Article
Chemistry, Multidisciplinary
Paul T. Ludford, Shenghua Yang, Marcela S. Bucardo, Yitzhak Tor
Summary: This study describes a new fluorescent ribonucleoside alphabet consisting of pyrimidine and purine analogues, which show large bathochromic shifts and high microenvironmental susceptibility. Enzymatic tests indicate that all but one enzyme can accommodate the substrates of this alphabet.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Shuai Li, Feng Li, Yuhang Dong, Nachuan Song, Li Pan, Dayong Yang
Summary: Carbon dots synthesized from ribonucleosides can mimic artificial enzymes and regulate the structure and oxidative cleavage of DNA.
Article
Chemistry, Organic
Young Eum Hyun, Dnyandev B. Jarhad, Minjae Kim, Ayeon Yang, Gyudong Kim, Hong-Rae Kim, Lak Shin Jeong
Summary: This study reports a concise synthetic route for the key amino sugar intermediate essential for the synthesis of (S)-MC ribonucleosides in a 100% stereoselective manner, and also the first synthesis of enantiomerically pure (S)-MC cytidine 1. These findings are expected to make significant contributions to the field of nucleoside chemistry and provide opportunities for novel nucleoside discovery.
Article
Biochemical Research Methods
Guangyuan Wang, Chuanping He, Jinrong Zou, Jiayun Liu, Yuhui Du, Tingjian Chen
Summary: The development of unnatural base pairs (UBPs) has the potential for numerous applications in the biotechnology and biopharmaceutical industry. Efficient synthesis of oligonucleotides containing unnatural nucleobases is essential, and the use of terminal deoxynucleotidyl transferases (TdTs) has shown great potential. This study reports the efficient incorporation of nucleotides of unnatural nucleobases into DNA oligonucleotides using TdT enzyme, as well as the orthogonal labeling of nucleic acids.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Daniel K. Carlin, Simon Larsen, Vikram Sirupurapu, Michael Cho, Edwin Silverman, Jan Baumbach, Trey Ideker
Summary: Many disease-causing genetic variants converge on common biological functions and pathways, but how to incorporate pathway knowledge in genetic association studies is still unclear. Previous approaches employ a two-step method, while a concise one-step approach called Hierarchical Genetic Analysis (Higana) directly computes phenotype associations against each function in the large hierarchy of biological functions documented by the Gene Ontology. Using Higana, risk genes and functions for Chronic Obstructive Pulmonary Disease (COPD) were identified, including microtubule transport, muscle adaptation, and nicotine receptor signaling pathways, which provide new insights into COPD.
Article
Chemistry, Multidisciplinary
Hai-Lun Xia, Jian Zhang, Jincheng Si, Hexiang Wang, Kang Zhou, Lei Wang, Jingbai Li, Wen Sun, Lulu Qu, Jing Li, Xiao-Yuan Liu
Summary: Researchers have successfully fabricated two series of nanoscaled luminescent metal-organic frameworks (nano-LMOFs) with precise size control and emission colors from blue to near-infrared, using specific organic linkers. These nano-LMOFs show promising potential in sensing, bioimaging, and photocatalysis due to their tunable emission behaviors and sizes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Engineering, Environmental
Hui Ding, Ran Zhao, Zi-Hui Zhang, Jia-Jia Yang, Zheng Wang, Lu-Lan Xiao, Xue-Hua Li, Xin-Jian He, Huan-Ming Xiong
Summary: This study reports the development of highly efficient solid-state fluorescent carbon dots using an aggregation-induced emission strategy. These carbon dots exhibit tunable emission throughout the visible spectrum and demonstrate enhanced optical properties in the aggregated state. The study also explores their applications in pattern encryption, luminescent fibrous membranes, LEDs, and fingerprint detection.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Multidisciplinary Sciences
Craig A. Jerome, Shuichi Hoshika, Kevin M. Bradley, Steven A. Benner, Elisa Biondi
Summary: The ability of nucleic acids to catalyze reactions is important for scientific research and applications. By constructing a library of nucleic acids with six nucleotide building blocks, the catalytic power of nucleic acids can be enhanced. Experimental results suggest that DNA libraries with increased chemical diversity and larger searchable sequence spaces are better reservoirs for catalytic molecules compared to libraries with standard four nucleotide building blocks.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Engineering, Mechanical
Kaipeng Ji, Peng Zhao, Chaojie Zhuo, Jian Chen, Xianghong Wang, Shiquan Gao, Jianzhong Fu
Summary: In this paper, an ultrasonic imaging method based on frequency-domain reverse-time migration (FD-RTM) was developed for defect detection in curved-surface components (CSC). The method showed high-quality imaging and obvious advantages compared to existing methods.
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
(2022)
Article
Chemistry, Physical
Danyang Zhang, Daiyong Chao, Chunyu Yu, Qi Zhu, Shihong Zhou, Long Tian, Liang Zhou
Summary: A simple strategy for developing full-color carbon quantum dots (CQDs) was proposed, resulting in the synthesis of blue, green, yellow-green, and orange-red CQDs doped with heteroatoms. The study also explored how luminescence can be tuned and improved in CQDs. Furthermore, a high-efficiency white light-emitting diode was successfully fabricated with high color rendering index.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Automation & Control Systems
Shshank Chaube
Summary: This paper introduces a novel method, triangular conflicting bifuzzy set (TCBFS), for dealing with conflicting uncertainty. Non-linear programming is used to derive a number of functions to generate membership and non-membership functions for different system configurations. The validity of the suggested method is demonstrated through illustrated scenarios, improving the precision and resilience of system reliability estimations.
ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE
(2023)
Article
Agronomy
Lazaro Jose Chaves
Summary: Quantifying genetic variability in plant populations is essential for selection plans. The study introduces an alternative method to estimate genetic variance components for recurrent selection using biparental cyclic crossing with three parents. The method allows for different selection strategies and provides expected genetic gain equal to or greater than unrelated full-sib selection, without any further advantage of using more than three parents in each chain-cross.
Article
Neurosciences
Yujiang Wang, Karoline Leiberg, Tobias Ludwig, Bethany Little, Joe H. Necus, Gavin Winston, Sjoerd B. Vos, Jane de Tisi, John S. Duncan, Peter N. Taylor, Bruno Mota
Summary: Research has shown covariance between cortical morphology measures and introduced new independent measures. Applying these measures can provide new insights, revealing distinct morphological alterations underlying healthy aging and temporal lobe epilepsy.
Article
Mathematics
Bai-Nian Shen, Wen-Xin Qin
Summary: In this paper, Morse decompositions are studied for a class of twist maps on the high-dimensional cylinder, based on the connected components of rotation sets. It is found that if the rotation set is contained in the union of n pairwise disjoint closed intervals, a Morse decomposition with n Morse sets can be constructed. Furthermore, this decomposition can be extended to nearby systems, with the Morse sets being upper semicontinuous. The dynamics within the Morse sets are also investigated.
JOURNAL OF DIFFERENTIAL EQUATIONS
(2023)
Article
Biochemistry & Molecular Biology
Samudrala Rajendra Prasad, Srishylam Penjarla, Paidi Yella Reddy, B. Purna Chandra Rao, Rambabu Gundla, Yogesh S. Sanghvi, Shyamapada Banerjee
Summary: An easy and efficient synthesis of 1,2,-di-O-acetyl-5-O-benzoyl-3-O-methyl-D-ribofuranose was achieved, and its utility in synthesizing nucleoside analogues was demonstrated. Five novel base modified nucleosides were generated via functional group manipulations. The 3'-O-modified nucleosides showed antiviral activity. This synthesis strategy provides a direct route to 3'-O-alkylated nucleosides with wide applications.
CARBOHYDRATE RESEARCH
(2023)
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
Biswarup Jash, Eric T. Kool
Summary: In this study, we investigated the acylation reactivity of RNA 2'-OH groups and identified the strong influence of steric and inductive effects on the reaction. These findings provide insights into new strategies for enhancing conjugation and mapping of RNA.
CHEMICAL COMMUNICATIONS
(2022)
Article
Microbiology
Mericien Venzon, Ritika Das, Daniel J. Luciano, Julia Burnett, Hyun Shin Park, Joseph Cooper Devlin, Eric T. Kool, Joel G. Belasco, E. Jane Albert Hubbard, Ken Cadwell
Summary: Microbial byproducts play a crucial role in the reproductive development of nematodes by affecting their fertility and hatching abilities through alterations in arginine and aldehyde levels.
CELL HOST & MICROBE
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Emily M. Harcourt, Yong Woong Jun, David L. Wilson, Emily D. Ledgerwood, Eric T. Kool
Article
Biochemistry & Molecular Biology
Yujeong Lee, Yoshiyuki Onishi, Lisa McPherson, Anna M. Kietrys, Marian Hebenbrock, Yong Woong Jun, Ishani Das, Shanthi Adimoolam, Debin Ji, Michael G. Mohsen, James M. Ford, Eric T. Kool
Summary: Impaired DNA repair activity is associated with increased cancer rates. This study found that certain tyrosine kinase inhibitors, such as nilotinib, can activate the repair enzyme MTH1, which cleanses oxidatively damaged nucleotides. Structural optimization resulted in compounds that strongly activate MTH1 and decrease mutagenic nucleotides in cellular DNA. These findings suggest that MTH1 activators may be a promising strategy to suppress tumorigenesis in individuals with elevated cancer risks.
ACS CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yong Woong Jun, Emily M. Harcourt, Lu Xiao, David L. Wilson, Eric T. Kool
Summary: This article presents a convenient and versatile method for general fluorescence labeling of DNAs. It utilizes deaminated DNA bases and aminooxy-substituted rotor dyes to mark label positions and trap AP sites, resulting in high emission intensities for fluorescence labeling of oligonucleotides and dsDNA.
NATURE COMMUNICATIONS
(2022)
Review
Chemistry, Multidisciplinary
Yong Woong Jun, Eric T. Kool
Summary: DNA repair enzymes play a significant role in protecting cellular DNA from damage and are closely associated with cancer and inflammation pathways. The development of new tools and methods has greatly contributed to the study of these enzymes and their potential applications in diagnostics and therapies. This article provides an overview of the development of chemical tools for studying DNA repair processes and discusses the insights gained from their application. The article also highlights the importance of future research in the field of biomedicine and human health.
ACCOUNTS OF CHEMICAL RESEARCH
(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
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
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.
