Review
Biochemistry & Molecular Biology
Barry S. Cooperman
Summary: The introduction of fluorophores into RNA for both in vitro and in cellulo studies of RNA function and cellular distribution is a subject of great current interest. Various methods for site-specific fluorescent labeling of RNAs are reviewed, including the utilization of natural posttranslational modifications, enzymatic transferase reactions, nucleic acid-assisted labeling, and de novo preparation of specifically labeled RNAs.
Article
Biochemistry & Molecular Biology
Ksenia A. Sapozhnikova, Evgeny L. Gulyak, Vsevolod A. Misyurin, Maria A. Simonova, Ekaterina V. Ryabukhina, Anastasiya V. Alexeeva, Nataliya A. Tikhonova, Natalia A. Lyzhko, Galina P. Popova, Andrey V. Misyurin, Alexey V. Ustinov, Vladimir A. Korshun, Vera A. Alferova, Dmitry Yu. Ryazantsev, Vladimir A. Brylev
Summary: Fluorescent antibodies are essential in molecular biology and diagnostics. This study introduces a methodology for synthesizing site-specific antibody-dye conjugates with a high degree of labeling, which was demonstrated to successfully detect PRAME protein on cell surfaces using flow cytometry.
Review
Chemistry, Multidisciplinary
Qi Tang, Xing Chen
Summary: Cellular proteins are dynamically regulated in response to environmental stimuli. Conventional proteomics compares the entire proteome in different cellular states to identify differentially expressed proteins, but it has limited sensitivity for analyzing acute and subtle changes. To address this challenge, nascent proteomics selectively analyzes the newly synthesized proteins, offering a more sensitive and timely insight into the dynamic changes of the proteome. In this Minireview, recent advancements in nascent proteomics are discussed, with an emphasis on methodological developments. The current challenges and future prospects of this exciting field are also explored.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Plant Sciences
Kasia Dinkeloo, Zoe Pelly, John M. McDowell, Guillaume Pilot
Summary: Translating ribosome affinity purification (TRAP) is a method that uses transgenic plants to purify ribosomes and translating mRNAs. It can be used for studying actively translated mRNAs by quantitative PCR or RNA sequencing. This approach allows researchers to isolate the translatome of specific cell types using condition- or cell-specific promoters. However, it may lack sensitivity in cases where the condition/cell-specific promoter is weak, ribosome turnover is low, or the targeted cells are short-lived. To overcome these limitations, a new TRAP system was developed that utilizes two transgenes and provides increased sensitivity and better temporal resolution.
Article
Biochemistry & Molecular Biology
Juan Tang, Chenfei Yu, Axel Loredo, Yuda Chen, Han Xiao
Summary: Photoactivatable fluorophores are limited in their applications due to their size and the need for ultraviolet light activation. Research has focused on more efficient protein labeling technologies, including single-step labeling processes. By using genetic code expansion and replacing oxygen with sulfur within existing fluorescent amino acids, the photoactivatable fluorescent amino acid thioacridonylalanine (SAcd) has been successfully incorporated into proteins in a single step.
Article
Biochemistry & Molecular Biology
Mateusz Chwastyk, Marek Cieplak
Summary: The study revealed differences in the geometry of the exit tunnel of ribosomes from different domains of life, leading to varying behaviors of proteins within them. One protein, bacterial YibK, showed knotting in its native state, with the highest probability observed in bacterial ribosomes. Relaxing the rigidity condition of ribosomes could enhance proper folding and avoid trapping.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemical Research Methods
Guozhang Zou, Vera B. Ivleva, Jeremy J. Wolff, Rong Sylvie Yang, Casper Alabanza, Nathan Barefoot, Cindy Cai, Yanhong Yang, Daniel B. Gowetski, Jason G. Gall, Q. . Paula Lei
Summary: To qualitatively localize HA trimers displayed on assembled tetravalent HA nanoparticles, hemagglutinantigen binding fragments (Fabs) were labeled with fluorescent (FLR) dyes as probes. The labeling profile, including labeling ratio, distribution, and site-specific labeling occupancy, was evaluated to determine the labeling efficiency. A combination of intact mass measurement and peptide mapping was used to accurately profile the labeling pattern of FLR-labeled 1H01-Fabs. The data showed site-specific and semiquantitative labeling, ensuring consistency in single-particle fluorescent imaging experiments.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Engineering, Biomedical
Xiao Liu, Takeru Yamazaki, Haw-Young Kwon, Satoshi Arai, Young-Tae Chang
Summary: Researchers have developed a new fluorescent thermometer, Thermo Greens (TGs), which can visualize temperature changes in almost all typical organelles, making it crucial for understanding intracellular temperature fluctuations.
MATERIALS TODAY BIO
(2022)
Article
Biology
Ryo Tamura, Fangchao Jiang, Jin Xie, Daichi Kamiyama
Summary: The article describes a method to expand the number of orthogonal split FP systems with spectrally distinct colors, utilizing rational design and cycles of directed evolution to broaden the spectral color palette of FP1-10/11. They demonstrate a multiplexing approach using the new orthogonal split FP systems, allowing simultaneous imaging of four distinct proteins in single cells.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xue Li, Lu Zhang, Suyang Wang, Xiangqin Liu, Ying Lin
Summary: A novel site-specific internal protein labeling method using two atypical split inteins was demonstrated, allowing for the incorporation of a fluorescent probe into recombinant proteins. The number of native extein amino acids was shown to affect trans-splicing activity.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemical Research Methods
Aparna Biswas, Yu-Fong Peng, Vikas Kaushik, Sofia Origanti
Summary: The Shwachman-Diamond syndrome (SDS) is a rare genetic disorder caused by mutations in the SBDS gene. SBDS is a ribosomal maturation factor that is crucial for the release of eIF6 during the late stages of ribosomal subunit maturation. Researchers have successfully labeled specific domains of SBDS with a fluorescent marker to study their dynamics upon binding to 60S and assess the effects of SDS-specific mutations.
Article
Biochemical Research Methods
Debayan Sarkar, Satyajit Mishra, Rahul Nisal, Sumita Majhi, Rohit Shrivas, Yashaswi Singh, V. S. Anusree, Jeet Kalia
Summary: Peptide toxins secreted by venomous animals can bind to and modulate the function of mammalian ion channel proteins. These toxins are highly specific to their target ion channels, making them powerful tools for ion channel biology. However, producing fluorescently labeled toxins rich in cysteine residues presents technical challenges. In this study, we evaluate different protein bioconjugation approaches and find that C-terminal bioconjugation via the sortase technology is successful in producing fluorescently labeled toxins.
BIOCONJUGATE CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Soumya Jyoti Singha Roy, Conor Loynd, Delilah Jewel, Sarah E. Canarelli, Elise D. Ficaretta, Quan A. Pham, Eranthie Weerapana, Abhishek Chatterjee
Summary: We have developed a novel visible-light-catalyzed bioconjugation reaction, PhotoCLIC, for selective modification of 5-hydroxytryptophan residue (5HTP) on full-length proteins. This reaction enables rapid and site-specific protein bioconjugation using catalytic amounts of methylene blue and blue/red light-emitting diodes. The PhotoCLIC product has a unique structure likely formed through singlet oxygen-dependent modification of 5HTP. PhotoCLIC has a wide substrate scope and is compatible with strain-promoted azide-alkyne click reaction, allowing for site-specific dual-labeling of a target protein.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Kenta Tanaka, Yoshiya Hatano, Junko Ohkanda
Summary: The 14-3-3 family of proteins plays a central role in regulating signaling pathways driven by serine/threonine kinases. Although there are seven highly conserved isoforms of 14-3-3 in humans, the specific functions of each isoform are still not fully understood. This study focused on evaluating the sigma isoform of 14-3-3 and designing a fluorescent labeling agent using a natural product as a base. The results showed that the labeled agent exhibited selective fluorescent detection of 14-3-3 sigma, indicating its potential use for studying the biological roles of this isoform.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Victoria Aladin, Arun K. Sreemantula, Thomas Biedenbaender, Alexander Marchanka, Bjoern Corzilius
Summary: An approach is presented to enhance NMR spectroscopic signals by site-specific enhancement of the protein-RNA binding site within a ribonucleoprotein (RNP) using dynamic nuclear polarization (DNP). This approach utilizes biochemical techniques for sparse isotope labeling and exploits the molecular dynamics of C-13-labeled methyl groups exclusively present in the protein, resulting in improved sensitivity and specificity for solid-state NMR structure determination of large biomolecules.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Sunil Kumar, Diana E. Schlamadinger, Mark A. Brown, Joanna M. Dunn, Brandon Mercado, James A. Hebda, Ishu Saraogi, Elizabeth Rhoades, Andrew D. Hamilton, Andrew D. Miranker
CHEMISTRY & BIOLOGY
(2015)
Article
Multidisciplinary Sciences
Aileen Ariosa, Jae Ho Lee, Shuai Wang, Ishu Saraogi, Shu-ou Shan
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Editorial Material
Neurosciences
Sandhya Chandrasekaran, Schahram Akbarian
BIOLOGICAL PSYCHIATRY
(2016)
Article
Genetics & Heredity
Yan Jiang, Yong-Hwee Eddie Loh, Prashanth Rajarajan, Teruyoshi Hirayama, Will Liao, Bibi S. Kassim, Behnam Javidfar, Brigham J. Hartley, Lisa Kleofas, Royce B. Park, Benoit Labonte, Seok-Man Ho, Sandhya Chandrasekaran, Catherine Do, Brianna R. Ramirez, Cyril J. Peter, T. C. W. Julia, Brian M. Safaie, Hirofumi Morishita, Panos Roussos, Eric J. Nestler, Anne Schaefer, Benjamin Tycko, Kristen J. Brennand, Takeshi Yagi, Li Shen, Schahram Akbarian
Article
Chemistry, Multidisciplinary
Oleg V. Kulikov, Yulia V. Sevryugina, Arshad Mehmood, Ishu Saraogi
NEW JOURNAL OF CHEMISTRY
(2017)
Article
Chemistry, Multidisciplinary
Sudipta Ghosh, Snehlata Saini, Ishu Saraogi
CHEMICAL COMMUNICATIONS
(2018)
Article
Neurosciences
Prashanth Rajarajan, Tyler Borrman, Will Liao, Sergio Espeso-Gil, Sandhya Chandrasekaran, Yan Jiang, Zhiping Weng, Kristen J. Brennand, Schahram Akbarian
CURRENT OPINION IN NEUROBIOLOGY
(2019)
Article
Multidisciplinary Sciences
Lucy K. Bicks, Kazuhiko Yamamuro, Meghan E. Flanigan, Julia Minjung Kim, Daisuke Kato, Elizabeth K. Lucas, Hiroyuki Koike, Michelle S. Peng, Daniel M. Brady, Sandhya Chandrasekaran, Kevin J. Norman, Milo R. Smith, Roger L. Clem, Scott J. Russo, Schahram Akbarian, Hirofumi Morishita
NATURE COMMUNICATIONS
(2020)
Article
Genetics & Heredity
Sergio Espeso-Gil, Tobias Halene, Jaroslav Bendl, Bibi Kassim, Gabriella Ben Hutta, Marina Iskhakova, Neda Shokrian, Pavan Auluck, Behnam Javidfar, Prashanth Rajarajan, Sandhya Chandrasekaran, Cyril J. Peter, Alanna Cote, Rebecca Birnbaum, Will Liao, Tyler Borrman, Jennifer Wiseman, Aaron Bell, Michael J. Bannon, Panagiotis Roussos, John F. Crary, Zhiping Weng, Stefano Marenco, Barbara Lipska, Nadejda M. Tsankova, Laura Huckins, Yan Jiang, Schahram Akbarian
Article
Medicine, Research & Experimental
Anirban Das, Yogesh M. Gangarde, Viniti Tomar, Omkar Shinde, Tulsi Upadhyay, Sarfaraz Alam, Sudipta Ghosh, Varun Chaudhary, Ishu Saraogi
MOLECULAR PHARMACEUTICS
(2020)
Article
Chemistry, Analytical
Anirban Das, Tanoy Dutta, Laxmikant Gadhe, Apurba Lal Koner, Ishu Saraogi
ANALYTICAL CHEMISTRY
(2020)
Article
Chemistry, Multidisciplinary
Yogesh M. Gangarde, T. K. Sajeev, Nihar R. Panigrahi, Ram K. Mishra, Ishu Saraogi
Article
Multidisciplinary Sciences
Sandhya Chandrasekaran, Sergio Espeso-Gil, Yong-Hwee Eddie Loh, Behnam Javidfar, Bibi Kassim, Yueyan Zhu, Yuan Zhang, Yuhao Dong, Lucy K. Bicks, Haixin Li, Prashanth Rajarajan, Cyril J. Peter, Daijing Sun, Esperanza Agullo-Pascual, Marina Iskhakova, Molly Estill, Bluma J. Lesch, Li Shen, Yan Jiang, Schahram Akbarian
Summary: The study reveals the role of upregulation of endogenous retroviral sequences in brain structure, with a specific focus on ERV2 sequences in neuron-specific chromatin domains in the cerebral cortex of adult mice. Comparative analysis between wild-derived and laboratory inbred mice further demonstrates the impact of recent ERV2 expansions on neuronal reconfigurations and chromosomal contact frequencies in the murine germline, highlighting the importance of neuronal chromosomal organization in transcriptional regulation and neuronal tropism.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Bapurao A. Bhoge, Purnima Mala, Jo S. Kurian, Varadharajan Srinivasan, Ishu Saraogi
CHEMICAL COMMUNICATIONS
(2020)
Article
Chemistry, Multidisciplinary
Vaibhav V. Karekar, Bapurao A. Bhoge, Ishu Saraogi
NEW JOURNAL OF CHEMISTRY
(2019)
