Article
Chemistry, Organic
Fabian Lang, Franziska Roenicke, Hans-Achim Wagenknecht
Summary: Aminophthalimide and N,N-dimethylaminophthalimide are fluorescent mimetics of purines that can be used in RNA imaging in live cells. They can be incorporated into RNA and act as nonspecific fluorescent base analogs with flexible hydrogen bonding capabilities. These molecules exhibit solvatochromic fluorescence.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Juri Eyberg, Mark Ringenberg, Clemens Richert
Summary: A new type of deoxynucleoside was reported in this study, which can control the pairing strength of nucleobases in DNA through reactions with compounds found inside the cell. The deoxynucleoside exhibits reactivity towards soft nucleophiles, changes its fluorescence, and has potential applications in controlled release, chemical biology, sensing, and diagnostics.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Review
Food Science & Technology
Ting Ding, Ge Song, Xinran Liu, Meihong Xu, Yong Li
Summary: Nucleotides are the basic units of nucleic acid macromolecules, playing important physiological and biochemical functions in organisms. Recent studies have shown that exogenous nucleotides are essential nutrients under specific physiological conditions, entering tissues, reducing the body's synthesis needs, and enhancing immune function and regulating intestinal flora.
JOURNAL OF FUNCTIONAL FOODS
(2021)
Article
Chemistry, Physical
Arusha Acharyya, Wenkai Zhang, Feng Gai
Summary: Most biological systems are complex, diverse, and non-fluorescent, requiring the development of diverse fluorescence reporters for studying their structures, dynamics, and interactions without affecting their native properties. Tryptophan-based fluorescent amino acids have been identified as a potential solution for this need, with recent progress and future directions towards their development.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Multidisciplinary
Pulak Ghosh, Heike M. Kropp, Karin Betz, Samra Ludmann, Kay Diederichs, Andreas Marx, Seergazhi G. Srivatsan
Summary: This study demonstrates the use of environment-sensitive heterocycle-modified fluorescent nucleotide substrates to probe the incorporation mechanism of DNA polymerases in real-time and at the atomic level. The results show that different nucleotide analogs have varying incorporation efficiencies in different DNA polymerase families, and some modified nucleotides can serve as reporters for monitoring enzyme activity.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Mariah J. Austin, Hattie Schunk, Carolyn Watkins, Natalie Ling, Jeremy Chauvin, Logan Morton, Adrianne M. Rosales
Summary: This study developed a system of peptomers to investigate the impact of non-natural residues on MMP specificity. The results showed that peptoid residues were well tolerated in certain substrate sites and had a moderate influence on the rate of cleavage. Furthermore, the study demonstrated that peptomers can be used in hydrogels to control degradation kinetics. This work has important implications for diagnostic and prognostic applications.
Article
Chemistry, Analytical
Zhen Wang, Xumei Zhou, Jing Han, Gang Xie, Juewen Liu
Summary: In this study, a series of homobimetallic MOFs were synthesized by tuning the metal contents, and selective recognition of specific nucleoside triphosphates was achieved using fluorescent probes. Co50Zn50-ZIF showed high selectivity and sensitivity towards GTP. A ZIF fluorescent sensor array was also designed to discriminate different nucleoside triphosphates.
ANALYTICA CHIMICA ACTA
(2022)
Article
Chemistry, Multidisciplinary
Lihua Feng, Yumeng Zhou, Wenqin Wang
Summary: In this study, Ag(NH3)(2)NO3 microcubes were obtained by evaporating the silver ammonia complex solution directly. In a Na(3)Cit solution, each Ag(NH3)(2)NO3 microcube can be broken into numerous Ag(3)Cit sub-microcubes with uniform size, serving as sacrificial templates for generating Ag sub-microcages. The resulting Ag cages exhibit ultra-high surface-enhanced Raman scattering (SERS) sensitivity towards R6G and thiram.
CHEMICAL COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Maurizio Righini, Justin Costa, Wei Zhou
Summary: DNA molecular combing is a technique that stretches individual DNA molecules into a parallel configuration on a surface for sequencing. A novel approach has been introduced to address challenges such as overstretching and enzymatic access limitations, by attaching DNA molecules to a removable surface with tunable stretching factor. This new platform shows promise for high-throughput sequencing of Mbp-long molecules and potential genomic applications.
Article
Chemistry, Applied
Jigyasa, Harminder Singh, Jaspreet Kaur Rajput
Summary: Fluorescent g-C3N4 nanosheets with laminar morphology and ultrathin thickness were fabricated for efficient detection of food colorants and photocatalytic degradation. They served as non-toxic and low-cost photocatalyst, capable of selectively detecting low concentrations of food colorants and degrading them under UV light.
Article
Chemistry, Multidisciplinary
Facai Wei, Hengyue Xu, Tingting Zhang, Wenda Li, Lingyan Huang, Yonghui Peng, Haitao Guo, Yuexi Wang, Shaojian Guan, Jianwei Fu, Chengbin Jing, Jiangong Cheng, Shaohua Liu
Summary: A mesoporous conductive polymer of poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) with adjustable size, large specific surface area, and high electrical conductivity was developed by introducing polystyrenesulfonate (PSS) as a multifunctional bridging molecule. It was demonstrated that the iodine-loaded mesoporous PEDOT:PSS nanospheres can serve as a promising cathode for aqueous zinc-iodine batteries with high specific capacity, excellent rate performance, and long cycle life.
Article
Chemistry, Physical
Tongxiang Tao, Shuai Xu, Jin Bai, Sajid ur Rehman, Peiyao Wang, Xianglong Zhao, Ruiguo Chen, Huangtao Xu, Hong Bi, Bangchuan Zhao, Kun Ma, Junfeng Wang
Summary: Protein templates have great potential in preparing LIB anode, but the biodiversity of proteins is not fully utilized. In this study, biomineralized protein BSA was selected as the template and successfully regulated the structure, obtaining high-quality electrode materials.
ACS APPLIED ENERGY MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Houyu Han, Jingyu Cui, Dianming Zhou, Deping Hua, Weipan Peng, Mengyao Lin, Yating Zhang, Fangya Li, Xiaoqun Gong, Jianyu Zhang
Summary: Terminal deoxynucleotidyl transferase (TdT) is a template-independent polymerase that uses single-stranded DNA (ssDNA) as primers to generate random oligonucleotides. However, the extension performance of TdT on single-stranded RNA (ssRNA) is unclear. By comparing and contrasting the efficiency of TdT-catalyzed ssDNA and ssRNA extension, it was found that the catalytic efficiency of ssRNA as primers was about three times lower than ssDNA. Understanding the catalytic performance of TdT is believed to be valuable in designing strategies for synthesizing chimeric DNA on ssRNA 3'-OH.
CHINESE CHEMICAL LETTERS
(2023)
Article
Multidisciplinary Sciences
Hannah M. Work, Sylvie E. Kandel, Jed N. Lampe
Summary: CYP3A7, a member of the CYP3A enzyme sub-family expressed in fetuses and neonates, plays a critical role in drug metabolism. However, it is often overlooked in preclinical drug testing. Screening for CYP3A7 inhibitors is essential to identify chemical entities with potential toxicity risks for neonates. A fluorescent compound DBF has been identified as superior for high-throughput screening, showing promise for future drug screening in the neonatal population.
SCIENTIFIC REPORTS
(2021)
Article
Engineering, Environmental
Seyyed Ebrahim Moosavifard, Abdolkhaled Mohammadi, Mohammad Ebrahimnejad Darzi, Asadollah Kariman, Mahnaz M. Abdi, Gholamreza Karimi
Summary: The study focuses on the design and optimization of electrode materials for fast energy storage devices in the electronics industries. By utilizing smart structural design and bimetallic synergy, the synthesized electrode demonstrates high capacity retention and exceptional specific capacitance, leading to remarkable electrochemical output. This approach offers a novel way to enhance the performance of hybrid supercapacitors for modern electronic devices.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Yong Woong Jun, Eddy Albarran, David L. Wilson, Jun Ding, Eric T. Kool
Summary: Mitochondrial function declines with aging and neurodegeneration, largely due to accumulated mutations in mtDNA from deficient DNA repair. A fluorescent probe, UBER, was used to visualize mitochondrial BER activity, showing increased repair under oxidative stress and time delay between stress onset and BER initiation. Cells lacking MTH1 exhibited elevated demand for BER activity during extended stress, while absence of OGG1 limited glycosylation capacity.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Fa-Jie Chen, Mengmeng Zheng, Vincent Nobile, Jianmin Gao
Summary: The novel method demonstrates fast reaction kinetics and excellent selectivity for cysteine residues, allowing modification of peptides and proteins under physiologic conditions.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Rahi M. Reja, Wenjian Wang, Yuhan Lyu, Fredrik Haeffner, Jianmin Gao
Summary: We report a new reversible lysine conjugation method that shows a unique diazaborine product and slower dissociation kinetics compared to the known iminoboronate chemistry. By incorporating the diazaborine-forming warhead RMR1 into a peptide ligand, we have developed potent and long-acting reversible covalent inhibitors of staphylococcal sortase. The efficacy of sortase inhibition is demonstrated through biochemical and cell-based assays. A comparative study between RMR1 and an iminoboronate-forming warhead emphasizes the importance and potential of modulating bond dissociation kinetics in achieving long-acting reversible covalent inhibitors.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Lu Xiao, Linglan Fang, Sayantan Chatterjee, Eric T. Kool
Summary: RNA 2'-OH acylation is widely used for structure mapping and conjugation, and depends on selective reactions with unpaired nucleotides. We prepared a range of structurally diverse acylimidazole reagents and used deep sequencing to study their reactivity and selectivity in a variety of RNA structures. Our results demonstrate that the reagent scaffold significantly affects reactivity profiles and highlight new acylating agents with altered selectivity, including compounds that show elevated selectivity within loops and reduced off-target reactivity in loop closing base pairs. We also discovered a simple reagent that is cell permeable and can map RNA structure in the presence of protein contacts, and describe reagents with elevated selectivity within small loops for site-selective labeling.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Fa-Jie Chen, Nicole Pinnette, Fan Yang, Jianmin Gao
Summary: In this study, we report a cysteine-directed proximity-driven strategy for constructing bicyclic peptides from simple natural peptide precursors. This linear to bicycle transformation involves rapid cysteine labeling and subsequent amine-selective cyclization. The bicyclization process occurs rapidly under physiological conditions, resulting in bicyclic peptides with Cys-Lys-Cys, Lys-Cys-Lys, or N-terminus-Cys-Cys stapling patterns. We demonstrate the utility and power of this strategy by constructing bicyclic peptides fused to proteins and the M13 phage, enabling the phage display of novel bicyclic peptide libraries.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Organic
Rahi M. Reja, Brittney Chau, Jianmin Gao
Summary: Multicyclic peptides are potential candidates for peptide-based drug discovery. A new cross-linker, DCA-RMR1, has been developed for efficient bicyclization of native peptides via N-terminus Cys-Cys cross-linking. The resulting diazaborine linkage is stable at neutral pH and can reversibly change under mild acidification, enabling the production of pH-responsive peptides.
Article
Chemistry, Multidisciplinary
Sayantan Chatterjee, Ryuta Shioi, Eric T. Kool
Summary: The nucleophilic reactivity of RNA 2'-OH groups has been applied in various RNA-related processes. In this study, it is discovered that activated small-molecule sulfonyl species can retain their reactivity in water. Reactions with ribose 2'-OH show high yields, especially for aryl sulfonyltriazole species. Additionally, an azide-substituted sulfonyltriazole reagent is developed for labeling RNA via click chemistry.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Yong Woong Jun, Melis Kant, Erdem Coskun, Takamitsu A. A. Kato, Pawel Jaruga, Elizabeth Palafox, Miral Dizdaroglu, Eric T. T. Kool
Summary: High-temperature cooking damages DNA in food, which can then enter the cellular DNA and lead to genetic risks.
ACS CENTRAL SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Mengmeng Zheng, Jianmin Gao
Summary: Peptides, as a therapeutic modality between small molecules and antibodies, are gaining attention for their ability to combine the benefits of both. This study presents a novel phage library that incorporates two distinct designer groups, allowing the screening of peptides with diverse and non-natural functional motifs. The modification of phage-displayed peptides through sequential chemical reactions resulted in the discovery of potent peptide inhibitors against TEV protease.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Linglan Fang, Lu Xiao, Yong Woong Jun, Yoshiyuki Onishi, Eric T. T. Kool
Summary: The presence of a hydroxyl group at the 2'-position in ribose makes RNA susceptible to hydrolysis. In this study, reversible 2'-OH acylation was presented as a general strategy to preserve RNA stability. High-yield polyacylation of 2'-hydroxyls effectively protected RNAs from degradation, and subsequent treatment with nucleophilic reagents removed acylation adducts and recovered a wide range of RNA functions.
Article
Chemistry, Multidisciplinary
Ryuta Shioi, Lu Xiao, Sayantan Chatterjee, Eric T. Kool
Summary: The reactivity of RNA 2'-OH groups with acylating agents has been studied for high-yield conjugation of RNA strands. This study focuses on the stereoselectivity of chiral acylimidazoles in RNA reactions. The results reveal that positional selectivity and reactivity vary greatly with local RNA macro-chirality, and the chirality of the reagents has a significant impact on their reactivity. This study demonstrates new chemical strategies for selective RNA modification and probing.
Article
Biochemical Research Methods
Reema Baskar, Amy F. Chen, Patricia Favaro, Warren Reynolds, Fabian Mueller, Luciene Borges, Sizun Jiang, Hyun Shin Park, Eric T. Kool, William J. Greenleaf, Sean C. Bendall
Summary: Master transcription factors regulate cell states by driving gene-expression programs, and their abundance affects cell fate at the chromatin level. InTAC-seq method allows the study of the relationship between protein abundance and gene regulation in cells.
CELL REPORTS METHODS
(2022)
Article
Biochemistry & Molecular Biology
Lu Xiao, Linglan Fang, Eric T. Kool
Summary: The reactivity of RNA 2'-OH acylation has been extensively studied in this research. The results show that there is a wide range of reactivity among single-stranded RNA sequences, with nearest neighbors playing a significant role. Interestingly, certain small loops exhibit much higher reactivity compared to single-stranded RNAs, which is attributed to conformational constraints.
CELL CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Sergio M. Marques, Michaela Slanska, Klaudia Chmelova, Radka Chaloupkova, Martin Marek, Spencer Clark, Jiri Damborsky, Eric T. Kool, David Bodnar, Zbynek Prokop
Summary: HaloTag labeling technology has revolutionized protein chemistry and cellular biology, and a systematic analysis of different ligands has led to the discovery of an optimal protein tag selection protocol, eliminating the need for expensive and complex protein engineering.
Article
Chemistry, Multidisciplinary
Mengmeng Zheng, Fredrik Haeffner, Jianmin Gao
Summary: Phage display is an invention for evaluating peptide libraries, and it has mainly been used for natural peptides. Recently, there has been increasing interest in modifying phage libraries to create nonnatural cyclic peptides. This study presents a novel strategy for creating backbone-side chain cyclized peptide libraries on phage, and potent inhibitors for two model proteins were discovered using this strategy.