Article
Chemistry, Organic
Haihui Peng, Son Vu, Parker Retes, Samuel Ward, Anil Kumar, Michael D. Sevilla, Amitava Adhikary, Marc M. Greenberg
Summary: We independently generated dC center dot from oxime esters under UV-irradiation or single electron transfer conditions, which is a strong oxidant that can abstract hydrogen atoms from carbon-hydrogen bonds and is produced in various DNA damaging processes. Product studies, electron spin resonance (ESR) characterization, and density functional theory (DFT) calculations supported the generation of this sigma-type iminyl radical. These experiments suggest that oxime esters are reliable sources of nitrogen radicals in nucleic acids and can be useful mechanistic tools and possibly radiosensitizing agents when incorporated in DNA.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Yong Zheng, Julong Jiang, Mingoo Jin, Daiyo Miura, Fei Xue Lu, Koji Kubota, Tasuku Nakajima, Satoshi Maeda, Hajime Ito, Jian Ping Gong
Summary: In this study, a novel strategy for real-time visualization of mechanochemical damages in hydrogels was developed using prefluorescent probes via oxygen-relayed free-radical trapping. This method allows for the detection of mechanochemical damages in hydrogels made from brittle networks of varied chemical structures, without introducing any chemical structural changes in the materials.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Organic
Arnab Das, Atanu Ghosh, Surajit Sinha
Summary: C5-substituted uridine and cytidine morpholino chlorophosphoramidate monomers were incorporated into a Phosphorodiamidate Morpholino Oligonucleotide (PMO) to enhance its thermal stability and binding affinity with RNA. These modified PMOs exhibited B-type helical conformation and greater lipophilicity compared to regular PMOs, indicating their potential for developing improved antisense technologies.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Article
Engineering, Environmental
Ke Zhang, Joseph Hodge, Anamika Chatterjee, Tae Seok Moon, Kimberly M. Parker
Summary: Double-stranded RNA undergoes alkaline hydrolysis at orders-of-magnitude slower rates compared to single-stranded RNA, and can remain intact for months at neutral pH. Increasing pH effectively attenuates enzymatic degradation of dsRNA without inducing alkaline hydrolysis, which differs significantly from ssRNA. Understanding these unique properties of dsRNA allows for greater control of stability in RNAi technology and provides insights into various applications, including isolation, detection, and inactivation of dsRNA viruses.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Dhruva Katrekar, James Yen, Yichen Xiang, Anushka Saha, Dario Meluzzi, Yiannis Savva, Prashant Mali
Summary: In this study, circular ADAR-recruiting guide RNAs (cadRNAs) were engineered to achieve more efficient and durable RNA editing without the need for exogenous proteins. The cadRNAs demonstrated robust and long-lasting RNA editing across multiple sites and cell lines, with high specificity. In vivo delivery of cadRNAs via adeno-associated viruses showed significant RNA editing in mouse livers and correction of a genetic mutation. cadRNAs enable programmable RNA editing with potential gene therapeutic applications.
NATURE BIOTECHNOLOGY
(2022)
Article
Agronomy
Ningbo Chen, Xin Dai, Qian Hu, Hongxiao Tan, Liping Qiao, Laifeng Lu
Summary: Postharvest quality deterioration is a major issue in food loss and waste, but the technique of spray-induced gene silencing (SIGS) offers a new solution. By spraying double-stranded RNA (dsRNA) onto the surface of plants, specific genes can be targeted for RNA interference, effectively reducing browning in freshly-cut potatoes. This study highlights the potential application of SIGS in controlling postharvest quality deterioration.
POSTHARVEST BIOLOGY AND TECHNOLOGY
(2023)
Article
Chemistry, Analytical
Steven R. Strezsak, Penny J. Beuning, Nicholas J. Skizim
Summary: A method for accurately determining the concentration of long dsRNA was developed using nucleic acid digestion and reversed-phase HPLC/UV methods. The study found that sequence design can dramatically change the extinction coefficient of the molecule, with ssRNA overhangs leading to a 5% reduction in the calculated extinction coefficient.
ANALYTICAL METHODS
(2021)
Article
Plant Sciences
Atrayee Sarkar, Subhankar Roy-Barman
Summary: RNA interference (RNAi) has been utilized as a promising combat strategy against a wide range of pests and pathogens by inducing highly specific posttranscriptional regulation of target essential genes through the application of long, non-coding double-stranded RNA (dsRNA) molecules. This approach has been successfully exploited in combating fungal blast disease caused by Magnaporthe oryzae.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Wenbo Xu, Miao Zhang, Yangcun Li, Wanwan He, Shengchun Li, Jiang Zhang
Summary: RNA interference (RNAi) is an effective technology for pest management. This study demonstrates that RNAi can be used to control the 28-spotted potato ladybird by targeting the beta-Actin gene. Transgenic potato plants expressing the target gene showed enhanced resistance to the pest. These findings expand the application range of RNAi technology to Coccinellidae pests.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Microbiology
Alexander Stevens, Katherine Muratore, Yanxiang Cui, Patricia J. Johnson, Z. Hong Zhou
Summary: The atomic structure of TVV2 reveals the interactions driving capsid assembly and the properties governing viral genome organization. Comparison with other dsRNA viruses suggests conserved strategies of RNA release and potential domains involved in viral RNA maintenance. This provides insights for future investigations into the interactions between Trichomonas vaginalis and its viruses.
Article
Chemistry, Analytical
Nan Ma, Yu Zhao, Lianzhi Li, Jinming Kong, Xueji Zhang
Summary: This paper reports an ultrasensitive biosensor based on ferritin-enhanced atom transfer radical polymerization (Ft-ATRP) for the accurate detection of microRNA-21, a early marker of lung cancer. The biosensor uses peptide nucleic acid probes on a gold electrode to bind the target marker, and ferritin induces Ft-ATRP on the electrode surface. The biosensor shows low limit of detection, wide detection concentration range, and has the potential for screening and identifying lung cancer.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Sijie Liu, Yu Hua, Jingna Wang, Lingyan Li, Junjie Yuan, Bo Zhang, Ziyang Wang, Jianguo Ji, Daochun Kong
Summary: Protection of 30 overhangs in DNA double-strand breaks (DSBs) repair is achieved through the transient formation of RNA-DNA hybrids, with RNA polymerase III (RNAPIII) responsible for synthesizing the RNA strand. CtIP and MRN nuclease activity are required for initiating RNAPIII-mediated RNA synthesis at DSBs. Reduced RNAPIII levels suppress homologous recombination (HR) and lead to genetic loss > 30 bp at DSBs.
Article
Plant Sciences
Jinqiu Fu, Shijing Xu, Huan Lu, Fanchi Li, Shengchun Li, Ling Chang, David G. Heckel, Ralph Bock, Jiang Zhang
Summary: Plant-mediated RNA interference (RNAi) using dsRNA or siRNA has shown promise in pest control, but little is known about the molecular mechanisms. This study found that siRNAs derived from transgenic plants may be more effective triggers of RNAi in Lepidoptera than dsRNAs.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Chemistry, Analytical
Shiwen Zhou, Menghui Qi, Yuanqing Luo, Wangyu Li, Yaqin Liu, Cheng Guo, Wei Wei, Guanru Chen, Peijun Tu, Hongru Feng, Yuanjiang Pan
Summary: This study demonstrates a method of oligonucleotide sequencing using TiO2/ZnAl-layered double oxide (LDO)-assisted laser desorption/ionization (LDI)-MS based on radical-induced dissociation (RID). They show that RID can sequence oligonucleotides with modifications and provide advantages such as single-charged signals, fewer types of fragments, and a lower proportion of unknown noise peaks compared to collision-based methods.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Xuefeng Zhu, Xie Xie, Hrishikesh Das, Benedict G. Tan, Yonghong Shi, Ali Al-Behadili, Bradley Peter, Elisa Motori, Sebastian Valenzuela, Viktor Posse, Claes M. Gustafsson, B. Martin Haellberg, Maria Falkenberg
Summary: The non-coding RNA molecule 7S RNA regulates mitochondrial transcription in mammalian cells by inducing POLRMT dimerization, which prevents transcription initiation.
Article
Chemistry, Organic
Joseph C. Nguyen, Yannick Kokouvi Dzowo, Carly Wolfbrandt, Justin Townsend, Stanislav Kukatin, Haobin Wang, Marino J. E. Resendiz
JOURNAL OF ORGANIC CHEMISTRY
(2016)
Article
Biochemistry & Molecular Biology
Yu J. Choi, Krzysztof S. Gibala, Tewoderos Ayele, Katherine V. Deventer, Marino J. E. Resendiz
NUCLEIC ACIDS RESEARCH
(2017)
Article
Multidisciplinary Sciences
Andrew J. Francis, Marino J. E. Resendiz
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2017)
Article
Biochemistry & Molecular Biology
Cassandra Herbert, Yannick Kokouvi Dzowo, Anthony Urban, Courtney N. Kiggins, Marino J. E. Resendiz
Article
Chemistry, Multidisciplinary
Yannick Kokouvi Dzowo, Carly Wolfbrandt, Marino J. E. Resendiz, Haobin Wang
NEW JOURNAL OF CHEMISTRY
(2018)
Article
Chemistry, Physical
Issac Torres, Mauro Ruiz, Hung Phan, Noemi Dominguez, Jacobo Garcia, Thuc-Quyen Nguyen, Hayden Evans, Marino J. Resendiz, Tunna Baruah, Alejandro Metta, Atta Arif, Juan C. Noveron
Article
Chemistry, Organic
Chelsea O'Hara, Chou-Hsun Yang, Andrew J. Francis, Brian S. Newell, Haobin Wang, Marino J. E. Resendiz
JOURNAL OF ORGANIC CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Courtney Kiggins, Austin Skinner, Marino J. E. Resendiz
Article
Multidisciplinary Sciences
Madeline M. Glennon, Austin Skinner, Mara Krutsinger, Marino J. E. Resendiz
Article
Biochemistry & Molecular Biology
Austin Skinner, Chou-Hsun Yang, Kazuki Hincks, Haobin Wang, Marino J. E. Resendiz
Article
Biochemistry & Molecular Biology
Cheyenne N. Phillips, Shawn Schowe, Conner J. Langeberg, Namoos Siddique, Erich G. Chapman, Marino J. E. Resendiz
Summary: The research shows that the exonuclease Xrn-1 stalls when encountering RNA with 8-oxoG, possibly due to spatial constraints and conformational changes. However, these factors alone do not fully explain the higher stalling yields observed, suggesting that additional factors like altered pi-pi stacking and induced H-bonding interactions may also contribute to the decreased Xrn-1 efficiency.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Shawn W. Schowe, Conner J. Langeberg, Erich G. Chapman, Kitty Brown, Marino J. E. Resendiz
Summary: RNA is a biopolymer that interacts with other molecules and undergoes various reactions, leading to biologically relevant species with distinct functions and implications. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry is a widely used method to characterize RNA reactions, such as guanine oxidation.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Editorial Material
Biochemistry & Molecular Biology
Lynn Htet Htet Aung, Peifeng Li, Claudia Perez-Cruz, Norbert Polacek, Marino J. E. Resendiz
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Cheyenne N. Phillips, Madeline Choi, Kim Ngan Huynh, Haobin Wang, Marino J. E. Resendiz
Summary: This study focuses on the chemical modification of RNA and DNA oligonucleotides, exploring their unique structural features and behavior. The findings provide a useful method to study modified oligonucleotides.
Review
Chemistry, Multidisciplinary
Yu Jung Choi, Stephanie J. Chang, Krzysztof S. Gibala, Marino J. E. Resendiz
CHEMISTRY-A EUROPEAN JOURNAL
(2017)