Article
Multidisciplinary Sciences
Ryo Amano, Masato Namekata, Masataka Horiuchi, Minami Saso, Takuya Yanagisawa, Yoichiro Tanaka, Farhana Ishrat Ghani, Masakuni Yamamoto, Taiichi Sakamoto
Summary: FGF5 is a key regulator of hair growth and an oncogenic factor in certain human cancers. Novel RNA aptamers have been developed to inhibit FGF5-induced cell proliferation, with high affinity and specificity, making them potential candidates for therapeutic use in FGF5-related diseases.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Analytical
Taehwi Yoon, Seokjoon Kim, Jiye Shin, Yu Zhou, Ki Soo Park
Summary: MicroRNAs involved in various biological processes can be important biomarkers for early cancer diagnosis. A simple and cost-effective strategy for multiplex detection of miRNA using light-up RNA aptamers has been developed. This method has been successfully applied for quantification of miRNAs in different cell lines, showing practical utility in clinical diagnosis and prognosis.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Chemistry, Multidisciplinary
Claire Husser, Stephane Vuilleumier, Michael Ryckelynck
Summary: This paper introduces a RNA-based biosensor, FluorMango, which can specifically detect fluoride. The biosensor is composed of two RNA modules, one of which can change its structure to sense fluoride, while the other module emits fluorescence when bound to a fluorogen. The study illustrates the value and efficiency of this biosensor in directly monitoring defluorinase activity in bacterial cells.
Article
Chemistry, Multidisciplinary
Po-Jung Jimmy Huang, Juewen Liu
Summary: In this study, DNA aptamers for L-lactate were obtained through library-immobilization selection method with high affinity and selectivity. A fluorescent biosensor based on the strand displacement method was constructed, allowing simultaneous detection of lactate and glucose in the same solution. This research expands the application of aptamers to simple metabolites and provides a useful tool for continuous and multiplexed monitoring.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Yu Gu, Li-Juan Huang, Wei Zhao, Ting-Ting Zhang, Mei-Rong Cui, Xue-Jiao Yang, Xue-Li Zhao, Hong-Yuan Chen, Jing-Juan Xu
Summary: This study demonstrates the utilization of Corn as a split aptamer system combined with RNA-initiated fluorescence complementation (RIFC) for monitoring RNA self-assembly and sensing microRNA. The split aptamers show good photostability and can deliver a light-up fluorescent response to miR-21 in mammalian cells. This method has potential for real-time visualization and mechanistic analysis of nucleic acids.
Article
Medicine, Research & Experimental
Dan Shu, Long Zhang, Xuefeng Bai, Jianhua Yu, Peixuan Guo
Summary: This study describes the development of a novel Ab-like RNA nanoparticle platform carrying multiple ligands for immunotherapy. Optimized trispecific RNA NPs showed efficient T cell activation, promoted the strongest anti-tumor function of immune cells, and inhibited cancer growth in animal trials. This Ab-like RNA NP platform provides a promising alternative to protein antibodies for tumor immunotherapy.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Article
Biochemistry & Molecular Biology
Kevin M. Pham, Scott R. Suter, Shannon S. Lu, Peter A. Beal
Summary: MicroRNAs (miRNAs) are essential in gene regulation, and deregulation of their expression is linked to diseases. Antisense oligonucleotides targeting disease-associated miRNAs show therapeutic potential. Chemical modifications of anti-miRNA oligonucleotides are being explored to enhance their activity, with a focus on improving nuclease resistance and binding affinity.
BIOORGANIC & MEDICINAL CHEMISTRY
(2021)
Article
Engineering, Biomedical
Abhichart Krissanaprasit, Carson M. Key, Kristen Froehlich, Sahil Pontula, Emily Mihalko, Daniel M. Dupont, Ebbe S. Andersen, Jorgen Kjems, Ashley C. Brown, Thomas H. LaBean
Summary: The RNA origami platform displaying RNA aptamers shows improved anticoagulation activity compared to free aptamers, with the ability for immediate thrombin inhibition switch-off by specific reversal agents. Single-stranded DNA (ssDNA) and single-stranded peptide nucleic acid (PNA) antidotes can restore coagulation activity, indicating the potential for practical, long-term storage for clinical use. RNA origami-based molecules demonstrate promise as safer alternatives with rapid activity switching compared to current commercial intravenous anticoagulants.
ADVANCED HEALTHCARE MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Imran Ozer, George A. Pitoc, Juliana M. Layzer, Angelo Moreno, Lyra B. Olson, Kyle D. Layzer, Angus M. Hucknall, Bruce A. Sullenger, Ashutosh Chilkoti
Summary: RNA aptamers are a promising class of therapeutics, but their poor blood circulation has limited their clinical potential. In this study, researchers address this limitation by conjugating RNA aptamers with a next-generation PEG-like brush polymer. The conjugate retains the therapeutic action of the drug and can be easily reversed, while avoiding the reactivity of pre-existing PEG antibodies. These findings have important implications for rescuing the PEGylation of RNA therapeutics and vaccines from the adverse effects of PEG.
ADVANCED MATERIALS
(2022)
Article
Chemistry, Analytical
Yanan Wu, Zhijun Li, Mingqing Shi, Kun Yuan, Hong-Min Meng, Lingbo Qu, Zhaohui Li
Summary: A reconfigurable DNA hybridization-based reaction was developed to assemble DNAzyme computing for specific in vivo tumor imaging, demonstrating high specificity and sensitivity. This design may have broad applications in biological research and personalized medicine.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Aurora Eliana Merulla, Michele Stella, Cristina Barbagallo, Rosalia Battaglia, Angela Caponnetto, Giuseppe Broggi, Roberto Altieri, Francesco Certo, Rosario Caltabiano, Marco Ragusa, Giuseppe Maria Vincenzo Barbagallo, Cinzia Di Pietro, Michele Purrello, Davide Barbagallo
Summary: This study investigates the role of circSMARCA5 in controlling miRNAs 126-3p and 515-5p in GBM cells, revealing a new subnetwork regulated by circSMARCA5 which affects downstream mRNA targets IGFBP2 and NRAS.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Lei Shi, Peter Magee, Matteo Fassan, Sudhakar Sahoo, Hui Sun Leong, Dave Lee, Robert Sellers, Laura Brulle-Soumare, Stefano Cairo, Tiziana Monteverde, Stefano Volinia, Duncan D. Smith, Gianpiero Di Leva, Francesca Galuppini, Athanasios R. Paliouras, Kang Zeng, Raymond O'Keefe, Michela Garofalo
Summary: This study reveals the role of KIMAT1 in maintaining KRAS signaling in lung cancer progression, suggesting that targeting it may be a strategy to prevent KRAS-induced tumorigenesis.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Tong Li, Mengxu Sun, Suping Xia, Ting Huang, Rong-Tian Li, Chunrong Li, Zong Dai, Jin-Xiang Chen, Jun Chen, Nuan Jia
Summary: Here, we developed a binary system based on DNA tetrahedron and fluorogenic RNA aptamers for highly specific and label-free mRNA imaging in living cells. This system achieved high specificity label-free detection of nucleic acids with a detection limit of 1.34 nM. The method has potential applications in early disease diagnosis and new drug development.
Article
Agriculture, Multidisciplinary
Emily Mastronardi, Kathryn Cyr, Carlos M. Monreal, Maria C. DeRosa
Summary: By conducting SELEX experiments, L-serine-binding DNA aptamers with micromolar affinity were successfully developed. Further truncation improved the binding affinity, leading to the creation of a Spiegelmer with improved nuclease resistance. This L-serine-binding Spiegelmer can be used in aptamer-based biosensors for agricultural applications.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Chloe Maucort, Duc Duy Vo, Samy Aouad, Coralie Charrat, Stephane Azoulay, Audrey Di Giorgio, Maria Duca
Summary: Targeting RNAs with small molecules is a promising field in medicinal chemistry, with microRNAs being particularly interesting targets due to their involvement in pathologies such as cancer.
ACS MEDICINAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Wenrui Zhong, Jonathan T. Sczepanski
Article
Chemistry, Multidisciplinary
Charles E. Deckard, Deb Ranjan Banerjee, Jonathan T. Sczepanski
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Article
Biochemistry & Molecular Biology
Adam M. Kabza, Jonathan T. Sczepanski
Article
Biochemistry & Molecular Biology
Sougata Dey, Jonathan T. Sczepanski
NUCLEIC ACIDS RESEARCH
(2020)
Article
Chemistry, Multidisciplinary
Katrina F. Tjhung, Jonathan T. Sczepanski, Eric R. Murtfeldt, Gerald F. Joyce
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Biochemical Research Methods
Wenrui Zhong, Jonathan T. Sczepanski
Summary: This study directly compares the functional stability and kinetics of D-DNA and L-DNA strand-displacement in live cells for the first time, showing that L-DNA systems have minimal leak, fast reaction kinetics, and prolonged stability inside living cells compared to conventional D-DNA. Additionally, the study demonstrates that biostable L-DNA components can be easily integrated with native DNA inside cells through heterochiral strand-displacement, supporting the broader adoption of L-DNA in the field of DNA molecular circuitry, especially for in vivo applications.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Charles E. Deckard, Jonathan T. Sczepanski
Summary: Thymine DNA glycosylase (TDG) has the ability to directly alter chromatin structure through physical interactions with DNA, inducing decompaction and condensation of chromatin fibers. This process is reversible with factors like GADD45a and sensitive to the methylation status of DNA, implying dynamic control of chromatin architecture by TDG and its binding partners.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Alexander Shaver, Nandini Kundu, Brian E. Young, Philip A. Vieira, Jonathan T. Sczepanski, Netzahualcoyotl Arroyo-Curras
Summary: Electrochemical aptamer-based sensors have the potential for real-time monitoring of drug concentrations in the body, but their in vivo operational life is limited by time-dependent degradation of the bioelectronic interface. The dominant cause of signal loss in these sensors is the loss of monolayer elements rather than nuclease hydrolysis of DNA aptamers.
Article
Biochemistry & Molecular Biology
Nandini Kundu, Brian E. Young, Jonathan T. Sczepanski
Summary: This study demonstrates that heterochiral strand displacement can be used to interface robust L-DNA nanodevices with endogenous D-nucleic acids in a sequence-specific manner, with reaction rates predictably tunable based on design parameters (including toehold length and mismatches).
NUCLEIC ACIDS RESEARCH
(2021)
Review
Nanoscience & Nanotechnology
Adam M. Kabza, Nandini Kundu, Wenrui Zhong, Jonathan T. Sczepanski
Summary: This article summarizes the recent progress in integrating chemically modified nucleotides with DNA strand displacement reactions to develop robust systems and devices that operate in living organisms. It also discusses the factors to consider when applying modified oligonucleotides to living cells.
WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jing Li, Jonathan T. Sczepanski
Summary: In this study, researchers identified l-DNA aptamers that bind to a conserved RNA structure in the SARS-CoV-2 genome. These aptamers have the potential for diagnosing and treating COVID-19. They can selectively bind to and differentiate between different RNA structures, and can also distinguish between SARS-CoV-2 and SARS-CoV-1. Furthermore, the binding of the aptamers induces conformational changes in the RNA structure, potentially blocking protein interactions.
RSC CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Alexander T. Piwko, Xuan Han, Adam M. Kabza, Sougata Dey, Jonathan T. Sczepanski
Summary: L-aptamers, composed of mirror-image L-(deoxy)ribose nucleic acids, are a promising class of RNA-binding reagents. A comprehensive analysis of their selectivity using an inverse in vitro selection approach revealed previously unidentified off-target RNA binding behaviors, providing valuable information for assessing potential off-target interactions.
Article
Chemistry, Analytical
Miguel Aller Pellitero, Nandini Kundu, Jonathan Sczepanski, Netzahualcoyotl Arroyo-Curras
Summary: DNA-based electrochemical sensors use Os(ii/iii) complex as a redox reporter, which shows pH-insensitive electron transfer and better operational stability compared to methylene blue, making it a promising candidate for continuous molecular monitoring applications.
Article
Chemistry, Multidisciplinary
Chen-Hsu Yu, Jonathan T. Sczepanski
Summary: l-oligonucleotides have intrinsic nuclease resistance and are increasingly used in biomedical research and therapeutics. However, their behavior and interactions with endogenous biomacromolecules in living systems and the resulting consequences are not well understood. This study characterizes the intracellular behavior of l-oligonucleotides, showing that they can be highly cytotoxic depending on backbone chemistry, sequence, and structure. The study also suggests that G-rich l-oligonucleotides stimulate an innate immune response and pro-inflammatory cytokine production. These findings challenge the perception that l-oligonucleotides are non-toxic and non-immunogenic and reveal new therapeutic opportunities.
Article
Chemistry, Multidisciplinary
Chen-Hsu Yu, Adam M. Kabza, Jonathan T. Sczepanski
Summary: L-oligonucleotides, known for their intrinsic nuclease resistance, are increasingly used in the development of molecular tools and sensors. Researchers have introduced a straightforward and versatile method to assemble long L-RNAs using T4 RNA ligase 1, demonstrating compatibility with different functional classes of L-RNA.
CHEMICAL COMMUNICATIONS
(2021)
