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Kekić T, Milisavljević N, Troussier J, Tahir A, Debart F, Lietard J. Accelerated, high-quality photolithographic synthesis of RNA microarrays in situ. SCIENCE ADVANCES 2024; 10:eado6762. [PMID: 39083603 PMCID: PMC11290486 DOI: 10.1126/sciadv.ado6762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/26/2024] [Indexed: 08/02/2024]
Abstract
Nucleic acid photolithography is the only microarray fabrication process that has demonstrated chemical versatility accommodating any type of nucleic acid. The current approach to RNA microarray synthesis requires long coupling and photolysis times and suffers from unavoidable degradation postsynthesis. In this study, we developed a series of RNA phosphoramidites with improved chemical and photochemical protection of the 2'- and 5'-OH functions. In so doing, we reduced the coupling time by more than half and the photolysis time by a factor of 4. Sequence libraries that would otherwise take over 6 hours to synthesize can now be prepared in half the time. Degradation is substantially lowered, and concomitantly, hybridization signals can reach over seven times those of the previous state of the art. Under those conditions, high-density RNA microarrays and RNA libraries can now be synthesized at greatly accelerated rates. We also synthesized fluorogenic RNA Mango aptamers on microarrays and investigated the effect of sequence mutations on their fluorogenic properties.
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Affiliation(s)
- Tadija Kekić
- Institute of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | | | - Joris Troussier
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Amina Tahir
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Françoise Debart
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Jory Lietard
- Institute of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
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2
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Yu Y, Li Q, Shi W, Yang Y, He H, Dai J, Mao G, Ma Y. Programmable Aptasensor for Regulating CRISPR/Cas12a Activity. ACS Sens 2024; 9:244-250. [PMID: 38085648 DOI: 10.1021/acssensors.3c01881] [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] [Indexed: 01/27/2024]
Abstract
CRISPR-mediated aptasensors have gained prevalence for detecting non-nucleic acid targets. However, there is an urgent need to develop an easily customizable design to improve the signal-to-noise ratio, enhance universality, and expand the detection range. In this article, we report a CRISPR-mediated programmable aptasensor (CPAS) platform. The platform includes single-stranded DNA comprising the aptamer sequence, locker DNA, and a crRNA recognition region, forming a hairpin structure through complementary hybridization. With T4 DNA polymerase, the crRNA recognition region was transformed into a complete double-stranded DNA through stem-loop extension, thereby activating the trans-cleavage activity of Cas 12a and generating fluorescence signals. The specific binding between the target molecule and aptamer disrupted the formation of the hairpin structure, altering the fluorescence signals. Notably, the CPAS platform allows for easy customization by simply changing the aptamer sequence and locker DNA, without entailing adjustments to the crRNA. The optimal number of bases in the locker DNA was determined to be seven nucleotides for the SARS-CoV-2 spike (S) protein and four nucleotides for ATP. The CPAS platform exhibited high sensitivity for S protein and ATP detection. Integration with a lateral flow assay enabled sensitive detection within 1 h, revealing its excellent potential for portable analysis.
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Affiliation(s)
- Yao Yu
- College of Chemistry & Pharmacy, Northwest A&F University Yangling, Shaanxi 712100, China
| | - Qiaoyu Li
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wen Shi
- College of Chemistry & Pharmacy, Northwest A&F University Yangling, Shaanxi 712100, China
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuxin Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Hongpeng He
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Junbiao Dai
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Guobin Mao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yingxin Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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3
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Kekić T, Lietard J. A Canvas of Spatially Arranged DNA Strands that Can Produce 24-bit Color Depth. J Am Chem Soc 2023; 145:22293-22297. [PMID: 37787949 PMCID: PMC10591465 DOI: 10.1021/jacs.3c06500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Indexed: 10/04/2023]
Abstract
Nucleic acid microarray photolithography combines density, throughput, and positional control in DNA synthesis. These surface-bound sequence libraries are conventionally used in large-scale hybridization assays against fluorescently labeled, perfect-match DNA strands. Here, we introduce another layer of control for in situ microarray synthesis─hybridization affinity─to precisely modulate fluorescence intensity upon duplex formation. Using a combination of Cy3-, Cy5-, and fluorescein-labeled targets and an ensemble of truncated DNA probes, we organize 256 shades of red, green, and blue intensities that can be superimposed and merged. In so doing, hybridization alone is able to produce a large palette of 16 million colors or 24-bit color depth. Digital images can be reproduced with high fidelity at the micrometer scale by using a simple process that assigns sequence to any RGB value. Largely automated, this approach can be seen as miniaturized DNA-based painting.
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Affiliation(s)
- Tadija Kekić
- Institute of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Jory Lietard
- Institute of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
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4
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Generation of Functional-RNA Arrays by In Vitro Transcription and In Situ RNA Capture for the Detection of RNA-RNA Interactions. Methods Mol Biol 2023; 2633:163-184. [PMID: 36853464 DOI: 10.1007/978-1-0716-3004-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
RNA performs a wide variety of vital cellular functions. These functions typically require interactions with other biological macromolecules, often as part of an intricate communication network. High-throughput techniques capable of analyzing RNA-based interactions are therefore essential. Functional-RNA arrays address this need, providing the capability of performing hundreds of miniature assays in parallel. Here we describe a method to generate functional-RNA arrays using in vitro transcription of a DNA template array and in situ RNA capture. We also suggest how functional-RNA arrays could be applied to investigating RNA-RNA interactions.
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Schaudy E, Lietard J, Somoza MM. Enzymatic Synthesis of High-Density RNA Microarrays. Curr Protoc 2023; 3:e667. [PMID: 36794904 PMCID: PMC10946701 DOI: 10.1002/cpz1.667] [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] [Indexed: 02/17/2023]
Abstract
Oligonucleotide microarrays are used to investigate the interactome of nucleic acids. DNA microarrays are commercially available, whereas equivalent RNA microarrays are not. This protocol describes a method to convert DNA microarrays of any density and complexity into RNA microarrays using only readily available materials and reagents. This simple conversion protocol will facilitate the accessibility of RNA microarrays to a wide range of researchers. In addition to general considerations for the design of a template DNA microarray, this procedure describes the experimental steps of hybridization of an RNA primer to the immobilized DNA, followed by its covalent attachment via psoralen-mediated photocrosslinking. The subsequent enzymatic processing steps comprise the extension of the primer with T7 RNA polymerase to generate complementary RNA, and finally the removal of the DNA template with TURBO DNase. Beyond the conversion process, we also describe approaches to detect the RNA product either by internal labeling with fluorescently labeled NTPs or via hybridization to the product strand, a step that can then be complemented by an RNase H assay to confirm the nature of the product. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Conversion of a DNA microarray to an RNA microarray Alternate Protocol: Detection of RNA via incorporation of Cy3-UTP Support Protocol 1: Detection of RNA via hybridization Support Protocol 2: RNase H assay.
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Affiliation(s)
- Erika Schaudy
- Faculty of Chemistry, Institute of Inorganic ChemistryUniversity of ViennaJosef‐Holaubek‐Platz 2 (UZA 2)ViennaAustria
| | - Jory Lietard
- Faculty of Chemistry, Institute of Inorganic ChemistryUniversity of ViennaJosef‐Holaubek‐Platz 2 (UZA 2)ViennaAustria
| | - Mark M. Somoza
- Faculty of Chemistry, Institute of Inorganic ChemistryUniversity of ViennaJosef‐Holaubek‐Platz 2 (UZA 2)ViennaAustria
- Chair of Food Chemistry and Molecular Sensory ScienceTechnical University of MunichLise‐Meitner‐Straße 34FreisingGermany
- Leibniz Institute for Food Systems Biology at the Technical University of MunichLise‐Meitner‐Straße 30FreisingGermany
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Simple synthesis of massively parallel RNA microarrays via enzymatic conversion from DNA microarrays. Nat Commun 2022; 13:3772. [PMID: 35773271 PMCID: PMC9246885 DOI: 10.1038/s41467-022-31370-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/14/2022] [Indexed: 11/20/2022] Open
Abstract
RNA catalytic and binding interactions with proteins and small molecules are fundamental elements of cellular life processes as well as the basis for RNA therapeutics and molecular engineering. In the absence of quantitative predictive capacity for such bioaffinity interactions, high throughput experimental approaches are needed to sufficiently sample RNA sequence space. Here we report on a simple and highly accessible approach to convert commercially available customized DNA microarrays of any complexity and density to RNA microarrays via a T7 RNA polymerase-mediated extension of photocrosslinked methyl RNA primers and subsequent degradation of the DNA templates. RNA microarrays have many potential applications, but are difficult to produce. Here, the AUs present a method for converting commercial, customizable DNA microarrays into RNA microarrays using an accessible three-step process involving primer photocrosslinking, extension, and template degradation.
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7
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Henderson CA, Vincent HA, Callaghan AJ. Reprogramming Gene Expression by Targeting RNA-Based Interactions: A Novel Pipeline Utilizing RNA Array Technology. ACS Synth Biol 2021; 10:1847-1858. [PMID: 34283568 DOI: 10.1021/acssynbio.0c00603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Regulatory RNA-based interactions are critical for coordinating gene expression and are increasingly being targeted in synthetic biology, antimicrobial, and therapeutic fields. Bacterial trans-encoded small RNAs (sRNAs) regulate the translation and/or stability of mRNA targets through base-pairing interactions. These interactions are often integral to complex gene circuits which coordinate critical bacterial processes. The ability to predictably modulate these gene circuits has potential for reprogramming gene expression for synthetic biology and antibacterial purposes. Here, we present a novel pipeline for targeting such RNA-based interactions with antisense oligonucleotides (ASOs) in order to reprogram gene expression. As proof-of-concept, we selected sRNA-mRNA interactions that are central to the Vibrio cholerae quorum sensing pathway, required for V. cholerae pathogenesis, as a regulatory RNA-based interaction input. We rationally designed anti-sRNA ASOs to target the sRNAs and synthesized them as peptide nucleic acids (PNAs). Next, we devised an RNA array-based interaction assay to allow screening of the anti-sRNA ASOs in vitro. Finally, an Escherichia coli-based gene expression reporter assay was developed and used to validate anti-sRNA ASO regulatory activity in a cellular environment. The output from the pipeline was an anti-sRNA ASO that targets sRNAs to inhibit sRNA-mRNA interactions and modulate gene expression. This anti-sRNA ASO has potential for reprogramming gene expression for synthetic biology and/or antibacterial purposes. We anticipate that this pipeline will find widespread use in fields targeting RNA-based interactions as modulators of gene expression.
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Affiliation(s)
- Charlotte A. Henderson
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
| | - Helen A. Vincent
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
| | - Anastasia J. Callaghan
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
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Lin SH, Wu KT, Wang CC, Huang KT, Chen KD, Lin CC, Hsu LW, Chiu KW. HCV RNA in serum and liver samples of patients undergoing living donor liver transplantation. J Int Med Res 2021; 49:3000605211034945. [PMID: 34344219 PMCID: PMC8358508 DOI: 10.1177/03000605211034945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Objective To compare hepatitis C virus (HCV) RNA levels from serum and explanted native liver samples from patients undergoing living donor liver transplantation (LDLT). Methods This was a prospective observational study. Serum and liver samples were collected from consecutive serum anti-HCV-positive transplant recipients between February 2016 to August 2019. HCV RNA was extracted from liver samples and subjected to one-step reverse-transcription qPCR. using the TopScript One Step qRT-PCR Probe Kit with HCV qPCR probe assay and human GAPDH qPCR probe assay on a ViiA7 Real-Time PCR System. Results Among the 80 patients, 36% (29/80) were HCV RNA positive in serum and 85% (68/80) had positive hepatic HCV RNA. Post-liver transplantation, 4% (3/80) patients were serum positive. Conclusions Our study suggests that pre-transplant serum HCV RNA levels may give an underestimate of the number of positive HCV RNA cases and that hepatic HCV RNA data may be more accurate.
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Affiliation(s)
- Shu-Hsien Lin
- Division of Hepato-Gastroenterology, Department of Internal Medicine, Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Liver Transplantation Centre, Department of Surgery, Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Kun-Ta Wu
- Division of General Surgery, Department of Surgery, Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Chih-Chi Wang
- Liver Transplantation Centre, Department of Surgery, Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Division of General Surgery, Department of Surgery, Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Kuang-Tzu Huang
- Liver Transplantation Centre, Department of Surgery, Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Institute for Translational Research in Biomedicine, Chang Gung Memorial Hospital, Kaohsiung¸ Taiwan
| | - Kuang-Den Chen
- Liver Transplantation Centre, Department of Surgery, Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Institute for Translational Research in Biomedicine, Chang Gung Memorial Hospital, Kaohsiung¸ Taiwan
| | - Chih-Che Lin
- Liver Transplantation Centre, Department of Surgery, Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Division of General Surgery, Department of Surgery, Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Li-Wen Hsu
- Liver Transplantation Centre, Department of Surgery, Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Division of General Surgery, Department of Surgery, Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - King-Wah Chiu
- Division of Hepato-Gastroenterology, Department of Internal Medicine, Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Liver Transplantation Centre, Department of Surgery, Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Chang Gung University, College of Medicine, Taoyuan, Taiwan
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Krämer SD, Wöhrle J, Meyer PA, Urban GA, Roth G. How to copy and paste DNA microarrays. Sci Rep 2019; 9:13940. [PMID: 31558745 PMCID: PMC6763488 DOI: 10.1038/s41598-019-50371-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Analogous to a photocopier, we developed a DNA microarray copy technique and were able to copy patterned original DNA microarrays. With this process the appearance of the copied DNA microarray can also be altered compared to the original by producing copies of different resolutions. As a homage to the very first photocopy made by Chester Charlson and Otto Kornei, we performed a lookalike DNA microarray copy exactly 80 years later. Those copies were also used for label-free real-time kinetic binding assays of apo-dCas9 to double stranded DNA and of thrombin to single stranded DNA. Since each DNA microarray copy was made with only 5 µl of spPCR mix, the whole process is cost-efficient. Hence, our DNA microarray copier has a great potential for becoming a standard lab tool.
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Affiliation(s)
- Stefan D Krämer
- ZBSA - Center for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Habsburgerstrasse. 49, D-79104, Freiburg, Germany. .,Faculty for Biology, Albert-Ludwigs-University Freiburg, Schaenzlestrasse 1, D-79104, Freiburg, Germany.
| | - Johannes Wöhrle
- ZBSA - Center for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Habsburgerstrasse. 49, D-79104, Freiburg, Germany.,IMTEK - Dep. of Microsystems Engineering, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 103, D-79110, Freiburg, Germany
| | - Philipp A Meyer
- ZBSA - Center for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Habsburgerstrasse. 49, D-79104, Freiburg, Germany.,IMTEK - Dep. of Microsystems Engineering, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 103, D-79110, Freiburg, Germany
| | - Gerald A Urban
- IMTEK - Dep. of Microsystems Engineering, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 103, D-79110, Freiburg, Germany.,BIOSS - Center for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Schaenzlestrasse 18, D-79104, Freiburg, Germany
| | - Günter Roth
- ZBSA - Center for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Habsburgerstrasse. 49, D-79104, Freiburg, Germany.,Faculty for Biology, Albert-Ludwigs-University Freiburg, Schaenzlestrasse 1, D-79104, Freiburg, Germany.,BioCopy GmbH, Spechtweg 25, D-79110, Freiburg, Germany.,BIOSS - Center for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Schaenzlestrasse 18, D-79104, Freiburg, Germany.,BioCopy Holding AG, Industriestrasse 15, 8355, Aadorf, Switzerland
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Henderson CA, Rail CA, Butt LE, Vincent HA, Callaghan AJ. Generation of small molecule-binding RNA arrays and their application to fluorogen-binding RNA aptamers. Methods 2019; 167:39-53. [PMID: 31055072 PMCID: PMC7068705 DOI: 10.1016/j.ymeth.2019.04.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/04/2019] [Accepted: 04/29/2019] [Indexed: 12/23/2022] Open
Abstract
The discovery and engineering of more and more functions of RNA has highlighted the utility of RNA-targeting small molecules. Recently, several fluorogen-binding RNA aptamers have been developed that have been applied to live cell imaging of RNA and metabolites as RNA tags or biosensors, respectively. Although the design and application of these fluorogen-binding RNA aptamer-based devices is straightforward in theory, in practice, careful optimisation is required. For this reason, high throughput in vitro screening techniques, capable of quantifying fluorogen-RNA aptamer interactions, would be beneficial. We recently developed a method for generating functional-RNA arrays and demonstrated that they could be used to detect fluorogen-RNA aptamer interactions. Specifically, we were able to visualise the interaction between malachite green and the malachite green-binding aptamer. Here we expand this study to demonstrate that functional-RNA arrays can be used to quantify fluorogen-aptamer interactions. As proof-of-concept, we provide detailed protocols for the production of malachite green-binding RNA aptamer and DFHBI-binding Spinach RNA aptamer arrays. Furthermore, we discuss the potential utility of the technology to fluorogen-binding RNA aptamers, including application as a molecular biosensor platform. We anticipate that functional-RNA array technology will be beneficial for a wide variety of biological disciplines.
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Affiliation(s)
- Charlotte A Henderson
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Callum A Rail
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Louise E Butt
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Helen A Vincent
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom.
| | - Anastasia J Callaghan
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom.
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Lietard J, Somoza MM. Spotting, Transcription and In Situ Synthesis: Three Routes for the Fabrication of RNA Microarrays. Comput Struct Biotechnol J 2019; 17:862-868. [PMID: 31321002 PMCID: PMC6612525 DOI: 10.1016/j.csbj.2019.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/04/2019] [Accepted: 06/08/2019] [Indexed: 12/11/2022] Open
Abstract
DNA microarrays have become commonplace in the last two decades, but the synthesis of other nucleic acids biochips, most importantly RNA, has only recently been developed to a similar extent. RNA microarrays can be seen as organized surfaces displaying a potentially very large number of unique sequences and are of invaluable help in understanding the complexity of RNA structure and function as they allow the probing and treatment of each of the many different sequences simultaneously. Three approaches have emerged for the fabrication of RNA microarrays. The earliest examples used a direct, manual or mechanical, deposition of pre-synthesized, purified RNA oligonucleotides onto the surface in a process called spotting. In a second approach, pre-spotted or in situ-synthesized DNA microarrays are employed as templates for the transcription of RNA, subsequently or immediately captured on the surface. Finally, a third approach attempts to mirror the phosphoramidite-based protocols for in situ synthesis of high-density DNA arrays in order to produce in situ synthesized RNA microarrays. In this mini-review, we describe the chemistry and the engineering behind the fabrications methods, underlining the advantages and shortcomings of each, and illustrate how versatile these platforms can be by presenting some of their applications.
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12
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Norouzi M, Pickford AR, Butt LE, Vincent HA, Callaghan AJ. Application of mRNA Arrays for the Production of mCherry Reporter-Protein Arrays for Quantitative Gene Expression Analysis. ACS Synth Biol 2019; 8:207-215. [PMID: 30682244 DOI: 10.1021/acssynbio.8b00266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The development of programmable regulators that precisely and predictably control gene expression is a major goal of synthetic biology. Consequently, rapid high-throughput biochemical methods capable of quantitatively analyzing all components of gene expression would be of value in the characterization and optimization of regulator performance. In this study we demonstrate a novel application of RNA arrays, involving the production of reporter-protein arrays, to gene expression analysis. This method enables simultaneous quantification of both the transcription and post-transcription/translation components of gene expression, and it also allows the assessment of the orthogonality of multiple regulators. We use our method to directly compare the performance of a series of previously characterized synthetic post-transcriptional riboregulators, thus demonstrating its utility in the development of synthetic regulatory modules and evaluation of gene expression regulation in general.
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Affiliation(s)
- Masoud Norouzi
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Andrew R. Pickford
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Louise E. Butt
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Helen A. Vincent
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Anastasia J. Callaghan
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
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