemical diversity has therefore been an important thrust for improving their properties for analytical and biomedical applications. Herein, we briefly describe the current state-of-the-art for the sequence-defined incorporatio

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Tafeenko, V. A., V. V. Chernyshev, A. V. Yatsenko, et al. "Intermolecular —CH3...O2N— contacts in two polymorphic modifications of (1E)-N'-[(E)-2-cyano-1-(dimethylamino)-2-nitrovinyl]-N,N-dimethylethanimidamide." Acta Crystallographica Section B Structural Science 59, no. 4 (2003): 492–97. http://dx.doi.org/10.1107/s0108768103010231.

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The title compound was synthesized and isolated in two crystal modifications. The structure of the orthorhombic modification was determined by the X-ray powder diffraction method and the structure of the monoclinic modification was determined using the X-ray single-crystal diffraction technique. The molecules in both polymorphs are E,E isomers. Intermolecular H3C...NO2 contacts and their role in the formation of the polymorphic modifications are analyzed.

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Zhang, Linhui, Yuelong Li, Liqing Li, et al. "Detection, molecular function and mechanisms of m5C in cancer." Clinical and Translational Medicine 15, no. 3 (2025). https://doi.org/10.1002/ctm2.70239.

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AbstractInterest in RNA posttranscriptional modifications, particularly 5‐methylcytosine (m5C), has surged in recent years. Studies have shown that m5C plays a key role in cellular processes and is closely linked to tumourigenesis. This growing focus emphasises the importance of understanding the diverse impacts of m5C modifications in both normal cellular functions and cancer development. Moreover, strides in methodologies for discerning m5C have facilitated intricate transcriptome cartography of RNA methylation at the solitary nucleotide echelon. This technical progress has fueled a surge in

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Porat, Jennifer. "Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function." RNA, March 5, 2025, rna.080421.125. https://doi.org/10.1261/rna.080421.125.

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Continued advances in high throughput detection of post-transcriptional RNA modifications have enabled large-scale, mechanistic studies into the importance of RNA modifications in regulating the structure, function, and stability of coding and noncoding RNAs. More recently, this has expanded beyond investigations of independent single modifications, revealing the breadth of modification complexities in single transcripts and the biogenesis pathways involved that lead to coordinately modified RNA species. This has resulted in the concept of modification circuits, where one modification can prom

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Ali, Ashiq, Tehreem Ajmal, Aisha Khatoon, et al. "Molecular Insights into RNA Modifications and their Role in Shaping Immune Responses and Tumor Microenvironments." Current Gene Therapy 25 (January 21, 2025). https://doi.org/10.2174/0115665232335322241205063758.

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Abstract: RNA modifications play crucial roles in immune system development and function, with dynamic changes essential for diverse cellular processes. Innovative profiling technologies are invaluable for understanding the significance of these modifications in immune cells, both in healthy and diseased states. This review explores the utility of such technologies in uncovering the functions of RNA modifications and their impact on immune responses. Additionally, it delves into the mechanisms through which aberrant RNA modifications influence the tumor microenvironments immune milieu. Despite

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Yu, Ningxi, Manasses Jora, Beulah Solivio, et al. "tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii." Journal of Bacteriology 201, no. 9 (2019). http://dx.doi.org/10.1128/jb.00690-18.

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ABSTRACT tRNAs play a critical role in mRNA decoding, and posttranscriptional modifications within tRNAs drive decoding efficiency and accuracy. The types and positions of tRNA modifications in model bacteria have been extensively studied, and tRNA modifications in a few eukaryotic organisms have also been characterized and localized to particular tRNA sequences. However, far less is known regarding tRNA modifications in archaea. While the identities of modifications have been determined for multiple archaeal organisms, Haloferax volcanii is the only organism for which modifications have been

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Fagre, Christian, and Wendy Gilbert. "Beyond reader proteins: RNA binding proteins and RNA modifications in conversation to regulate gene expression." WIREs RNA 15, no. 2 (2024). http://dx.doi.org/10.1002/wrna.1834.

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AbstractPost‐transcriptional mRNA modifications play diverse roles in gene expression and RNA function. In many cases, RNA modifications function by altering how cellular machinery such as RNA binding proteins (RBPs) interact with RNA substrates. For instance, N6‐methyladenosine (m6A) is recognized by the well‐characterized YTH domain‐containing family of “reader” proteins. For other mRNA modifications, similar global readers of modification status have not been clearly defined. Rather, most interactions between RBPs and RNA modifications have a more complicated dependence on sequence context

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Zhu, Xiping, Zhijun Cao, Huake Liu, and Shaohui Zheng. "Utilizing hybridization effects to tune morphology and electron mobility of Y6 through asymmetric small- and large-scale modifications of terminal groups." Journal of Chemical Physics 162, no. 16 (2025). https://doi.org/10.1063/5.0255271.

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While exploring molecular modifications of the high-performance acceptor Y6 with an A-DA′D-A framework, researchers have discovered that asymmetric modification of terminal groups (TGs) appears to be a promising approach as it frequently enhances the photovoltaic performance of organic solar cells (OSCs) effectively. However, the underlying mechanism about how asymmetric TG modifications influence morphology and charge carrier mobility remains unclear. We have conducted a systematic study in this work to investigate the morphology and electron mobility of two asymmetric Y6 derivatives with the

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Chen, Hui-Ming, Hang Li, Meng-Xian Lin, et al. "Research Progress for RNA Modifications in Physiological and Pathological Angiogenesis." Frontiers in Genetics 13 (July 22, 2022). http://dx.doi.org/10.3389/fgene.2022.952667.

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As a critical layer of epigenetics, RNA modifications demonstrate various molecular functions and participate in numerous biological processes. RNA modifications have been shown to be essential for embryogenesis and stem cell fate. As high-throughput sequencing and antibody technologies advanced by leaps and bounds, the association of RNA modifications with multiple human diseases sparked research enthusiasm; in addition, aberrant RNA modification leads to tumor angiogenesis by regulating angiogenesis-related factors. This review collected recent cutting-edge studies focused on RNA modificatio

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Li, Hengzhen, WenFeng Xiao, Yuqiong He, et al. "Novel Insights Into the Multifaceted Functions of RNA n6-Methyladenosine Modification in Degenerative Musculoskeletal Diseases." Frontiers in Cell and Developmental Biology 9 (December 27, 2021). http://dx.doi.org/10.3389/fcell.2021.766020.

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N6-methyladenosine (m6A) is an important modification of eukaryotic mRNA. Since the first discovery of the corresponding demethylase and the subsequent identification of m6A as a dynamic modification, the function and mechanism of m6A in mammalian gene regulation have been extensively investigated. “Writer”, “eraser” and “reader” proteins are key proteins involved in the dynamic regulation of m6A modifications, through the anchoring, removal, and interpretation of m6A modifications, respectively. Remarkably, such dynamic modifications can regulate the progression of many diseases by affecting

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Biswas, Pritam, Aniruddha Adhikari, Uttam Pal, et al. "A combined spectroscopic and molecular modeling Study on structure-function-dynamics under chemical modification: Alpha-chymotrypsin with formalin preservative." Frontiers in Chemistry 10 (August 31, 2022). http://dx.doi.org/10.3389/fchem.2022.978668.

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Enzyme function can be altered via modification of its amino acid residues, side chains and large-scale domain modifications. Herein, we have addressed the role of residue modification in catalytic activity and molecular recognition of an enzyme alpha-chymotrypsin (CHT) in presence of a covalent cross-linker formalin. Enzyme assay reveals reduced catalytic activity upon increased formalin concentration. Polarization gated anisotropy studies of a fluorophore 8-Anilino-1-naphthalenesulfonic acid (ANS) in CHT show a dip rise pattern in presence of formalin which is consistent with the generation

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Xue, Chen, Qingfei Chu, Qiuxian Zheng, et al. "Role of main RNA modifications in cancer: N6-methyladenosine, 5-methylcytosine, and pseudouridine." Signal Transduction and Targeted Therapy 7, no. 1 (2022). http://dx.doi.org/10.1038/s41392-022-01003-0.

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AbstractCancer is one of the major diseases threatening human life and health worldwide. Epigenetic modification refers to heritable changes in the genetic material without any changes in the nucleic acid sequence and results in heritable phenotypic changes. Epigenetic modifications regulate many biological processes, such as growth, aging, and various diseases, including cancer. With the advancement of next-generation sequencing technology, the role of RNA modifications in cancer progression has become increasingly prominent and is a hot spot in scientific research. This review studied severa

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Kazarian, Ruben, Nikolay Komarov, Vitaly Chulkov, and Dora Cazarian. "Variability and adaptive norm in the system "man-technology-environment, MTE"." On-line Journal "Naukovedenie" 9, no. 5 (2017). http://dx.doi.org/10.15862/108tvn517.

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Distinguish between hereditary (mutational and combinative) and non-hereditary (modification or phenotypic) variability in the human body. Modificational variability arises as a result of interaction with the surrounding environment, the effects of factors which different people react differently. There is the concept of "reaction norm" as the limit of modification variability, within the capabilities of a particular person. In most cases, modification is a useful adaptive response of the organism, is adaptive in nature (adaptive norm). Adaptive nature is usually inherent in modifications that

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Zhao, Xiaohong, Qinyi Li, Xiaolong Zhu, Yuanyuan Jiao, Huan Yang, and Jiao Feng. "Protein modifications in hepatic ischemia-reperfusion injury: molecular mechanisms and targeted therapy." Frontiers in Immunology 16 (April 11, 2025). https://doi.org/10.3389/fimmu.2025.1553298.

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Ischemia-reperfusion injury refers to the damage that occurs when blood supply is restored to organs or tissues after a period of ischemia. This phenomenon is commonly observed in clinical contexts such as organ transplantation and cardiac arrest resuscitation. Among these, hepatic ischemia-reperfusion injury is a prevalent complication in liver transplantation, significantly impacting the functional recovery of the transplanted liver and potentially leading to primary graft dysfunction. With the growing demand for organ transplants and the limited availability of donor organs, effectively add

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Gao, MingZe, ZhongYuan Li, and WeiFeng Sun. "Molecular Simulation Insights into Chemical-Grafted EPDM for Improving Charge Traps, Moisture Resistance, and Pyrolysis Tolerance." ECS Journal of Solid State Science and Technology, August 7, 2024. http://dx.doi.org/10.1149/2162-8777/ad6c7e.

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Abstract This study explores and verifies the chemical modifications achieved by grafting 4-formylcyclohexyl heptanoate (FH) and 4-(2,5-dioxopyrrolidin-1-yl) cyclohexane-1-carbaldehyde (CC) onto ethylene propylene diene monomer (EPDM) elastomer, a prevalent dielectric material used for reinforced insulation in cable accessories. Employing a rigorous theoretical methodology combining first-principles calculations, molecular dynamics, and Monte Carlo molecular simulations, we elucidate the intricate effects of these chemical-graft modifications on the polymeric structure of EPDM to resist charge

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Lang, Xiaoqiang, Chunyan Yu, Mengyuan Shen, et al. "PRMD: an integrated database for plant RNA modifications." Nucleic Acids Research, October 13, 2023. http://dx.doi.org/10.1093/nar/gkad851.

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Abstract The scope and function of RNA modifications in model plant systems have been extensively studied, resulting in the identification of an increasing number of novel RNA modifications in recent years. Researchers have gradually revealed that RNA modifications, especially N6-methyladenosine (m6A), which is one of the most abundant and commonly studied RNA modifications in plants, have important roles in physiological and pathological processes. These modifications alter the structure of RNA, which affects its molecular complementarity and binding to specific proteins, thereby resulting in

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