1
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Guo J, Chen S, Onishi Y, Shi Q, Song Y, Mei H, Chen L, Kool ET, Zhu RY. RNA Control via Redox-Responsive Acylation. Angew Chem Int Ed Engl 2024; 63:e202402178. [PMID: 38480851 DOI: 10.1002/anie.202402178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Indexed: 04/05/2024]
Abstract
Incorporating stimuli-responsive components into RNA constructs provides precise spatiotemporal control over RNA structures and functions. Despite considerable advancements, the utilization of redox-responsive stimuli for the activation of caged RNAs remains scarce. In this context, we present a novel strategy that leverages post-synthetic acylation coupled with redox-responsive chemistry to exert control over RNA. To achieve this, we design and synthesize a series of acylating reagents specifically tailored for introducing disulfide-containing acyl adducts into the 2'-OH groups of RNA ("cloaking"). Our data reveal that these acyl moieties can be readily appended, effectively blocking RNA catalytic activity and folding. We also demonstrate the traceless release and reactivation of caged RNAs ("uncloaking") through reducing stimuli. By employing this strategy, RNA exhibits rapid cellular uptake, effective distribution and activation in the cytosol without lysosomal entrapment. We anticipate that our methodology will be accessible to laboratories engaged in RNA biology and holds promise as a versatile platform for RNA-based applications.
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Affiliation(s)
- Junsong Guo
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Siqin Chen
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Yoshiyuki Onishi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Qi Shi
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599, Singapore
| | - Hui Mei
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599, Singapore
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Ru-Yi Zhu
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
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2
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Wang LL, Wu CQ, Zhang QL, Wang Y, Liu Y, Yang WJ, Ye SL, Tian Y, Xu L. Chemically Cross-Linked Hammerhead Ribozyme as an Efficient RNA Interference Tool. J Am Chem Soc 2024; 146:6665-6674. [PMID: 38412223 DOI: 10.1021/jacs.3c12702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
RNA-cleaving ribozymes are promising candidates as general tools of RNA interference (RNAi) in gene manipulation. However, compared with other RNA systems, such as siRNA and CRISPR technologies, the ribozyme tools are still far from broad applications on RNAi due to their poor performance in the cellular context. In this work, we report an efficient RNAi tool based on chemically modified hammerhead ribozyme (HHR). By the introduction of an intramolecular linkage into the minimal HHR to reconstruct the distal interaction within the tertiary ribozyme structure, this cross-linked HHR exhibits efficient RNA substrate cleavage activities with almost no sequence constraint. Cellular experiments suggest that both exogenous and endogenous RNA expression can be dramatically knocked down by this HHR tool with levels comparable to those of siRNA. Unlike the widely applied protein-recruiting RNA systems (siRNA and CRISPR), this ribozyme tool functions solely on RNA itself with great simplicity, which may provide a new approach for gene manipulation in both fundamental and translational studies.
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Affiliation(s)
- Liang-Liang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Chao-Qun Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Qiu-Long Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
- School of Pharmacy and Medical Technology, Key Laboratory of Pharmaceutical Analysis and Laboratory Medicine of Fujian Province, Putian University, Putian 351100, China
| | - Yang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yan Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wen-Jian Yang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Sen-Lin Ye
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yongqiang Tian
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
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3
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Wang J, Yu H. Threose nucleic acid as a primitive genetic polymer and a contemporary molecular tool. Bioorg Chem 2024; 143:107049. [PMID: 38150936 DOI: 10.1016/j.bioorg.2023.107049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 12/29/2023]
Abstract
Nucleic acids serve a dual role as both genetic materials in living organisms and versatile molecular tools for various applications. Threose nuclei acid (TNA) stands out as a synthetic genetic polymer, holding potential as a primitive genetic material and as a contemporary molecular tool. In this review, we aim to provide an extensive overview of TNA research progress in these two key aspects. We begin with a retrospect of the initial discovery of TNA, followed by an in-depth look at the structural features of TNA duplex and experimental assessment of TNA as a possible RNA progenitor during early evolution of life on Earth. In the subsequent section, we delve into the recent development of TNA molecular tools such as aptamers, catalysts and antisense oligonucleotides. We emphasize the practical application of functional TNA molecules in the realms of targeted protein degradation and selective gene silencing. Our review culminates with a discussion of future research directions and the technical challenges that remain to be addressed in the field of TNA research.
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Affiliation(s)
- Juan Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hanyang Yu
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China.
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4
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Assmann SM, Chou HL, Bevilacqua PC. Rock, scissors, paper: How RNA structure informs function. THE PLANT CELL 2023; 35:1671-1707. [PMID: 36747354 DOI: 10.1093/plcell/koad026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 01/30/2023] [Indexed: 05/30/2023]
Abstract
RNA can fold back on itself to adopt a wide range of structures. These range from relatively simple hairpins to intricate 3D folds and can be accompanied by regulatory interactions with both metabolites and macromolecules. The last 50 yr have witnessed elucidation of an astonishing array of RNA structures including transfer RNAs, ribozymes, riboswitches, the ribosome, the spliceosome, and most recently entire RNA structuromes. These advances in RNA structural biology have deepened insight into fundamental biological processes including gene editing, transcription, translation, and structure-based detection and response to temperature and other environmental signals. These discoveries reveal that RNA can be relatively static, like a rock; that it can have catalytic functions of cutting bonds, like scissors; and that it can adopt myriad functional shapes, like paper. We relate these extraordinary discoveries in the biology of RNA structure to the plant way of life. We trace plant-specific discovery of ribozymes and riboswitches, alternative splicing, organellar ribosomes, thermometers, whole-transcriptome structuromes and pan-structuromes, and conclude that plants have a special set of RNA structures that confer unique types of gene regulation. We finish with a consideration of future directions for the RNA structure-function field.
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Affiliation(s)
- Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Li Chou
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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5
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Forstmeier PC, Meyer MO, Bevilacqua PC. The Functional RNA Identification (FRID) Pipeline: Identification of Potential Pseudoknot-Containing RNA Elements as Therapeutic Targets for SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535424. [PMID: 37066195 PMCID: PMC10103974 DOI: 10.1101/2023.04.03.535424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The COVID-19 pandemic persists despite the development of effective vaccines. As such, it remains crucial to identify new targets for antiviral therapies. The causative virus of COVID-19, SARS-CoV-2, is a positive-sense RNA virus with RNA structures that could serve as therapeutic targets. One such RNA with established function is the frameshift stimulatory element (FSE), which promotes programmed ribosomal frameshifting. To accelerate identification of additional functional RNA elements, we introduce a novel computational approach termed the Functional RNA Identification (FRID) pipeline. The guiding principle of our pipeline, which uses established component programs as well as customized component programs, is that functional RNA elements have conserved secondary and pseudoknot structures that facilitate function. To assess the presence and conservation of putative functional RNA elements in SARS-CoV-2, we compared over 6,000 SARS-CoV-2 genomic isolates. We identified 22 functional RNA elements from the SARS-CoV-2 genome, 14 of which have conserved pseudoknots and serve as potential targets for small molecule or antisense oligonucleotide therapeutics. The FRID pipeline is general and can be applied to identify pseudoknotted RNAs for targeted therapeutics in genomes or transcriptomes from any virus or organism.
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6
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Cardador CM, Muehlmann LA, Coelho CM, Silva LP, Garay AV, Carvalho AMDS, Bastos IMD, Longo JPF. Nucleotides Entrapped in Liposome Nanovesicles as Tools for Therapeutic and Diagnostic Use in Biomedical Applications. Pharmaceutics 2023; 15:873. [PMID: 36986734 PMCID: PMC10056227 DOI: 10.3390/pharmaceutics15030873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
The use of nucleotides for biomedical applications is an old desire in the scientific community. As we will present here, there are references published over the past 40 years with this intended use. The main problem is that, as unstable molecules, nucleotides require some additional protection to extend their shelf life in the biological environment. Among the different nucleotide carriers, the nano-sized liposomes proved to be an effective strategic tool to overcome all these drawbacks related to the nucleotide high instability. Moreover, due to their low immunogenicity and easy preparation, the liposomes were selected as the main strategy for delivery of the mRNA developed for COVID-19 immunization. For sure this is the most important and relevant example of nucleotide application for human biomedical conditions. In addition, the use of mRNA vaccines for COVID-19 has increased interest in the application of this type of technology to other health conditions. For this review article, we will present some of these examples, especially focused on the use of liposomes to protect and deliver nucleotides for cancer therapy, immunostimulatory activities, enzymatic diagnostic applications, some examples for veterinarian use, and the treatment of neglected tropical disease.
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Affiliation(s)
- Camila Magalhães Cardador
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília (UnB), Brasilia 70910-900, DF, Brazil
| | | | - Cíntia Marques Coelho
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasilia 70910-900, DF, Brazil
| | - Luciano Paulino Silva
- Laboratório de Nanobiotecnologia (LNANO), Embrapa Recursos Genéticos e Biotecnologia, Brasilia 70770-917, DF, Brazil
| | - Aisel Valle Garay
- Molecular Biophysics Laboratory, Department of Cell Biology, Institute of Biological Science, University of Brasília (UnB), Brasília 70910-900, DF, Brazil
| | | | - Izabela Marques Dourado Bastos
- Pathogen-Host Interface Laboratory, Department of Cell Biology, University of Brasilia (UnB), Brasilia 70910-900, DF, Brazil
| | - João Paulo Figueiró Longo
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília (UnB), Brasilia 70910-900, DF, Brazil
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7
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Ono H, Saito H. Sensing intracellular signatures with synthetic mRNAs. RNA Biol 2023; 20:588-602. [PMID: 37582192 PMCID: PMC10431736 DOI: 10.1080/15476286.2023.2244791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/30/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
The bottom-up assembly of biological components in synthetic biology has contributed to a better understanding of natural phenomena and the development of new technologies for practical applications. Over the past few decades, basic RNA research has unveiled the regulatory roles of RNAs underlying gene regulatory networks; while advances in RNA biology, in turn, have highlighted the potential of a wide variety of RNA elements as building blocks to construct artificial systems. In particular, synthetic mRNA-based translational regulators, which respond to signals in cells and regulate the production of encoded output proteins, are gaining attention with the recent rise of mRNA therapeutics. In this Review, we discuss recent progress in RNA synthetic biology, mainly focusing on emerging technologies for sensing intracellular protein and RNA molecules and controlling translation.
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Affiliation(s)
- Hiroki Ono
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Sakyo-Ku, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Sakyo-Ku, Japan
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8
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Ouyang Y, O'Hagan MP, Willner I. Functional catalytic nanoparticles (nanozymes) for sensing. Biosens Bioelectron 2022; 218:114768. [DOI: 10.1016/j.bios.2022.114768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/29/2022]
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9
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Mao D, Li Q, Li Q, Wang P, Mao C. A conformational study of the 10-23 DNAzyme via programmed DNA self-assembly. Chem Commun (Camb) 2022; 58:6188-6191. [PMID: 35521655 DOI: 10.1039/d2cc01144a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This communication measures the inter-helical angle of the 10-23 DNAzyme-substrate complex by atomic force microscopy (AFM). Herein, we have devised a strategy to assemble the DNAzyme-substrate complex into a periodic DNA 2D array, which allows reliable study of the conformation of the 10-23 DNAzyme by AFM imaging and fast Fourier transform (FFT). Specifically, the angle between the two flanking helical domains of the catalytic core has been determined via the repeating distance of the 2D array. We expect that the same strategy can generally be applicable for studying other nucleic acid structures.
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Affiliation(s)
- Dake Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
| | - Qian Li
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA. .,College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qian Li
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
| | - Pengfei Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
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10
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Terai G, Asai K. QRNAstruct: a method for extracting secondary structural features of RNA via regression with biological activity. Nucleic Acids Res 2022; 50:e73. [PMID: 35390152 PMCID: PMC9303433 DOI: 10.1093/nar/gkac220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/15/2022] [Accepted: 03/24/2022] [Indexed: 12/04/2022] Open
Abstract
Recent technological advances have enabled the generation of large amounts of data consisting of RNA sequences and their functional activity. Here, we propose a method for extracting secondary structure features that affect the functional activity of RNA from sequence–activity data. Given pairs of RNA sequences and their corresponding bioactivity values, our method calculates position-specific structural features of the input RNA sequences, considering every possible secondary structure of each RNA. A Ridge regression model is trained using the structural features as feature vectors and the bioactivity values as response variables. Optimized model parameters indicate how secondary structure features affect bioactivity. We used our method to extract intramolecular structural features of bacterial translation initiation sites and self-cleaving ribozymes, and the intermolecular features between rRNAs and Shine–Dalgarno sequences and between U1 RNAs and splicing sites. We not only identified known structural features but also revealed more detailed insights into structure–activity relationships than previously reported. Importantly, the datasets we analyzed here were obtained from different experimental systems and differed in size, sequence length and similarity, and number of RNA molecules involved, demonstrating that our method is applicable to various types of data consisting of RNA sequences and bioactivity values.
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Affiliation(s)
- Goro Terai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8561, Japan
| | - Kiyoshi Asai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8561, Japan
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11
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Abstract
In recent years, it has become clear that RNA molecules are involved in almost all vital cellular processes and pathogenesis of human disorders. The functional diversity of RNA comes from its structural richness. Although composed of only four nucleotides, RNA molecules present a plethora of secondary and tertiary structures critical for intra and intermolecular contacts with other RNAs and ligands (proteins, small metabolites, etc.). In order to fully understand RNA function it is necessary to define its spatial structure. Crystallography, nuclear magnetic resonance and cryogenic electron microscopy have demonstrated considerable success in determining the structures of biologically important RNA molecules. However, these powerful methods require large amounts of sample. Despite their limitations, chemical synthesis and in vitro transcription are usually employed to obtain milligram quantities of RNA for structural studies, delivering simple and effective methods for large-scale production of homogenous samples. The aim of this paper is to provide an overview of methods for large-scale RNA synthesis with emphasis on chemical synthesis and in vitro transcription. We also present our own results of testing the efficiency of these approaches in order to adapt the material acquisition strategy depending on the desired RNA construct.
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12
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Piao M, Li P, Zeng X, Wang XW, Kang L, Zhang J, Wei Y, Zhang S, Tang L, Zhu J, Kwok CK, Hu X, Zhang QC. An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages. FUNDAMENTAL RESEARCH 2022; 2:2-13. [PMID: 38933905 PMCID: PMC11197792 DOI: 10.1016/j.fmre.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/10/2021] [Accepted: 12/20/2021] [Indexed: 11/17/2022] Open
Abstract
To enable diverse functions and precise regulation, an RNA sequence often folds into complex yet distinct structures in different cellular states. Probing RNA in its native environment is essential to uncovering RNA structures of biological contexts. However, current methods generally require large amounts of input RNA and are challenging for physiologically relevant use. Here, we report smartSHAPE, a new RNA structure probing method that requires very low amounts of RNA input due to the largely reduced artefact of probing signals and increased efficiency of library construction. Using smartSHAPE, we showcased the profiling of the RNA structure landscape of mouse intestinal macrophages upon inflammation, and provided evidence that RNA conformational changes regulate immune responses. These results demonstrate that smartSHAPE can greatly expand the scope of RNA structure-based investigations in practical biological systems, and also provide a research paradigm for the study of post-transcriptional regulation.
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Affiliation(s)
- Meiling Piao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Pan Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaomin Zeng
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xi-Wen Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Lan Kang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jinsong Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yifan Wei
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Shaojun Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Lei Tang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jianghui Zhu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong, China
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Xiaoyu Hu
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
- Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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13
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Sanbonmatsu K. Getting to the bottom of lncRNA mechanism: structure-function relationships. Mamm Genome 2021; 33:343-353. [PMID: 34642784 PMCID: PMC8509902 DOI: 10.1007/s00335-021-09924-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022]
Abstract
While long non-coding RNAs are known to play key roles in disease and development, relatively few structural studies have been performed for this important class of RNAs. Here, we review functional studies of long non-coding RNAs and expose the need for high-resolution 3-D structural studies, discussing the roles of long non-coding RNAs in the cell and how structure–function relationships might be used to elucidate further understanding. We then describe structural studies of other classes of RNAs using chemical probing, nuclear magnetic resonance, small-angle X-ray scattering, X-ray crystallography, and cryogenic electron microscopy (cryo-EM). Next, we review early structural studies of long non-coding RNAs to date and describe the way forward for the structural biology of long non-coding RNAs in terms of cryo-EM.
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14
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Brewer KI, Greenlee EB, Higgs G, Yu D, Mirihana Arachchilage G, Chen X, King N, White N, Breaker RR. Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes. RNA Biol 2021; 18:2417-2432. [PMID: 33970790 PMCID: PMC8632094 DOI: 10.1080/15476286.2021.1917891] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022] Open
Abstract
Comparative sequence analysis methods are highly effective for uncovering novel classes of structured noncoding RNAs (ncRNAs) from bacterial genomic DNA sequence datasets. Previously, we developed a computational pipeline to more comprehensively identify structured ncRNA representatives from individual bacterial genomes. This search process exploits the fact that genomic regions serving as templates for the transcription of structured RNAs tend to be present in longer than average noncoding 'intergenic regions' (IGRs) that are enriched in G and C nucleotides compared to the remainder of the genome. In the present study, we apply this computational pipeline to identify structured ncRNA candidates from 26 diverse bacterial species. Numerous novel structured ncRNA motifs were discovered, including several riboswitch candidates, one whose ligand has been identified and others that have yet to be experimentally validated. Our findings support recent predictions that hundreds of novel ribo-switch classes and other ncRNAs remain undiscovered among the limited number of bacterial species whose genomes have been completely sequenced.
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Affiliation(s)
- Kenneth I Brewer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Etienne B Greenlee
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Gadareth Higgs
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Diane Yu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Xi Chen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Nicholas King
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Neil White
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
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15
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Huber RG, Marzinek JK, Boon PLS, Yue W, Bond PJ. Computational modelling of flavivirus dynamics: The ins and outs. Methods 2021; 185:28-38. [PMID: 32526282 PMCID: PMC7278654 DOI: 10.1016/j.ymeth.2020.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/24/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Enveloped viruses such as the flaviviruses represent a significant burden to human health around the world, with hundreds of millions of people each year affected by dengue alone. In an effort to improve our understanding of the molecular basis for the infective mechanisms of these viruses, extensive computational modelling approaches have been applied to elucidate their conformational dynamics. Multiscale protocols have been developed to simulate flavivirus envelopes in close accordance with biophysical data, in particular derived from cryo-electron microscopy, enabling high-resolution refinement of their structures and elucidation of the conformational changes associated with adaptation both to host environments and to immunological factors such as antibodies. Likewise, integrative modelling efforts combining data from biophysical experiments and from genome sequencing with chemical modification are providing unparalleled insights into the architecture of the previously unresolved nucleocapsid complex. Collectively, this work provides the basis for the future rational design of new antiviral therapeutics and vaccine development strategies targeting enveloped viruses.
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Affiliation(s)
- Roland G Huber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, 138671, Singapore
| | - Jan K Marzinek
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, 138671, Singapore
| | - Priscilla L S Boon
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, 138671, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore (NUS), University Hall, Tan Chin Tuan Wing #04-02, 119077, Singapore; Department of Biological Sciences (DBS), National University of Singapore (NUS), 16 Science Drive 4, Building S3, Singapore
| | - Wan Yue
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, 138672, Singapore
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, 138671, Singapore; Department of Biological Sciences (DBS), National University of Singapore (NUS), 16 Science Drive 4, Building S3, Singapore.
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16
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Jain S, Kaur J, Prasad S, Roy I. Nucleic acid therapeutics: a focus on the development of aptamers. Expert Opin Drug Discov 2020; 16:255-274. [PMID: 32990095 DOI: 10.1080/17460441.2021.1829587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Aptamers provide exciting opportunities for the development of specific and targeted therapeutic approaches. AREAS COVERED In this review, the authors discuss different therapeutic options available with nucleic acids, including aptamers, focussing on similarities and differences between them. The authors concentrate on case studies with specific aptamers, which exemplify their distinct advantages. The reasons for failure, wherever available, are deliberated upon. Attempts to accelerate the in vitro selection process have been discussed. Challenges with aptamers in terms of their specificity and targeted delivery and strategies to overcome these are described. Examples of precise regulation of systemic half-life of aptamers using antidotes are discussed. EXPERT OPINION Despite their nontoxic nature, a variety of reasons limit the therapeutic potential of aptamers in the clinic. The analysis of adverse effects observed with the pegnivacogin/anivamersen pair has highlighted the need to screen for preexisting PEG antibodies in any clinical trial involving pegylated molecules. Surprisingly, and promisingly, the ability of nucleic acid therapeutics to breach the blood brain barrier seems achievable. The recognition of specific motifs, e.g. G-quadruplex in thrombin-binding aptamers, or a 'nucleation' zone while designing aptamer-antidote pairs, is likely to accelerate the discovery of therapeutically efficacious molecules.
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Affiliation(s)
- Swati Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Jaskirat Kaur
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Shivcharan Prasad
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
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17
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Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki J, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, Ding F, Geniesse C, Jiang Y, Joshi A, Krokhotin A, Magnus M, Mailhot O, Major F, Mann TH, Piątkowski P, Pluta R, Popenda M, Sarzynska J, Sun L, Szachniuk M, Tian S, Wang J, Wang J, Watkins AM, Wiedemann J, Xiao Y, Xu X, Yesselman JD, Zhang D, Zhang Y, Zhang Z, Zhao C, Zhao P, Zhou Y, Zok T, Żyła A, Ren A, Batey RT, Golden BL, Huang L, Lilley DM, Liu Y, Patel DJ, Westhof E. RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. RNA (NEW YORK, N.Y.) 2020; 26:982-995. [PMID: 32371455 PMCID: PMC7373991 DOI: 10.1261/rna.075341.120] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/03/2020] [Indexed: 05/21/2023]
Abstract
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of the crystal structures. We now report the prediction of 3D structures for six RNA sequences: four nucleolytic ribozymes and two riboswitches. Systematic protocols for comparing models and crystal structures are described and analyzed. In these six puzzles, we discuss (i) the comparison between the automated web servers and human experts; (ii) the prediction of coaxial stacking; (iii) the prediction of structural details and ligand binding; (iv) the development of novel prediction methods; and (v) the potential improvements to be made. We show that correct prediction of coaxial stacking and tertiary contacts is essential for the prediction of RNA architecture, while ligand binding modes can only be predicted with low resolution and simultaneous prediction of RNA structure with accurate ligand binding still remains out of reach. All the predicted models are available for the future development of force field parameters and the improvement of comparison and assessment tools.
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Affiliation(s)
- Zhichao Miao
- Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, CB10 1SD, United Kingdom
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Ryszard W Adamiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Maciej Antczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Michał J Boniecki
- International Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland
| | - Janusz Bujnicki
- International Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland
| | - Shi-Jie Chen
- Department of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA
| | - Clarence Yu Cheng
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Yi Cheng
- Department of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA
| | - Fang-Chieh Chou
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, 17033, USA
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, 17033, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Caleb Geniesse
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Yangwei Jiang
- Department of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA
| | - Astha Joshi
- International Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland
| | - Andrey Krokhotin
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Departments of Pathology, Genetics and Developmental Biology, Howard Hughes Medical Institute, Stanford Medical School, Palo Alto, California, 94305, USA
| | - Marcin Magnus
- International Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland
| | - Olivier Mailhot
- Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, H3C 3J7, Canada
| | - Francois Major
- Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, H3C 3J7, Canada
| | - Thomas H Mann
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Paweł Piątkowski
- International Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland
| | - Radoslaw Pluta
- International Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland
| | - Mariusz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Lizhen Sun
- Department of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA
| | - Marta Szachniuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Siqi Tian
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jian Wang
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, 17033, USA
| | - Jun Wang
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jakub Wiedemann
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Yi Xiao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Xiaojun Xu
- Department of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA
| | - Joseph D Yesselman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Dong Zhang
- Department of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA
| | - Yi Zhang
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Zhenzhen Zhang
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Chenhan Zhao
- Department of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA
| | - Peinan Zhao
- Department of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA
| | - Yuanzhe Zhou
- Department of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA
| | - Tomasz Zok
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Adriana Żyła
- International Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Robert T Batey
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, Colorado 80309-0596, USA
| | - Barbara L Golden
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P. R. China
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P. R. China
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - David M Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Eric Westhof
- Arch et Reactivite de l'ARN, Univ de Strasbourg, Inst de Biol Mol et Cell du CNRS, 67084 Strasbourg, France
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18
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Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions. Molecules 2020; 25:molecules25122881. [PMID: 32585844 PMCID: PMC7357161 DOI: 10.3390/molecules25122881] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022] Open
Abstract
In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range base-pairing ("kissing") interactions, self-annealing of palindromic or complementary sequences, and stable tertiary contact motifs, such as the GNRA tetraloop-receptors. To explore the general mechanics of RNA dimerization, we performed a meta-analysis of a collection of exemplary RNA homodimer structures consisting of viral genomic elements, ribozymes, riboswitches, etc., encompassing both functional and fortuitous dimers. Globally, we found that domain-swapped dimers and antiparallel, head-to-tail arrangements are predominant architectural themes. Locally, we observed that the same structural motifs, interfaces and forces that enable tertiary RNA folding also drive their higher-order assemblies. These feature prominently long-range kissing loops, pseudoknots, reciprocal base intercalations and A-minor interactions. We postulate that the scarcity of functional RNA multimers and limited diversity in multimerization motifs may reflect evolutionary constraints imposed by host antiviral immune surveillance and stress sensing. A deepening mechanistic understanding of RNA multimerization is expected to facilitate investigations into RNA and RNP assemblies, condensates, and granules and enable their potential therapeutical targeting.
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19
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Joseph NN, Roy RN, Steitz TA. Molecular dynamics analysis of Mg 2+ -dependent cleavage of a pistol ribozyme reveals a fail-safe secondary ion for catalysis. J Comput Chem 2020; 41:1345-1352. [PMID: 32091136 DOI: 10.1002/jcc.26179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 01/19/2020] [Indexed: 11/08/2022]
Abstract
Pistol ribozymes comprise a class of small, self-cleaving RNAs discovered via comparative genomic analysis. Prior work in the field has probed the kinetics of the cleavage reaction, as well as the influence of various metal ion cofactors that accelerate the process. In the current study, we performed unbiased and unconstrained molecular dynamics simulations from two current high-resolution pistol crystal structures, and we analyzed trajectory data within the context of the currently accepted ribozyme mechanistic framework. Root-mean-squared deviations, radial distribution functions, and distributions of nucleophilic angle-of-attack reveal insights into the potential roles of three magnesium ions with respect to catalysis and overall conformational stability of the molecule. A series of simulation trajectories containing in silico mutations reveal the relatively flexible and partially interchangeable roles of two particular magnesium ions within solvated hydrogen-bonding distances from the catalytic center.
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Affiliation(s)
- Newlyn N Joseph
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA, New Haven, Connecticut.,University of Connecticut School of Medicine, Farmington, Connecticut
| | - Raktim N Roy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA, New Haven, Connecticut.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA, New Haven, Connecticut
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20
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Cuturello F, Tiana G, Bussi G. Assessing the accuracy of direct-coupling analysis for RNA contact prediction. RNA (NEW YORK, N.Y.) 2020; 26:637-647. [PMID: 32115426 PMCID: PMC7161351 DOI: 10.1261/rna.074179.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/26/2020] [Indexed: 05/31/2023]
Abstract
Many noncoding RNAs are known to play a role in the cell directly linked to their structure. Structure prediction based on the sole sequence is, however, a challenging task. On the other hand, thanks to the low cost of sequencing technologies, a very large number of homologous sequences are becoming available for many RNA families. In the protein community, the idea of exploiting the covariance of mutations within a family to predict the protein structure using the direct-coupling-analysis (DCA) method has emerged in the last decade. The application of DCA to RNA systems has been limited so far. We here perform an assessment of the DCA method on 17 riboswitch families, comparing it with the commonly used mutual information analysis and with state-of-the-art R-scape covariance method. We also compare different flavors of DCA, including mean-field, pseudolikelihood, and a proposed stochastic procedure (Boltzmann learning) for solving exactly the DCA inverse problem. Boltzmann learning outperforms the other methods in predicting contacts observed in high-resolution crystal structures.
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Affiliation(s)
- Francesca Cuturello
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 34136 Trieste, Italy
| | - Guido Tiana
- Center for Complexity and Biosystems and Department of Physics, Università degli Studi di Milano and INFN, 20133 Milano, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies, 34136 Trieste, Italy
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21
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Velema WA, Kool ET. The chemistry and applications of RNA 2'-OH acylation. Nat Rev Chem 2020; 4:22-37. [PMID: 32984545 PMCID: PMC7513686 DOI: 10.1038/s41570-019-0147-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2019] [Indexed: 12/19/2022]
Abstract
RNA is a versatile biomolecule with a broad range of biological functions that go far beyond its initially described role as a simple information carrier. The development of chemical methods to control, manipulate and modify RNA has the potential to yield new insights into its many functions and properties. Traditionally, most of these methods involved the chemical modification of RNA structure using solid-state synthesis or enzymatic transformations. However, over the past 15 years, the direct functionalization of RNA by selective acylation of the 2'-hydroxyl (2'-OH) group has emerged as a powerful alternative that enables the simple modification of both synthetic and transcribed RNAs. In this Review, we discuss the chemical properties and design of effective reagents for RNA 2'-OH acylation, highlighting the unique problem of 2'-OH reactivity in the presence of water. We elaborate on how RNA 2'-OH acylation is being exploited to develop selective chemical probes that enable interrogation of RNA structure and function, and describe new developments and applications in the field.
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Affiliation(s)
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA, USA
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22
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A Novel G-Quadruplex Binding Protein in Yeast-Slx9. Molecules 2019; 24:molecules24091774. [PMID: 31067825 PMCID: PMC6539110 DOI: 10.3390/molecules24091774] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 01/01/2023] Open
Abstract
G-quadruplex (G4) structures are highly stable four-stranded DNA and RNA secondary structures held together by non-canonical guanine base pairs. G4 sequence motifs are enriched at specific sites in eukaryotic genomes, suggesting regulatory functions of G4 structures during different biological processes. Considering the high thermodynamic stability of G4 structures, various proteins are necessary for G4 structure formation and unwinding. In a yeast one-hybrid screen, we identified Slx9 as a novel G4-binding protein. We confirmed that Slx9 binds to G4 DNA structures in vitro. Despite these findings, Slx9 binds only insignificantly to G-rich/G4 regions in Saccharomyces cerevisiae as demonstrated by genome-wide ChIP-seq analysis. However, Slx9 binding to G4s is significantly increased in the absence of Sgs1, a RecQ helicase that regulates G4 structures. Different genetic and molecular analyses allowed us to propose a model in which Slx9 recognizes and protects stabilized G4 structures in vivo.
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23
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Ren GX, Guo XP, Sun YC. Regulatory 3' Untranslated Regions of Bacterial mRNAs. Front Microbiol 2017; 8:1276. [PMID: 28740488 PMCID: PMC5502269 DOI: 10.3389/fmicb.2017.01276] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/26/2017] [Indexed: 12/11/2022] Open
Abstract
The untranslated regions (UTRs) of mRNA contain important features that are relevant to the post-transcriptional and translational regulation of gene expression. Most studies of bacterial UTRs have focused on the 5′regions; however, 3′UTRs have recently emerged as a new class of post-transcriptional regulatory elements. 3′UTRs were found to regulate the decay and translation initiation in their own mRNAs. In addition, 3′UTRs constitute a rich reservoir of small regulatory RNAs, regulating target gene expression. In the current review, we describe several recently discovered examples of bacterial regulatory 3′UTRs, discuss their modes of action, and illustrate how they facilitate gene regulation in various environments.
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Affiliation(s)
- Gai-Xian Ren
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Xiao-Peng Guo
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Yi-Cheng Sun
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
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24
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Crystal structure of Pistol, a class of self-cleaving ribozyme. Proc Natl Acad Sci U S A 2017; 114:1021-1026. [PMID: 28096403 DOI: 10.1073/pnas.1611191114] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Small self-cleaving ribozymes have been discovered in all evolutionary domains of life. They can catalyze site-specific RNA cleavage, and as a result, they have relevance in gene regulation. Comparative genomic analysis has led to the discovery of a new class of small self-cleaving ribozymes named Pistol. We report the crystal structure of Pistol at 2.97-Å resolution. Our results suggest that the Pistol ribozyme self-cleavage mechanism likely uses a guanine base in the active site pocket to carry out the phosphoester transfer reaction. The guanine G40 is in close proximity to serve as the general base for activating the nucleophile by deprotonating the 2'-hydroxyl to initiate the reaction (phosphoester transfer). Furthermore, G40 can also establish hydrogen bonding interactions with the nonbridging oxygen of the scissile phosphate. The proximity of G32 to the O5' leaving group suggests that G32 may putatively serve as the general acid. The RNA structure of Pistol also contains A-minor interactions, which seem to be important to maintain its tertiary structure and compact fold. Our findings expand the repertoire of ribozyme structures and highlight the conserved evolutionary mechanism used by ribozymes for catalysis.
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25
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Gebetsberger J, Micura R. Unwinding the twister ribozyme: from structure to mechanism. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27863022 PMCID: PMC5408937 DOI: 10.1002/wrna.1402] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 09/12/2016] [Accepted: 10/10/2016] [Indexed: 11/12/2022]
Abstract
The twister ribozyme motif has been identified by bioinformatic means very recently. Currently, four crystal structures with ordered active sites together with a series of chemical and biochemical data provide insights into how this RNA accomplishes its efficient self‐cleavage. Of particular interest for a mechanistic proposal are structural distinctions observed in the active sites that concern the conformation of the U‐A cleavage site dinucleotide (in‐line alignment of the attacking 2′‐O nucleophile to the to‐be‐cleaved P—O5′ bond versus suboptimal alignments) as well as the presence/absence of Mg2+ ions at the scissile phosphate. All structures support the notion that an active site guanine and the conserved adenine at the cleavage site are important contributors to cleavage chemistry, likely being involved in general acid base catalysis. Evidence for innersphere coordination of a Mg2+ ion to the pro‐S nonbridging oxygen of the scissile phosphate stems from two of the four crystal structures. Together with the finding of thio/rescue effects for phosphorothioate substrates, this suggests the participation of divalent ions in the overall catalytic strategy employed by twister ribozymes. In this context, it is notable that twister retains wild‐type activity when the phylogenetically conserved stem P1 is deleted, able to cleave a single nucleotide only. WIREs RNA 2017, 8:e1402. doi: 10.1002/wrna.1402 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Jennifer Gebetsberger
- Institute of Organic Chemistry, Leopold-Franzens University and Center of Molecular Biosciences Innsbruck CMBI, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Leopold-Franzens University and Center of Molecular Biosciences Innsbruck CMBI, Innsbruck, Austria
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26
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Wagner A, Ortman S, Maxfield R. From the primordial soup to self-driving cars: standards and their role in natural and technological innovation. J R Soc Interface 2016; 13:20151086. [PMID: 26864893 DOI: 10.1098/rsif.2015.1086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Standards are specifications to which the elements of a technology must conform. Here, we apply this notion to the biochemical 'technologies' of nature, where objects like DNA and proteins, as well as processes like the regulation of gene activity are highly standardized. We introduce the concept of standards with multiple examples, ranging from the ancient genetic material RNA, to Palaeolithic stone axes, and digital electronics, and we discuss common ways in which standards emerge in nature and technology. We then focus on the question of how standards can facilitate technological and biological innovation. Innovation-enhancing standards include those of proteins and digital electronics. They share common features, such as that few standardized building blocks can be combined through standard interfaces to create myriad useful objects or processes. We argue that such features will also characterize the most innovation-enhancing standards of future technologies.
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Affiliation(s)
- Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland Santa Fe Institute, Santa Fe, NM, USA
| | - Scott Ortman
- Santa Fe Institute, Santa Fe, NM, USA Department of Anthropology, University of Colorado Boulder, Boulder, CO, USA
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Ren A, Vušurović N, Gebetsberger J, Gao P, Juen M, Kreutz C, Micura R, Patel DJ. Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage. Nat Chem Biol 2016; 12:702-8. [PMID: 27398999 PMCID: PMC4990474 DOI: 10.1038/nchembio.2125] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/08/2016] [Indexed: 12/20/2022]
Abstract
The field of small self-cleaving nucleolytic ribozymes has been invigorated by the recent discovery of the twister, twister-sister, pistol and hatchet ribozymes. We report the crystal structure of a pistol ribozyme termed env25, which adopts a compact tertiary architecture stabilized by an embedded pseudoknot fold. The G-U cleavage site adopts a splayed-apart conformation with in-line alignment of the modeled 2'-O of G for attack on the adjacent to-be-cleaved P-O5' bond. Highly conserved residues G40 (N1 position) and A32 (N3 and 2'-OH positions) are aligned to act as a general base and a general acid, respectively, to accelerate cleavage chemistry, with their roles confirmed by cleavage assays on variants, and an increased pKa of 4.7 for A32. Our structure of the pistol ribozyme defined how the overall and local topologies dictate the in-line alignment at the G-U cleavage site, with cleavage assays on variants revealing key residues that participate in acid-base-catalyzed cleavage chemistry.
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Affiliation(s)
- Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, China
- Structural Biology Program, Memorial Sloan-Kettering Cancer, New York, New York, USA
| | - Nikola Vušurović
- Institute of Organic Chemistry, Leopold Franzens University, Innsbruck, Austria
- Center of Molecular Biosciences (CMBI), Innsbruck, Austria
| | - Jennifer Gebetsberger
- Institute of Organic Chemistry, Leopold Franzens University, Innsbruck, Austria
- Center of Molecular Biosciences (CMBI), Innsbruck, Austria
| | - Pu Gao
- Structural Biology Program, Memorial Sloan-Kettering Cancer, New York, New York, USA
| | - Michael Juen
- Institute of Organic Chemistry, Leopold Franzens University, Innsbruck, Austria
- Center of Molecular Biosciences (CMBI), Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Leopold Franzens University, Innsbruck, Austria
- Center of Molecular Biosciences (CMBI), Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Leopold Franzens University, Innsbruck, Austria
- Center of Molecular Biosciences (CMBI), Innsbruck, Austria
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer, New York, New York, USA
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Nucleic acid polymeric properties and electrostatics: Directly comparing theory and simulation with experiment. Adv Colloid Interface Sci 2016; 232:49-56. [PMID: 26482088 DOI: 10.1016/j.cis.2015.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/18/2015] [Accepted: 09/29/2015] [Indexed: 11/24/2022]
Abstract
Nucleic acids are biopolymers that carry genetic information and are also involved in various gene regulation functions such as gene silencing and protein translation. Because of their negatively charged backbones, nucleic acids are polyelectrolytes. To adequately understand nucleic acid folding and function, we need to properly describe its i) polymer/polyelectrolyte properties and ii) associating ion atmosphere. While various theories and simulation models have been developed to describe nucleic acids and the ions around them, many of these theories/simulations have not been well evaluated due to complexities in comparison with experiment. In this review, I discuss some recent experiments that have been strategically designed for straightforward comparison with theories and simulation models. Such data serve as excellent benchmarks to identify limitations in prevailing theories and simulation parameters.
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Jacobson DR, Saleh OA. Quantifying the ion atmosphere of unfolded, single-stranded nucleic acids using equilibrium dialysis and single-molecule methods. Nucleic Acids Res 2016; 44:3763-71. [PMID: 27036864 PMCID: PMC4856996 DOI: 10.1093/nar/gkw196] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/14/2016] [Indexed: 12/31/2022] Open
Abstract
To form secondary structure, nucleic acids (NAs) must overcome electrostatic strand–strand repulsion, which is moderated by the surrounding atmosphere of screening ions. The free energy of NA folding therefore depends on the interactions of this ion atmosphere with both the folded and unfolded states. We quantify such interactions using the preferential ion interaction coefficient or ion excess: the number of ions present near the NA in excess of the bulk concentration. The ion excess of the folded, double-helical state has been extensively studied; however, much less is known about the salt-dependent ion excess of the unfolded, single-stranded state. We measure this quantity using three complementary approaches: a direct approach of Donnan equilibrium dialysis read out by atomic emission spectroscopy and two indirect approaches involving either single-molecule force spectroscopy or existing thermal denaturation data. The results of these three approaches, each involving an independent experimental technique, are in good agreement. Even though the single-stranded NAs are flexible polymers that are expected to adopt random-coil configurations, we find that their ion atmosphere is quantitatively described by rod-like models that neglect large-scale conformational freedom, an effect that we explain in terms of the competition between the relevant structural and electrostatic length scales.
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Affiliation(s)
- David R Jacobson
- Department of Physics, University of California, Santa Barbara, CA 93106, USA
| | - Omar A Saleh
- Materials Department and BMSE Program, University of California, Santa Barbara, CA, USA
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Henke PS, Mak CH. An implicit divalent counterion force field for RNA molecular dynamics. J Chem Phys 2016; 144:105104. [DOI: 10.1063/1.4943387] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Paul S. Henke
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Chi H. Mak
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
- Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089, USA
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Li J, Mo L, Lu CH, Fu T, Yang HH, Tan W. Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications. Chem Soc Rev 2016; 45:1410-31. [PMID: 26758955 PMCID: PMC4775362 DOI: 10.1039/c5cs00586h] [Citation(s) in RCA: 352] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hydrogels are crosslinked hydrophilic polymers that can absorb a large amount of water. By their hydrophilic, biocompatible and highly tunable nature, hydrogels can be tailored for applications in bioanalysis and biomedicine. Of particular interest are DNA-based hydrogels owing to the unique features of nucleic acids. Since the discovery of the DNA double helical structure, interest in DNA has expanded beyond its genetic role to applications in nanotechnology and materials science. In particular, DNA-based hydrogels present such remarkable features as stability, flexibility, precise programmability, stimuli-responsive DNA conformations, facile synthesis and modification. Moreover, functional nucleic acids (FNAs) have allowed the construction of hydrogels based on aptamers, DNAzymes, i-motif nanostructures, siRNAs and CpG oligodeoxynucleotides to provide additional molecular recognition, catalytic activities and therapeutic potential, making them key players in biological analysis and biomedical applications. To date, a variety of applications have been demonstrated with FNA-based hydrogels, including biosensing, environmental analysis, controlled drug release, cell adhesion and targeted cancer therapy. In this review, we focus on advances in the development of FNA-based hydrogels, which have fully incorporated both the unique features of FNAs and DNA-based hydrogels. We first introduce different strategies for constructing DNA-based hydrogels. Subsequently, various types of FNAs and the most recent developments of FNA-based hydrogels for bioanalytical and biomedical applications are described with some selected examples. Finally, the review provides an insight into the remaining challenges and future perspectives of FNA-based hydrogels.
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Affiliation(s)
- Juan Li
- The Key Lab of Analysis and Detection Technology for Food Safety of the MOE and Fujian Province, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China. and Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China.
| | - Liuting Mo
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China.
| | - Chun-Hua Lu
- The Key Lab of Analysis and Detection Technology for Food Safety of the MOE and Fujian Province, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China.
| | - Ting Fu
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China. and Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, University of Florida, Gainesville, FL 32611-7200, USA
| | - Huang-Hao Yang
- The Key Lab of Analysis and Detection Technology for Food Safety of the MOE and Fujian Province, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China.
| | - Weihong Tan
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China. and Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, University of Florida, Gainesville, FL 32611-7200, USA
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Frankel EA, Bevilacqua PC, Keating CD. Polyamine/Nucleotide Coacervates Provide Strong Compartmentalization of Mg²⁺, Nucleotides, and RNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:2041-9. [PMID: 26844692 DOI: 10.1021/acs.langmuir.5b04462] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Phase separation of aqueous solutions containing polyelectrolytes can lead to formation of dense, solute-rich liquid droplets referred to as coacervates, surrounded by a dilute continuous phase of much larger volume. This type of liquid-liquid phase separation is thought to help explain the appearance of polyelectrolyte-rich intracellular droplets in the cytoplasm and nucleoplasm of extant biological cells and may be relevant to protocellular compartmentalization of nucleic acids on the early Earth. Here we describe complex coacervates formed upon mixing the polycation poly(allylamine) (PAH, 15 kDa) with the anionic nucleotides adenosine 5'-mono-, di-, and triphosphate (AMP, ADP, and ATP). Droplet formation was observed over a wide range of pH and MgCl2 concentrations. The nucleotides themselves as well as Mg(2+) and RNA oligonucleotides were all extremely concentrated within the coacervates. Nucleotides present at just 2.5 mM in bulk solution had concentrations greater than 1 M inside the coacervate droplets. A solution with a total Mg(2+) concentration of 10 mM had 1-5 M Mg(2+) in the coacervates, and RNA random sequence (N54) partitioned ∼10,000-fold into the coacervates. Coacervate droplets are thus rich in nucleotides, Mg(2+), and RNA, providing a medium favorable for generating functional RNAs. Compartmentalization of nucleotides at high concentrations could have facilitated their polymerization to form oligonucleotides, which preferentially accumulate in the droplets. Locally high Mg(2+) concentrations could have aided folding and catalysis in an RNA world, making coacervate droplets an appealing platform for exploring protocellular environments.
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Affiliation(s)
- Erica A Frankel
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Philip C Bevilacqua
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Christine D Keating
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
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Harris KA, Lünse CE, Li S, Brewer KI, Breaker RR. Biochemical analysis of pistol self-cleaving ribozymes. RNA (NEW YORK, N.Y.) 2015; 21:1852-8. [PMID: 26385507 PMCID: PMC4604425 DOI: 10.1261/rna.052514.115] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 06/22/2015] [Indexed: 05/27/2023]
Abstract
Pistol RNAs are members of a distinct class of self-cleaving ribozymes that was recently discovered by using a bioinformatics search strategy. Several hundred pistol ribozymes share a consensus sequence including 10 highly conserved nucleotides and many other modestly conserved nucleotides associated with specific secondary structure features, including three base-paired stems and a pseudoknot. A representative pistol ribozyme from the bacterium Lysinibacillus sphaericus was found to promote RNA strand scission with a rate constant of ∼10 min(-1) under physiological Mg(2+) and pH conditions. The reaction proceeds via the nucleophilic attack of a 2'-oxygen atom on the adjacent phosphorus center, and thus adheres to the same general catalytic mechanism of internal phosphoester transfer as found with all other classes of natural self-cleaving ribozymes discovered to date. Analyses of the kinetic characteristics and the metal ion requirements of the cleavage reaction reveal that members of this ribozyme class likely use several catalytic strategies to promote the rapid cleavage of RNA.
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Affiliation(s)
- Kimberly A Harris
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Christina E Lünse
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Sanshu Li
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Kenneth I Brewer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ronald R Breaker
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
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35
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Qi X, Xia T. Structure, dynamics, and mechanism of the lead-dependent ribozyme. Biomol Concepts 2015; 2:305-14. [PMID: 25962038 DOI: 10.1515/bmc.2011.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 06/06/2011] [Indexed: 12/24/2022] Open
Abstract
Leadzyme is a small catalytic RNA that was identified by in vitro selection for Pb2+-dependent cleavage from a tRNA library. Leadzyme employs a unique two-step Pb2+-specific mechanism to cleave within its active site. NMR and crystal structures of the active site revealed different folding patterns, but neither features the in-line alignment for attack by the 2'-OH nucleophilic group. These experimentally determined structures most likely represent ground states and are catalytically inactive. There are significant dynamics of the active site and the motif samples multiple conformations at the ground states. Various metal ion binding sites have been identified, including one that may be occupied by a catalytic Pb2+. Based on functional group analysis, a computational model of the transition state has been proposed. This model features a unique base triple that is consistent with sequence and functional group requirements for catalysis. This structure is likely only populated transiently, but imposing appropriate conformational constraints may significantly stabilize this state thereby promoting catalysis. Other ions may inhibit the cleavage by competing for the Pb2+ binding site, or by stabilizing the ground state thereby suppressing its transition to the catalytically active conformation. Some rare earth ions can enhance the reaction via an unknown mechanism. Because of its unique chemistry and dynamic behavior, leadzyme can continue to serve as an excellent model system for teaching us RNA biology and chemistry.
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Zenk J, Schulman R. An assembly funnel makes biomolecular complex assembly efficient. PLoS One 2014; 9:e111233. [PMID: 25360818 PMCID: PMC4215988 DOI: 10.1371/journal.pone.0111233] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/30/2014] [Indexed: 11/18/2022] Open
Abstract
Like protein folding and crystallization, the self-assembly of complexes is a fundamental form of biomolecular organization. While the number of methods for creating synthetic complexes is growing rapidly, most require empirical tuning of assembly conditions and/or produce low yields. We use coarse-grained simulations of the assembly kinetics of complexes to identify generic limitations on yields that arise because of the many simultaneous interactions allowed between the components and intermediates of a complex. Efficient assembly occurs when nucleation is fast and growth pathways are few, i.e. when there is an assembly "funnel". For typical complexes, an assembly funnel occurs in a narrow window of conditions whose location is highly complex specific. However, by redesigning the components this window can be drastically broadened, so that complexes can form quickly across many conditions. The generality of this approach suggests assembly funnel design as a foundational strategy for robust biomolecular complex synthesis.
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Affiliation(s)
- John Zenk
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Rebecca Schulman
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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Riccitelli N, Lupták A. HDV family of self-cleaving ribozymes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 120:123-71. [PMID: 24156943 DOI: 10.1016/b978-0-12-381286-5.00004-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The hepatitis delta virus (HDV) ribozymes are catalytic RNAs capable of cleaving their own sugar-phosphate backbone. The HDV virus possesses the ribozymes in both sense and antisense genomic transcripts, where they are essential for processing during replication. These ribozymes have been the subject of intense biochemical scrutiny and have yielded a wealth of mechanistic insights. In recent years, many HDV-like ribozymes have been identified in nearly all branches of life. The ribozymes are implicated in a variety of biological events, including episodic memory in mammals and retrotransposition in many eukaryotes. Detailed analysis of additional HDV-like ribozyme isolates will likely reveal many more biological functions and provide information about the evolution of this unique RNA.
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Affiliation(s)
- Nathan Riccitelli
- Department of Chemistry, University of California, Irvine, California, USA
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Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′,5′-Cyclic GMP. ENTROPY 2013. [DOI: 10.3390/e15125362] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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40
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Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Moll I, Fabbretti A, Brandi L, Gualerzi CO. Inhibitors Targeting Riboswitches and Ribozymes. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Mohan U, Burai R, McNaughton BR. In vitro evolution of a Friedel-Crafts deoxyribozyme. Org Biomol Chem 2013; 11:2241-4. [PMID: 23443910 DOI: 10.1039/c3ob40080h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the in vitro selection of a single-stranded 72-nucleotide DNA enzyme (deoxyribozyme) that catalyzes a Friedel-Crafts reaction between an indole and acyl imidazole in good yield and in aqueous solvent. Appreciable Friedel-Crafts product requires addition of copper nitrate and the deoxyribozyme. We observe deoxyribozyme-mediated bond formation for both in cis and in trans Friedel-Crafts reactions.
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Affiliation(s)
- Utpal Mohan
- Department of Chemistry, Colorado State University, 200 West Lake Street, Fort Collins, CO, USA
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Zhang L, Yang L, Li JJ, Sun L. Potential use of nucleic acid-based agents in the sensitization of nasopharyngeal carcinoma to radiotherapy. Cancer Lett 2012; 323:1-10. [DOI: 10.1016/j.canlet.2012.03.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 03/26/2012] [Accepted: 03/26/2012] [Indexed: 11/27/2022]
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Abe H, Abe N, Shibata A, Ito K, Tanaka Y, Ito M, Saneyoshi H, Shuto S, Ito Y. Structure Formation and Catalytic Activity of DNA Dissolved in Organic Solvents. Angew Chem Int Ed Engl 2012; 51:6475-9. [DOI: 10.1002/anie.201201111] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 03/27/2012] [Indexed: 01/22/2023]
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45
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Abe H, Abe N, Shibata A, Ito K, Tanaka Y, Ito M, Saneyoshi H, Shuto S, Ito Y. Structure Formation and Catalytic Activity of DNA Dissolved in Organic Solvents. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201111] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Abstract
Detecting functional RNAs is increasingly accomplished through structure-based searches for patterns of conserved secondary structure. With large amounts of new sequencing data becoming available, there is a greater demand for efficient methods of identifying new RNAs. Here we present a method of identifying self-cleaving ribozymes and characterizing the in vitro activity.
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Halvorsen M, Martin JS, Broadaway S, Laederach A. Disease-associated mutations that alter the RNA structural ensemble. PLoS Genet 2010; 6:e1001074. [PMID: 20808897 PMCID: PMC2924325 DOI: 10.1371/journal.pgen.1001074] [Citation(s) in RCA: 244] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 07/15/2010] [Indexed: 12/28/2022] Open
Abstract
Genome-wide association studies (GWAS) often identify disease-associated mutations in intergenic and non-coding regions of the genome. Given the high percentage of the human genome that is transcribed, we postulate that for some observed associations the disease phenotype is caused by a structural rearrangement in a regulatory region of the RNA transcript. To identify such mutations, we have performed a genome-wide analysis of all known disease-associated Single Nucleotide Polymorphisms (SNPs) from the Human Gene Mutation Database (HGMD) that map to the untranslated regions (UTRs) of a gene. Rather than using minimum free energy approaches (e.g. mFold), we use a partition function calculation that takes into consideration the ensemble of possible RNA conformations for a given sequence. We identified in the human genome disease-associated SNPs that significantly alter the global conformation of the UTR to which they map. For six disease-states (Hyperferritinemia Cataract Syndrome, β-Thalassemia, Cartilage-Hair Hypoplasia, Retinoblastoma, Chronic Obstructive Pulmonary Disease (COPD), and Hypertension), we identified multiple SNPs in UTRs that alter the mRNA structural ensemble of the associated genes. Using a Boltzmann sampling procedure for sub-optimal RNA structures, we are able to characterize and visualize the nature of the conformational changes induced by the disease-associated mutations in the structural ensemble. We observe in several cases (specifically the 5′ UTRs of FTL and RB1) SNP–induced conformational changes analogous to those observed in bacterial regulatory Riboswitches when specific ligands bind. We propose that the UTR and SNP combinations we identify constitute a “RiboSNitch,” that is a regulatory RNA in which a specific SNP has a structural consequence that results in a disease phenotype. Our SNPfold algorithm can help identify RiboSNitches by leveraging GWAS data and an analysis of the mRNA structural ensemble. Genome-wide association studies identify mutations in the human genome that correlate with a particular disease. It is common to find mutations associated with disease in the non-coding region of the genome. These non-coding mutations are more difficult to interpret at a molecular level, because they do not affect the protein sequence. In this study, we analyze disease-associated mutations in non-coding regions of our genome in the context of their structural effect on the message of genetic information in our cells, Ribonucleic Acid (RNA). We focus in particular on the regulatory parts of our genes known as untranslated regions. We find that certain disease-associated mutations in these regulatory untranslated regions have a significant effect on the structure of the RNA message. We call these elements “RiboSNitches,” because they act like switches turning on and off genes, but are caused by Single Nucleotide Polymorphisms (SNPs), which are single point mutations in our genome. The RiboSNitches we identify are potentially a new class of pharmaceutical targets, as it is possible to change the structure of RNA with small drug-like molecules.
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Affiliation(s)
- Matthew Halvorsen
- Biomedical Sciences Department, University at Albany, Albany, New York, United States of America
| | - Joshua S. Martin
- Developmental Genetics and Bioinformatics, Wadsworth Center, Albany, New York, United States of America
| | - Sam Broadaway
- Developmental Genetics and Bioinformatics, Wadsworth Center, Albany, New York, United States of America
| | - Alain Laederach
- Biomedical Sciences Department, University at Albany, Albany, New York, United States of America
- Developmental Genetics and Bioinformatics, Wadsworth Center, Albany, New York, United States of America
- * E-mail:
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Marton S, Reyes-Darias JA, Sánchez-Luque FJ, Romero-López C, Berzal-Herranz A. In vitro and ex vivo selection procedures for identifying potentially therapeutic DNA and RNA molecules. Molecules 2010; 15:4610-38. [PMID: 20657381 PMCID: PMC6257598 DOI: 10.3390/molecules15074610] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 06/17/2010] [Accepted: 06/24/2010] [Indexed: 02/05/2023] Open
Abstract
It was only relatively recently discovered that nucleic acids participate in a variety of biological functions, besides the storage and transmission of genetic information. Quite apart from the nucleotide sequence, it is now clear that the structure of a nucleic acid plays an essential role in its functionality, enabling catalysis and specific binding reactions. In vitro selection and evolution strategies have been extremely useful in the analysis of functional RNA and DNA molecules, helping to expand our knowledge of their functional repertoire and to identify and optimize DNA and RNA molecules with potential therapeutic and diagnostic applications. The great progress made in this field has prompted the development of ex vivo methods for selecting functional nucleic acids in the cellular environment. This review summarizes the most important and most recent applications of in vitro and ex vivo selection strategies aimed at exploring the therapeutic potential of nucleic acids.
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Affiliation(s)
- Soledad Marton
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, P.T. Ciencias de la Salud, Av. del Conocimiento s/n, Armilla, 18100 Granada, Spain.
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Riccitelli NJ, Lupták A. Computational discovery of folded RNA domains in genomes and in vitro selected libraries. Methods 2010; 52:133-40. [PMID: 20554049 DOI: 10.1016/j.ymeth.2010.06.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 06/03/2010] [Indexed: 10/19/2022] Open
Abstract
Structured functional RNAs are conserved on the level of secondary and tertiary structure, rather than at sequence level, and so traditional sequence-based searches often fail to identify them. Structure-based searches are increasingly used to discover known RNA motifs in sequence databases. We describe the application of the program RNABOB, which performs such searches by allowing the user to define a desired motif's sequence, paired and spacer elements and then scans a sequence file for regions capable of assuming the prescribed fold. Structure descriptors of stem-loops, internal loops, three-way junctions, kissing loops, and the hammerhead and hepatitis delta virus ribozymes are shown as examples of implementation of structure-based searches.
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