In retroviruses, strand displacement DNA-dependent DNA polymerization catalyzed by the viral reverse transcriptase (RT) is required to synthesize double-stranded proviral DNA. In addition, strand displacement during RNA-dependent DNA synthesis is critical to generate high-quality cDNA for use in molecular biology and biotechnology. In this work, we show that the loss of RNase H activity due to inactivating mutations in HIV-1 RT (e.g. D443N or E478Q) has no significant effect on strand displacement while copying DNA templates, but has a large impact on DNA polymerization in reactions carried out with RNA templates. Similar effects were observed with β-thujaplicinol and other RNase H active site inhibitors, including compounds with dual activity (i.e., characterized also as inhibitors of HIV-1 integrase and/or the RT DNA polymerase). Among them, dual inhibitors of HIV-1 RT DNA polymerase/RNase H activities, containing a 7-hydroxy-6-nitro-2H-chromen-2-one pharmacophore were found to be very potent and effective strand displacement inhibitors in RNA-dependent DNA polymerization reactions. These findings might be helpful in the development of transcriptomics technologies to obtain more uniform read coverages when copying long RNAs and for the construction of more representative libraries avoiding biases towards 5' and 3' ends, while providing valuable information for the development of novel antiretroviral agents.
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http://dx.doi.org/10.1016/j.jmb.2022.167507 | DOI Listing |
Anal Chim Acta
February 2025
Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China; Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, Hangzhou, 310003, China. Electronic address:
Background: Amplified imaging of microRNA (miRNA) in cancer cells is essential for understanding of the underlying pathological process. Synthetic catalytic DNA circuits represent pivotal tools for miRNA imaging. However, most existing catalytic DNA circuits can not achieve the reactant recycling operation in cells and in vivo.
View Article and Find Full Text PDFAnal Chim Acta
February 2025
School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China. Electronic address:
Background: DNA methylation catalyzed by various DNA methyltransferases (DNA MTases) is one of the important epigenetic regulations in both eukaryotes and prokaryotes. Therefore, the detection of DNA MTase activity is a vital target and direction in the study of methylation-related diseases.
Results: In this study, an ultrasensitive and robust strategy was developed for DNA MTase activity sensing based on bifunctional probe propelling multipath strand displacement amplification and CRISPR/Cas12a techniques.
Adv Mater
January 2025
Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, P. R. China.
Metastasis, the leading cause of mortality in cancer patients, presents challenges for conventional photodynamic therapy (PDT) due to its reliance on localized light and oxygen application to tumors. To overcome these limitations, a self-sustained organelle-mimicking nanoreactor is developed here with programmable DNA switches that enables bio-chem-photocatalytic cascade-driven starvation-photodynamic synergistic therapy against tumor metastasis. Emulating the compartmentalization and positional assembly strategies found in living cells, this nano-organelle reactor allows quantitative co-compartmentalization of multiple functional modules for the designed self-illuminating chemiexcited PDT system.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125.
The diversity and heterogeneity of biomarkers has made the development of general methods for single-step quantification of analytes difficult. For individual biomarkers, electrochemical methods that detect a conformational change in an affinity binder upon analyte binding have shown promise. However, because the conformational change must operate within a nanometer-scale working distance, an entirely new sensor, with a unique conformational change, must be developed for each analyte.
View Article and Find Full Text PDFChembiochem
January 2025
Ludwig-Maximilians-Universitat Munchen, Chemistry, Butenandstr. 5-13, 81377, Muenchen, GERMANY.
In the last decade the important role of small non-coding RNAs such as micro RNAs (miRs) in gene regulation in healthy and disease states became more and more evident. The miR-200-family of miRs has been shown to play a critical role in many diseases such as cancer and neurodegenerative disorders and could be potentially important for diagnosis and treatment. However, the size of miRs of about ~21-23nt provide challenges for their investigation.
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