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Zhang M, Li K, Bai J, Velema WA, Yu C, van Damme R, Lee WH, Corpuz ML, Chen JF, Lu Z. Optimized photochemistry enables efficient analysis of dynamic RNA structuromes and interactomes in genetic and infectious diseases. Nat Commun 2021; 12:2344. [PMID: 33879794 PMCID: PMC8058046 DOI: 10.1038/s41467-021-22552-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
Direct determination of RNA structures and interactions in living cells is critical for understanding their functions in normal physiology and disease states. Here, we present PARIS2, a dramatically improved method for RNA duplex determination in vivo with >4000-fold higher efficiency than previous methods. PARIS2 captures ribosome binding sites on mRNAs, reporting translation status on a transcriptome scale. Applying PARIS2 to the U8 snoRNA mutated in the neurological disorder LCC, we discover a network of dynamic RNA structures and interactions which are destabilized by patient mutations. We report the first whole genome structure of enterovirus D68, an RNA virus that causes polio-like symptoms, revealing highly dynamic conformations altered by antiviral drugs and different pathogenic strains. We also discover a replication-associated asymmetry on the (+) and (-) strands of the viral genome. This study establishes a powerful technology for efficient interrogation of the RNA structurome and interactome in human diseases.
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MESH Headings
- Calcinosis/genetics
- Calcinosis/metabolism
- Central Nervous System Cysts/genetics
- Central Nervous System Cysts/metabolism
- Communicable Diseases/genetics
- Communicable Diseases/metabolism
- Cross-Linking Reagents
- Enterovirus D, Human/genetics
- Furocoumarins
- Genetic Diseases, Inborn/genetics
- Genetic Diseases, Inborn/metabolism
- Genome, Viral
- Humans
- Leukoencephalopathies/genetics
- Leukoencephalopathies/metabolism
- Models, Molecular
- Mutation
- Nucleic Acid Conformation
- Photochemical Processes
- Photochemistry/methods
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
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Affiliation(s)
- Minjie Zhang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Kongpan Li
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Jianhui Bai
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Willem A Velema
- Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Chengqing Yu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Ryan van Damme
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Wilson H Lee
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Maia L Corpuz
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Jian-Fu Chen
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Zhipeng Lu
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA.
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Guan Z, Liu J, Bai W, Lv Z, Jiang X, Yang S, Chen A, Lv G. Label-free and sensitive fluorescent detection of sequence-specific single-strand DNA based on S1 nuclease cleavage effects. PLoS One 2014; 9:e108401. [PMID: 25285445 PMCID: PMC4186753 DOI: 10.1371/journal.pone.0108401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 08/27/2014] [Indexed: 11/18/2022] Open
Abstract
The ability to detect sequence-specific single-strand DNA (ssDNA) in complex, contaminant-ridden samples, using a fluorescent method directly without a DNA extraction and PCR step could simplify the detection of pathogens in the field and in the clinic. Here, we have demonstrated a simple label-free sensing strategy to detect ssDNA by employing its complementary ssDNA, S1 nuclease and nucleic acid fluorescent dyes. Upon clearing away redundant complementary ssDNA and possibly mismatched double strand DNA by using S1 nuclease, the fluorescent signal-to-noise ratio could be increased dramatically. It enabled the method to be adaptable to three different types of DNA fluorescent dyes and the ability to detect target ssDNA in complex, multicomponent samples, like tissue homogenate. The method can distinguish a two-base mismatch from avian influenza A (H1N1) virus. Also, it can detect the appearance of 50 pM target ssDNA in 0.5 µg · mL(-1) Lambda DNA, and 50 nM target ssDNA in 5 µg · mL(-1) Lambda DNA or in tissue homogenate. It is facile and cost-effective, and could be easily extended to detect other ssDNA with many common nucleic acid fluorescent dyes.
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Affiliation(s)
- Zheng Guan
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
- Institute of Materia Medica, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jinchuan Liu
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Wenhui Bai
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Zhenzhen Lv
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Xiaoling Jiang
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Shuming Yang
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Ailiang Chen
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
- * E-mail: (AC); (GL)
| | - Guiyuan Lv
- Institute of Materia Medica, Zhejiang Chinese Medical University, Hangzhou, China
- * E-mail: (AC); (GL)
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