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ORP9-PH domain-based fluorescent reporters for visualizing phosphatidylinositol 4-phosphate dynamics in living cells RSC Chem. Biol. Pub Date : 2024-04-24 Moeka Ajiki, Masaru Yoshikawa, Tomoki Miyazaki, Asami Kawasaki, Kazuhiro Aoki, Fubito Nakatsu, Shinya Tsukiji
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Reverse transcription as key step in RNA in vitro evolution with unnatural base pairs RSC Chem. Biol. Pub Date : 2024-04-23 Eva S. Hoffmann, Mareike C. De Pascali, Lukas Neu, Christof Domnick, Alice Soldà, Stephanie Kath-Schorr
Unnatural base pairs (UBPs) augment the chemical diversity of artificial nucleic acids and can thus enable the generation of new aptamers and catalytic nucleic acids by in vitro selection. However, owing to a lack of methodologies, the reverse transcription of UBPs, a key step in RNA aptamer selection, has not been sufficiently characterized. Here, we present a series of versatile assays to investigate
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Why pyridoxal phosphate could be a functional predecessor of thiamine pyrophosphate and speculations on a primordial metabolism RSC Chem. Biol. Pub Date : 2024-04-18 Andreas Kirschning
The account attempts to substantiate the hypothesis that, from an evolutionary perspective, the coenzyme couple pyridoxal phosphate and pyridoxamine phosphate preceded the coenzyme thiamine pyrophosphate and acted as its less efficient chemical analogue in some form of early metabolism. The analysis combines mechanism-based chemical reactivity with biosynthetic arguments and provides evidences that
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Ancient and modern mechanisms compete in progesterone receptor activation RSC Chem. Biol. Pub Date : 2024-04-15 Sabab Hasan Khan, Namita Dube, Nishanti Sudhakar, Olivia Fraser, Priscilla Villalona, Sean M. Braet, Stephanie Leedom, Erin R. Reilly, Jacob Sivak, Kenidee Crittenden, C. Denise Okafor
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Reduction midpoint potential of a paradigm light–oxygen–voltage receptor and its modulation by methionine residues RSC Chem. Biol. Pub Date : 2024-04-09 Andrés García de Fuentes, Andreas Möglich
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Polyamines promote xenobiotic nucleic acid synthesis by modified thermophilic polymerase mutants RSC Chem. Biol. Pub Date : 2024-04-04 Hidekazu Hoshino, Yuuya Kasahara, Satoshi Obika
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Advances in the joint profiling technologies of 5mC and 5hmC RSC Chem. Biol. Pub Date : 2024-04-05 Bo He, Haojun Yao, Chengqi Yi
DNA cytosine methylation, a crucial epigenetic modification, involves the dynamic interplay of 5-methylcytosine (5mC) and its oxidized form, 5-hydroxymethylcytosine (5hmC), generated by ten-eleven translocation (TET) DNA dioxygenases. This process is central to regulating gene expression, influencing critical biological processes such as development, disease progression, and aging. Recognizing the
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Prevention of amyloid β fibril deposition on the synaptic membrane in the precuneus by ganglioside nanocluster-targeting inhibitors RSC Chem. Biol. Pub Date : 2024-04-04 Erika Miyamoto, Hideki Hayashi, Shigeo Murayama, Katsuhiko Yanagisawa, Toshinori Sato, Teruhiko Matsubara
Alzheimer's disease (AD), a progressive neurodegenerative condition, is one of the most common causes of dementia. Senile plaques, a hallmark of AD, are formed by the accumulation of amyloid β protein (Aβ), which starts to aggregate before the onset of the disease. Gangliosides, sialic acid-containing glycosphingolipids, play a key role in the formation of toxic Aβ aggregates. In membrane rafts, ganglioside-bound
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Genome-wide mapping of G-quadruplex DNA: a step-by-step guide to select the most effective method RSC Chem. Biol. Pub Date : 2024-03-25 Silvia Galli, Gem Flint, Lucie Růžičková, Marco Di Antonio
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Site-specific RNA modification via initiation of in vitro transcription reactions with m6A and isomorphic emissive adenosine analogs RSC Chem. Biol. Pub Date : 2024-03-27 Deyuan Cong, Kfir B. Steinbuch, Ryosuke Koyama, Tyler V. Lam, Jamie Y. Lam, Yitzhak Tor
The templated enzymatic incorporation of adenosine and its analogs, including m6A, thA and tzA into RNA transcripts, has been explored. Enforced transcription initiation with excess free nucleosides and the native triphosphates generates 5′-end modified transcripts, which can be 5′-phosphorylated and ligated to provide full length, singly modified RNA oligomers. To explore structural integrity, functionality
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Introduction to ‘Medicinal Chemistry Small Molecule Probes’ RSC Chem. Biol. Pub Date : 2024-03-25 Gemma Nixon, Khondaker Miraz Rahman, John Spencer
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Pseudouridine and N1-methylpseudouridine as potent nucleotide analogues for RNA therapy and vaccine development RSC Chem. Biol. Pub Date : 2024-03-19 Lyana L. Y. Ho, Gabriel H. A. Schiess, Pâmella Miranda, Gerald Weber, Kira Astakhova
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Leveraging machine learning models for peptide–protein interaction prediction RSC Chem. Biol. Pub Date : 2024-03-13 Song Yin, Xuenan Mi, Diwakar Shukla
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Discovery of potent and selective activity-based probes (ABPs) for the deubiquitinating enzyme USP30 RSC Chem. Biol. Pub Date : 2024-03-13 Milon Mondal, Fangyuan Cao, Daniel Conole, Holger W. Auner, Edward W. Tate
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Molecularly imprinted nanoparticles reveal regulatory scaffolding features in Pyk2 tyrosine kinase RSC Chem. Biol. Pub Date : 2024-03-13 Tania M. Palhano Zanela, Milad Zangiabadi, Yan Zhao, Eric S. Underbakke
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Introduction to ‘The Epitranscriptome’ RSC Chem. Biol. Pub Date : 2024-03-06 Ralph E. Kleiner, Claudia Höbartner, Guifang Jia
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Engineering cell-free systems by chemoproteomic-assisted phenotypic screening RSC Chem. Biol. Pub Date : 2024-03-06 Zarina Levitskaya, Zheng Ser, Hiromi Koh, Wang Shi Mei, Sharon Chee, Radoslaw Mikolaj Sobota, John F. Ghadessy
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Development of PCR primers enabling the design of flexible sticky ends for efficient concatenation of long DNA fragments RSC Chem. Biol. Pub Date : 2024-02-26 Kohei Nomura, Kaoru Onda, Hirotaka Murase, Fumitaka Hashiya, Yukiteru Ono, Goro Terai, Natsuhisa Oka, Kiyoshi Asai, Daisuke Suzuki, Naho Takahashi, Haruka Hiraoka, Masahito Inagaki, Yasuaki Kimura, Yoshihiro Shimizu, Naoko Abe, Hiroshi Abe
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Tracking the cellular uptake and phototoxicity of Ru(II)-polypyridyl-1,8-naphthalimide Tröger's base conjugates RSC Chem. Biol. Pub Date : 2024-02-21 Sandra A. Bright, MariaLuisa Erby, Fergus E. Poynton, Daniel Monteyne, David Pérez-Morga, Thorfinnur Gunnlaugsson, D. Clive Williams, Robert B. P. Elmes
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A covalent compound selectively inhibits RNA demethylase ALKBH5 rather than FTO RSC Chem. Biol. Pub Date : 2024-02-19 Gan-Qiang Lai, Yali Li, Heping Zhu, Tao Zhang, Jing Gao, Hu Zhou, Cai-Guang Yang
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Strategies for converting turn-motif and cyclic peptides to small molecules for targeting protein–protein interactions RSC Chem. Biol. Pub Date : 2024-02-16 Deanne Hayward, Andrew M. Beekman
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Sortase mediated protein ubiquitination with defined chain length and topology RSC Chem. Biol. Pub Date : 2024-02-07 Nicole R. Raniszewski, Jenna N. Beyer, Myles I. Noel, George M. Burslem
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Biomedical applications, perspectives and tag design concepts in the cell – silent Raman window RSC Chem. Biol. Pub Date : 2024-02-12 Martha Z. Vardaki, Vasilis G. Gregoriou, Christos L. Chochos
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Unusual cysteine modifications in natural product biosynthesis RSC Chem. Biol. Pub Date : 2024-02-09 Yaojie Gao, Yuhao Zhu, Takayoshi Awakawa, Ikuro Abe
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Genetically encodable biosensors for Ras activity RSC Chem. Biol. Pub Date : 2024-02-07 Ryan Weeks, Sohum Mehta, Jin Zhang
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Reversible oxidative dimerization of 4-thiouridines in tRNA isolates RSC Chem. Biol. Pub Date : 2024-02-01 Larissa Bessler, Jonathan Groß, Christopher J. Kampf, Till Opatz, Mark Helm
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Cell penetration of oxadiazole-containing macrocycles RSC Chem. Biol. Pub Date : 2024-01-15 Sungjoon Huh, Nefeli Batistatou, Jing Wang, George J. Saunders, Joshua A. Kritzer, Andrei K. Yudin
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Introduction to the themed collection on ‘Molecular and Nanotheranostics’ RSC Chem. Biol. Pub Date : 2024-01-12 Thimmaiah Govindaraju
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Evaluating Riboglow-FLIM probes for RNA sensing RSC Chem. Biol. Pub Date : 2024-01-08 Nadia Sarfraz, Luke K. Shafik, Zachary R. Stickelman, Uma Shankar, Emilia Moscoso, Esther Braselmann
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Click chemistry in the development of PROTACs RSC Chem. Biol. Pub Date : 2023-12-29 Ce Yang, Ravi Tripathi, Binghe Wang
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Engineered triphenylphosphonium-based, mitochondrial-targeted liposomal drug delivery system facilitates cancer cell killing actions of chemotherapeutics RSC Chem. Biol. Pub Date : 2023-12-21 Subramaniyam Sivagnanam, Kiran Das, Ieshita Pan, Adele Stewart, Atanu Barik, Biswanath Maity, Priyadip Das
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Sialic acids in infection and their potential use in detection and protection against pathogens RSC Chem. Biol. Pub Date : 2023-12-19 Simone Dedola, Sanaz Ahmadipour, Peterson de Andrade, Alexander N. Baker, Andrew N. Boshra, Simona Chessa, Matthew I. Gibson, Pedro J. Hernando, Irina M. Ivanova, Jessica E. Lloyd, María J. Marín, Alexandra J. Munro-Clark, Giulia Pergolizzi, Sarah-Jane Richards, Iakovia Ttofi, Ben A. Wagstaff, Robert A. Field
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Identifying ligands for the PHD1 finger of KDM5A through high-throughput screening RSC Chem. Biol. Pub Date : 2023-12-18 Gloria Ortiz, James E. Longbotham, Sophia L. Qin, Meng Yao Zhang, Gregory M. Lee, R. Jeffrey Neitz, Mark J. S. Kelly, Michelle R. Arkin, Danica Galonić Fujimori
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BrainBike peptidomimetic enables efficient transport of proteins across brain endothelium RSC Chem. Biol. Pub Date : 2023-12-11 Maria C. Lucana, Roberta Lucchi, Fabien Gosselet, Cristina Díaz-Perlas, Benjamí Oller-Salvia
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Cationic dextrin nanoparticles for effective intracellular delivery of cytochrome C in cancer therapy RSC Chem. Biol. Pub Date : 2023-11-24 Ankita Sarkar, Sanchita Sarkhel, Deepali Bisht, Amit Jaiswal
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Bioluminescent detection of viral surface proteins using branched multivalent protein switches RSC Chem. Biol. Pub Date : 2023-11-23 Alexander Gräwe, Cindy M. Spruit, Robert P. de Vries, Maarten Merkx
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N 4-Allylcytidine: a new nucleoside analogue for RNA labelling and chemical sequencing RSC Chem. Biol. Pub Date : 2023-11-22 Tengwei Li, Xiao Shu, Minsong Gao, Chenyang Huang, Ting Li, Jie Cao, Xiner Ying, Donghong Liu, Jianzhao Liu
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Discovery and engineering of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products RSC Chem. Biol. Pub Date : 2023-11-21 He Li, Wei Ding, Qi Zhang
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Identification and engineering of potent cyclic peptides with selective or promiscuous binding through biochemical profiling and bioinformatic data analysis RSC Chem. Biol. Pub Date : 2023-11-14 Thomas P. Smith, Bhaskar Bhushan, Daniele Granata, Christian S. Kaas, Birgitte Andersen, Klaas W. Decoene, Qiansheng Ren, Haimo Liu, Xinping Qu, Yang Yang, Jia Pan, Quijia Chen, Martin Münzel, Akane Kawamura
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Design, synthesis and modelling of photoreactive chemical probes for investigating target engagement of plasmepsin IX and X in Plasmodium falciparum RSC Chem. Biol. Pub Date : 2023-11-13 Monika Lisauskaitė, Gemma L. Nixon, Christopher M. Woodley, Neil G. Berry, Andy Coninckx, L. Charlie Qie, Suet C. Leung, Donatella Taramelli, Nicoletta Basilico, Silvia Parapini, Stephen A. Ward, Oscar Vadas, Dominique Soldati-Favre, W. David Hong, Paul M. O'Neill
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Monitoring host–pathogen interactions using chemical proteomics RSC Chem. Biol. Pub Date : 2023-11-10 Angela Weigert Muñoz, Weining Zhao, Stephan A. Sieber
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Helix-based screening with structure prediction using artificial intelligence has potential for the rapid development of peptide inhibitors targeting class I viral fusion RSC Chem. Biol. Pub Date : 2023-11-07 Satoshi Suzuki, Mio Kuroda, Keisuke Aoki, Kumi Kawaji, Yoshiki Hiramatsu, Mina Sasano, Akie Nishiyama, Kazutaka Murayama, Eiichi N. Kodama, Shinya Oishi, Hironori Hayashi
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An AIE-based monofunctional Pt(II) complex for photodynamic therapy through synergism of necroptosis–ferroptosis RSC Chem. Biol. Pub Date : 2023-11-06 Xiaoxue Zheng, Minglun Liu, Yanping Wu, Yuncong Chen, Weijiang He, Zijian Guo
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Increasing the functional density of threose nucleic acid RSC Chem. Biol. Pub Date : 2023-10-25 Biju Majumdar, Daisy Sarma, Yutong Yu, Adriana Lozoya-Colinas, John C. Chaput
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Studies on the selectivity of the SARS-CoV-2 papain-like protease reveal the importance of the P2′ proline of the viral polyprotein RSC Chem. Biol. Pub Date : 2023-10-24 H. T. Henry Chan, Lennart Brewitz, Petra Lukacik, Claire Strain-Damerell, Martin A. Walsh, Christopher J. Schofield, Fernanda Duarte
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An enhanced biophysical screening strategy to investigate the affinity of ASOs for their target RNA RSC Chem. Biol. Pub Date : 2023-10-23 Rouven Stulz, Michael Lerche, Olivia Luige, Agnes Taylor, Stefan Geschwindner, Alice Ghidini
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Small molecule modulators of immune pattern recognition receptors RSC Chem. Biol. Pub Date : 2023-10-23 Taku Tsukidate, Charles W. Hespen, Howard C. Hang
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Copper binding and protein aggregation: a journey from the brain to the human lens RSC Chem. Biol. Pub Date : 2023-10-17 Yanahi Posadas, Carolina Sánchez-López, Liliana Quintanar
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A cell-permeable probe for the labelling of a bacterial glycosyltransferase and virulence factor RSC Chem. Biol. Pub Date : 2023-10-19 Yong Xu, Gerd K. Wagner
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Red-light modulated ortho-chloro azobenzene photoswitch for peptide stapling via aromatic substitution RSC Chem. Biol. Pub Date : 2023-10-19 Mia Kapun, F. Javier Pérez-Areales, Nicola Ashman, Pamela J. E. Rowling, Tim Schober, Elaine Fowler, Laura S. Itzhaki, David R. Spring
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A unique binding mode of P1′ Leu-containing target sequences for Streptococcus pyogenes sortase A results in alternative cleavage RSC Chem. Biol. Pub Date : 2023-10-18 Brandon A. Vogel, Jadon M. Blount, Hanna M. Kodama, Noah J. Goodwin-Rice, Devin J. Andaluz, Sophie N. Jackson, John M. Antos, Jeanine F. Amacher
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Covalent targeting of non-cysteine residues in PI4KIIIβ RSC Chem. Biol. Pub Date : 2023-10-17 Brett Cosgrove, Emma K. Grant, Sophie Bertrand, Kenneth D. Down, Don O. Somers, John P. Evans, Nicholas C. O. Tomkinson, Michael D. Barker
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Biotransformation-coupled mutasynthesis for the generation of novel pristinamycin derivatives by engineering the phenylglycine residue RSC Chem. Biol. Pub Date : 2023-10-14 Oliver Hennrich, Leoni Weinmann, Andreas Kulik, Karen Harms, Philipp Klahn, Jung-Won Youn, Frank Surup, Yvonne Mast
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Stitched peptides as potential cell permeable inhibitors of oncogenic DAXX protein RSC Chem. Biol. Pub Date : 2023-10-11 Clare Jelinska, Srinivasaraghavan Kannan, Yuri Frosi, Siti Radhiah Ramlan, Fernaldo Winnerdy, Rajamani Lakshminarayanan, Charles W Johannes, Christopher J Brown, Anh-Tuan Phan, Daniela Rhodes, Chandra S Verma
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Quantitative mass spectrometric analysis of hepatocellular carcinoma biomarker alpha-fetoprotein RSC Chem. Biol. Pub Date : 2023-10-09 Chen-Chun Chen, Han-Wen Huang, Bo-Rui Chen, Chi-Huey Wong
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Reduction-cleavable desferrioxamine B pulldown system enriches Ni(II)-superoxide dismutase from a Streptomyces proteome RSC Chem. Biol. Pub Date : 2023-10-02 Jenny Ni, James L. Wood, Melanie Y. White, Norbert Lihi, Todd E. Markham, Joseph Wang, Peter T. Chivers, Rachel Codd
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Bringing enzymes to the proximity party RSC Chem. Biol. Pub Date : 2023-09-29 Gabrielle S. Tender, Carolyn R. Bertozzi
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Unlocking the potential of platinum drugs: organelle-targeted small-molecule platinum complexes for improved anticancer performance RSC Chem. Biol. Pub Date : 2023-10-03 Zhiqin Deng, Shu Chen, Gongyuan Liu, Guangyu Zhu
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Single-chain multicolor-reporter templates for subcellular localization of molecular events in mammalian cells RSC Chem. Biol. Pub Date : 2023-10-03 Sung-Bae Kim, Ramasamy Paulmurugan, Nobuo Kitada, Sojiro A. Maki