1
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Gupta K, Krieg E. Y-switch: a spring-loaded synthetic gene switch for robust DNA/RNA signal amplification and detection. Nucleic Acids Res 2024:gkae680. [PMID: 39149901 DOI: 10.1093/nar/gkae680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 07/04/2024] [Accepted: 07/31/2024] [Indexed: 08/17/2024] Open
Abstract
Nucleic acid tests (NATs) are essential for biomedical diagnostics. Traditional NATs, often complex and expensive, have prompted the exploration of toehold-mediated strand displacement (TMSD) circuits as an economical alternative. However, the wide application of TMSD-based reactions is limited by 'leakage'-the spurious activation of the reaction leading to high background signals and false positives. Here, we introduce the Y-Switch, a new TMSD cascade design that recognizes a custom nucleic acid input and generates an amplified output. The Y-Switch is based on a pair of thermodynamically spring-loaded DNA modules. The binding of a predefined nucleic acid target triggers an intermolecular reaction that activates a T7 promoter, leading to the perpetual transcription of a fluorescent aptamer that can be detected by a smartphone camera. The system is designed to permit the selective depletion of leakage byproducts to achieve high sensitivity and zero-background signal in the absence of the correct trigger. Using Zika virus (ZIKV)- and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-derived nucleic acid sequences, we show that the assay generates a reliable target-specific readout. Y-Switches detect native RNA under isothermal conditions without reverse transcription or pre-amplification, with a detection threshold as low as ∼200 attomole. The modularity of the assay allows easy re-programming for the detection of other targets by exchanging a single sequence domain. This work provides a low-complexity and high-fidelity synthetic biology tool for point-of-care diagnostics and for the construction of more complex biomolecular computations.
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Affiliation(s)
- Krishna Gupta
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
- Faculty of Chemistry and Food Chemistry, TU Dresden, Dresden, Germany
| | - Elisha Krieg
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
- Faculty of Chemistry and Food Chemistry, TU Dresden, Dresden, Germany
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2
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Lokras AG, Bobak TR, Baghel SS, Sebastiani F, Foged C. Advances in the design and delivery of RNA vaccines for infectious diseases. Adv Drug Deliv Rev 2024; 213:115419. [PMID: 39111358 DOI: 10.1016/j.addr.2024.115419] [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: 03/01/2024] [Revised: 07/19/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024]
Abstract
RNA medicines represent a paradigm shift in treatment and prevention of critical diseases of global significance, e.g., infectious diseases. The highly successful messenger RNA (mRNA) vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were developed at record speed during the coronavirus disease 2019 pandemic. A consequence of this is exceptionally shortened vaccine development times, which in combination with adaptability makes the RNA vaccine technology highly attractive against infectious diseases and for pandemic preparedness. Here, we review state of the art in the design and delivery of RNA vaccines for infectious diseases based on different RNA modalities, including linear mRNA, self-amplifying RNA, trans-amplifying RNA, and circular RNA. We provide an overview of the clinical pipeline of RNA vaccines for infectious diseases, and present analytical procedures, which are paramount for characterizing quality attributes and guaranteeing their quality, and we discuss future perspectives for using RNA vaccines to combat pathogens beyond SARS-CoV-2.
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Affiliation(s)
- Abhijeet Girish Lokras
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Thomas Rønnemoes Bobak
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Saahil Sandeep Baghel
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Federica Sebastiani
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark; Division of Physical Chemistry, Department of Chemistry, Lund University, 22100, Lund, Sweden
| | - Camilla Foged
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark.
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3
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Metzner E, Southard KM, Norman TM. Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605307. [PMID: 39091800 PMCID: PMC11291144 DOI: 10.1101/2024.07.26.605307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Single-cell CRISPR screens link genetic perturbations to transcriptional states, but high-throughput methods connecting these induced changes to their regulatory foundations are limited. Here we introduce Multiome Perturb-seq, extending single-cell CRISPR screens to simultaneously measure perturbation-induced changes in gene expression and chromatin accessibility. We apply Multiome Perturb-seq in a CRISPRi screen of 13 chromatin remodelers in human RPE-1 cells, achieving efficient assignment of sgRNA identities to single nuclei via an improved method for capturing barcode transcripts from nuclear RNA. We organize expression and accessibility measurements into coherent programs describing the integrated effects of perturbations on cell state, finding that ARID1A and SUZ12 knockdowns induce programs enriched for developmental features. Pseudotime analysis of perturbations connects accessibility changes to changes in gene expression, highlighting the value of multimodal profiling. Overall, our method provides a scalable and simply implemented system to dissect the regulatory logic underpinning cell state.
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Affiliation(s)
- Eli Metzner
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - Kaden M. Southard
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thomas M. Norman
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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4
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Lenk R, Kleindienst W, Szabó GT, Baiersdörfer M, Boros G, Keller JM, Mahiny AJ, Vlatkovic I. Understanding the impact of in vitro transcription byproducts and contaminants. Front Mol Biosci 2024; 11:1426129. [PMID: 39050733 PMCID: PMC11266732 DOI: 10.3389/fmolb.2024.1426129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/14/2024] [Indexed: 07/27/2024] Open
Abstract
The success of messenger (m)RNA-based vaccines against SARS-CoV-2 during the COVID-19 pandemic has led to rapid growth and innovation in the field of mRNA-based therapeutics. However, mRNA production, whether in small amounts for research or large-scale GMP-grade for biopharmaceutics, is still based on the In Vitro Transcription (IVT) reaction developed in the early 1980s. The IVT reaction exploits phage RNA polymerase to catalyze the formation of an engineered mRNA that depends on a linearized DNA template, nucleotide building blocks, as well as pH, temperature, and reaction time. But depending on the IVT conditions and subsequent purification steps, diverse byproducts such as dsRNA, abortive RNAs and RNA:DNA hybrids might form. Unwanted byproducts, if not removed, could be formulated together with the full-length mRNA and cause an immune response in cells by activating host pattern recognition receptors. In this review, we summarize the potential types of IVT byproducts, their known biological activity, and how they can impact the efficacy and safety of mRNA therapeutics. In addition, we briefly overview non-nucleotide-based contaminants such as RNases, endotoxin and metal ions that, when present in the IVT reaction, can also influence the activity of mRNA-based drugs. We further discuss current approaches aimed at adjusting the IVT reaction conditions or improving mRNA purification to achieve optimal performance for medical applications.
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5
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Jung JK, Dreyer KS, Dray KE, Muldoon JJ, George J, Shirman S, Cabezas MD, D’Aquino AE, Verosloff MS, Seki K, Rybnicky GA, Alam KK, Bagheri N, Jewett MC, Leonard JN, Mangan NM, Lucks JB. Developing, characterizing and modeling CRISPR-based point-of-use pathogen diagnostics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601853. [PMID: 39005318 PMCID: PMC11244977 DOI: 10.1101/2024.07.03.601853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Recent years have seen intense interest in the development of point-of-care nucleic acid diagnostic technologies to address the scaling limitations of laboratory-based approaches. Chief among these are combinations of isothermal amplification approaches with CRISPR-based detection and readouts of target products. Here, we contribute to the growing body of rapid, programmable point-of-care pathogen tests by developing and optimizing a one-pot NASBA-Cas13a nucleic acid detection assay. This test uses the isothermal amplification technique NASBA to amplify target viral nucleic acids, followed by Cas13a-based detection of amplified sequences. We first demonstrate an in-house formulation of NASBA that enables optimization of individual NASBA components. We then present design rules for NASBA primer sets and LbuCas13a guide RNAs for fast and sensitive detection of SARS-CoV-2 viral RNA fragments, resulting in 20 - 200 aM sensitivity without any specialized equipment. Finally, we explore the combination of high-throughput assay condition screening with mechanistic ordinary differential equation modeling of the reaction scheme to gain a deeper understanding of the NASBA-Cas13a system. This work presents a framework for developing a mechanistic understanding of reaction performance and optimization that uses both experiments and modeling, which we anticipate will be useful in developing future nucleic acid detection technologies.
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Affiliation(s)
- Jaeyoung K. Jung
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Center for Water Research, Northwestern University (Evanston, IL, USA)
| | - Kathleen S. Dreyer
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
| | - Kate E. Dray
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
| | - Joseph J. Muldoon
- Department of Medicine, University of California, San Francisco (San Francisco, CA, USA)
- Gladstone-UCSF Institute of Genomic Immunology (San Francisco, CA, USA)
| | - Jithin George
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Department of Engineering Sciences and Applied Mathematics, Northwestern University (Evanston, IL, USA)
- NSF-Simons Center for Quantitative Biology, Northwestern University (Evanston, IL, USA)
| | - Sasha Shirman
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- NSF-Simons Center for Quantitative Biology, Northwestern University (Evanston, IL, USA)
| | - Maria D. Cabezas
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Department of Biomedical Engineering, Northwestern University (Evanston, IL, USA)
| | - Anne E. D’Aquino
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Stemloop, Inc. (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
| | - Matthew S. Verosloff
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
| | - Kosuke Seki
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
| | - Grant A. Rybnicky
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
- Chemistry of Life Processes Institute, Northwestern University (Evanston, IL, USA)
| | | | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
- Departments of Biology and Chemical Engineering, University of Washington (Seattle, WA, USA)
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Department of Bioengineering, Stanford University (Stanford, CA)
| | - Joshua N. Leonard
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Interdisciplinary Biological Sciences Program, Northwestern University (Evanston, IL, USA)
| | - Niall M. Mangan
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Department of Engineering Sciences and Applied Mathematics, Northwestern University (Evanston, IL, USA)
- NSF-Simons Center for Quantitative Biology, Northwestern University (Evanston, IL, USA)
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University (Evanston IL, USA)
- Center for Synthetic Biology, Northwestern University (Evanston, IL, USA)
- Center for Water Research, Northwestern University (Evanston, IL, USA)
- Chemistry of Life Processes Institute, Northwestern University (Evanston, IL, USA)
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6
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Bhamidimarri PM, Salameh L, Mahdami A, Abdullah HW, Mahboub B, Hamoudi R. LINCATRA: Two-cycle method to amplify RNA for transcriptome analysis from formalin-fixed paraffin-embedded tissue. Heliyon 2024; 10:e32896. [PMID: 38988576 PMCID: PMC11234047 DOI: 10.1016/j.heliyon.2024.e32896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024] Open
Abstract
Whole transcriptome analysis (WTA) using RNA extracted from Formalin Fixed Paraffin Embedded (FFPE) tissue is an invaluable tool to understand the molecular pathology of disease. RNA extracted from FFPE tissue is either degraded and/or in very low quantities hampering gene expression analysis. Earlier studies described protocols applied for cellular RNA using poly-A primer-based linear amplification. The current study describes a method, LINCATRA (LINear amplifiCAtion of RNA for whole TRAnscriptome analysis). It employs random nonamer primer based method which can amplify short, fragmented RNA with high fidelity from as low as 5 ng to obtain enough material for WTA. The two-cycle method significantly amplified RNA at ∼1000 folds (p < 0.0001) improving the mean read lengths (p < 0.05) in WTA. Overall, increased mean read length positively correlated with on-target reads (Pearson's r = 0.71, p < 0.0001) in both amplified and unamplified RNA-seq analysis. Gene expression analysis compared between unamplified and amplified group displayed substantial overlap of the differentially expressed genes (DEGs) (log2 fold change cut-off < -2 and >2, p < 0.05) identified between lung cancer and asthma cohorts validating the method developed. This method is applicable in clinical molecular pathology field for both diagnostics and elucidation of disease mechanisms.
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Affiliation(s)
- Poorna Manasa Bhamidimarri
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Laila Salameh
- Rashid Hospital, Dubai Health, Dubai, 4545, United Arab Emirates
| | - Amena Mahdami
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Hanan Wael Abdullah
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Bassam Mahboub
- Rashid Hospital, Dubai Health, Dubai, 4545, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Sciences, University College London, London, United Kingdom
- BIMAI-Lab, Biomedically Informed Artificial Inelligence Laboratory, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Centre of Excelence for Precision Medicine, Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
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7
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Evans NM, Shivers LR, To AJ, Murphy GK, Dieckmann T. Biophysical characterization and design of a minimal version of the Hoechst RNA aptamer. Biochem Biophys Res Commun 2024; 711:149908. [PMID: 38613867 DOI: 10.1016/j.bbrc.2024.149908] [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] [Received: 02/02/2024] [Revised: 03/24/2024] [Accepted: 04/05/2024] [Indexed: 04/15/2024]
Abstract
RNA aptamers are oligonucleotides, selected through Systematic Evolution of Ligands by EXponential Enrichment (SELEX), that can bind to specific target molecules with high affinity. One such molecule is the RNA aptamer that binds to a blue-fluorescent Hoechst dye that was modified with bulky t-Bu groups to prevent non-specific binding to DNA. This aptamer has potential for biosensor applications; however, limited information is available regarding its conformation, molecular interactions with the ligand, and binding mechanism. The study presented here aims to biophysically characterize the Hoechst RNA aptamer when complexed with the t-Bu Hoechst dye and to further optimize the RNA sequence by designing and synthesizing new sequence variants. Each variant aptamer-t-Bu Hoechst complex was evaluated through a combination of fluorescence emission, native polyacrylamide gel electrophoresis, fluorescence titration, and isothermal titration calorimetry experiments. The results were used to design a minimal version of the aptamer consisting of only 21 nucleotides. The performed study also describes a more efficient method for synthesizing the t-Bu Hoechst dye derivative. Understanding the biophysical properties of the t-Bu Hoechst dye-RNA complex lays the foundation for nuclear magnetic resonance spectroscopy studies and its potential development as a building block for an aptamer-based biosensor that can be used in medical, environmental or laboratory settings.
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Affiliation(s)
- Natasha M Evans
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Lindsey R Shivers
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Avery J To
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Graham K Murphy
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Thorsten Dieckmann
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
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8
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Curry E, Sedelnikova S, Rafferty J, Hulley M, Pohle M, Muir G, Brown A. Expanding the RNA polymerase biocatalyst solution space for mRNA manufacture. Biotechnol J 2024; 19:e2400012. [PMID: 39031865 DOI: 10.1002/biot.202400012] [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: 01/05/2024] [Revised: 05/13/2024] [Accepted: 05/27/2024] [Indexed: 07/22/2024]
Abstract
All mRNA products are currently manufactured in in vitro transcription (IVT) reactions that utilize single-subunit RNA polymerase (RNAP) biocatalysts. Although it is known that discrete polymerases exhibit highly variable bioproduction phenotypes, including different relative processivity rates and impurity generation profiles, only a handful of enzymes are generally available for mRNA biosynthesis. This limited RNAP toolbox restricts strategies to design and troubleshoot new mRNA manufacturing processes, which is particularly undesirable given the continuing diversification of mRNA product lines toward larger and more complex molecules. Herein, we describe development of a high-throughput RNAP screening platform, comprising complementary in silico and in vitro testing modules, that enables functional characterization of large enzyme libraries. Utilizing this system, we identified eight novel sequence-diverse RNAPs, with associated active cognate promoters, and subsequently validated their performance as recombinant enzymes in IVT-based mRNA production processes. By increasing the number of available characterized functional RNAPs by more than 130% and providing a platform to rapidly identify further potentially useful enzymes, this work significantly expands the RNAP biocatalyst solution space for mRNA manufacture, thereby enhancing the capability for application-specific and molecule-specific optimization of both product yield and quality.
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Affiliation(s)
- Edward Curry
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | | | - John Rafferty
- School of Biosciences, University of Sheffield, Sheffield, UK
| | | | - Melinda Pohle
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - George Muir
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Adam Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
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9
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He W, Zhang X, Zou Y, Li J, Wang C, He Y, Jin Q, Ye J. Effective Synthesis of High-Integrity mRNA Using In Vitro Transcription. Molecules 2024; 29:2461. [PMID: 38893337 PMCID: PMC11173937 DOI: 10.3390/molecules29112461] [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] [Received: 04/10/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
mRNA vaccines are entering a period of rapid development. However, their synthesis is still plagued by challenges related to mRNA impurities and fragments (incomplete mRNA). Most impurities of mRNA products transcribed in vitro are mRNA fragments. Only full-length mRNA transcripts containing both a 5'-cap and a 3'-poly(A) structure are viable for in vivo expression. Therefore, RNA fragments are the primary product-related impurities that significantly hinder mRNA efficacy and must be effectively controlled; these species are believed to originate from either mRNA hydrolysis or premature transcriptional termination. In the manufacturing of commercial mRNA vaccines, T7 RNA polymerase-catalyzed in vitro transcription (IVT) synthesis is a well-established method for synthesizing long RNA transcripts. This study identified a pivotal domain on the T7 RNA polymerase that is associated with erroneous mRNA release. By leveraging the advantageous properties of a T7 RNA polymerase mutant and precisely optimized IVT process parameters, we successfully achieved an mRNA integrity exceeding 91%, thereby further unlocking the immense potential of mRNA therapeutics.
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Affiliation(s)
- Wei He
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China;
- Vazyme Biotech Co., Ltd., Nanjing 210037, China; (X.Z.); (Y.Z.); (J.L.); (C.W.)
| | - Xinya Zhang
- Vazyme Biotech Co., Ltd., Nanjing 210037, China; (X.Z.); (Y.Z.); (J.L.); (C.W.)
| | - Yangxiaoyu Zou
- Vazyme Biotech Co., Ltd., Nanjing 210037, China; (X.Z.); (Y.Z.); (J.L.); (C.W.)
| | - Ji Li
- Vazyme Biotech Co., Ltd., Nanjing 210037, China; (X.Z.); (Y.Z.); (J.L.); (C.W.)
| | - Chong Wang
- Vazyme Biotech Co., Ltd., Nanjing 210037, China; (X.Z.); (Y.Z.); (J.L.); (C.W.)
| | - Yucai He
- School of Pharmacy, Changzhou University, Changzhou 213164, China
| | - Qiuheng Jin
- Vazyme Biotech Co., Ltd., Nanjing 210037, China; (X.Z.); (Y.Z.); (J.L.); (C.W.)
| | - Jianren Ye
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China;
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10
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Popova PG, Lagace MA, Tang G, Blakney AK. Effect of in vitro transcription conditions on yield of high quality messenger and self-amplifying RNA. Eur J Pharm Biopharm 2024; 198:114247. [PMID: 38462138 DOI: 10.1016/j.ejpb.2024.114247] [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] [Received: 10/16/2023] [Revised: 02/12/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
Messenger RNA (mRNA) and self-amplifying RNA (saRNA) vaccines against SARS-CoV-2 produced using in vitro transcription (IVT) were clinically approved in 2020 and 2022, respectively. While the industrial production of mRNA using IVT has been extensively optimized, the optimal conditions for saRNA have been explored to a lesser extent. Most T7 polymerase IVT protocols have been specifically optimized for mRNA which is ∼5-10-fold smaller than saRNA and may have profound effects on both the quality and yield of longer transcripts. Here, we optimized IVT conditions for simultaneously increasing the yield of full-length transcripts and reducing dsRNA formation through Design of Experiments. Using a definitive screening approach, we found that the key parameters are temperature and magnesium in the outcome of RNA quality (% full length transcript) and yield in small scale synthesis. The most important parameter for reducing dsRNA formation for both mRNA and saRNA was Mg2+ concentration (10 mM). We observed that a lower temperature was vital for production of high quality saRNA transcripts. mRNA quality was optimal at higher Mg2+ concentration (>40 mM). High quality transcripts correspond to significantly reduced product yield for saRNA, but not for mRNA. The differences between mRNA and saRNA requirements for high quality product and the relationship between high quality large saRNA molecules and low temperature synthesis have not been reported previously. These findings are key for informing future IVT parameters design and optimization for smaller and larger RNA transcripts.
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Affiliation(s)
- Petya G Popova
- Michael Smith Laboratories, School of Biomedical Engineering, University of British Columbia, Canada
| | - Melissa A Lagace
- Michael Smith Laboratories, School of Biomedical Engineering, University of British Columbia, Canada
| | - George Tang
- Michael Smith Laboratories, School of Biomedical Engineering, University of British Columbia, Canada
| | - Anna K Blakney
- Michael Smith Laboratories, School of Biomedical Engineering, University of British Columbia, Canada.
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11
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Sari Y, Sousa Rosa S, Jeffries J, Marques MPC. Comprehensive evaluation of T7 promoter for enhanced yield and quality in mRNA production. Sci Rep 2024; 14:9655. [PMID: 38671016 PMCID: PMC11053036 DOI: 10.1038/s41598-024-59978-5] [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: 12/12/2023] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
The manufacturing of mRNA vaccines relies on cell-free based systems that are easily scalable and flexible compared with the traditional vaccine manufacturing processes. Typically, standard processes yield 2 to 5 g L-1 of mRNA, with recent process optimisations increasing yields to 12 g L-1. However, increasing yields can lead to an increase in the production of unwanted by-products, namely dsRNA. It is therefore imperative to reduce dsRNA to residual levels in order to avoid intensive purification steps, enabling cost-effective manufacturing processes. In this work, we exploit sequence modifications downstream of the T7 RNA polymerase promoter to increase mRNA yields whilst simultaneously minimising dsRNA. In particular, transcription performance was optimised by modifying the sequence downstream of the T7 promoter with additional AT-rich sequences. We have identified variants that were able to produce higher amounts of mRNA (up to 14 g L-1) in 45 min of reaction. These variants exhibited up to a 30% reduction in dsRNA byproduct levels compared to a wildtype T7 promoter, and have similar EGFP protein expression. The results show that optimising the non-coding regions can have an impact on mRNA production yields and quality, reducing overall manufacturing costs.
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Affiliation(s)
- Yustika Sari
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1E 6BT, UK
| | - Sara Sousa Rosa
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1E 6BT, UK
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Jack Jeffries
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1E 6BT, UK
| | - Marco P C Marques
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1E 6BT, UK.
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12
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Brunderová M, Havlíček V, Matyašovský J, Pohl R, Poštová Slavětínská L, Krömer M, Hocek M. Expedient production of site specifically nucleobase-labelled or hypermodified RNA with engineered thermophilic DNA polymerases. Nat Commun 2024; 15:3054. [PMID: 38594306 PMCID: PMC11004144 DOI: 10.1038/s41467-024-47444-9] [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: 10/28/2023] [Accepted: 03/26/2024] [Indexed: 04/11/2024] Open
Abstract
Innovative approaches to controlled nucleobase-modified RNA synthesis are urgently needed to support RNA biology exploration and to synthesize potential RNA therapeutics. Here we present a strategy for enzymatic construction of nucleobase-modified RNA based on primer-dependent engineered thermophilic DNA polymerases - SFM4-3 and TGK. We demonstrate introduction of one or several different base-modified nucleotides in one strand including hypermodified RNA containing all four modified nucleotides bearing four different substituents, as well as strategy for primer segment removal. We also show facile site-specific or segmented introduction of fluorophores or other functional groups at defined positions in variety of RNA molecules, including structured or long mRNA. Intriguing translation efficacy of single-site modified mRNAs underscores the necessity to study isolated modifications placed at designer positions to disentangle their biological effects and enable development of improved mRNA therapeutics. Our toolbox paves the way for more precise dissecting RNA structures and functions, as well as for construction of diverse types of base-functionalized RNA for therapeutic applications and diagnostics.
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Affiliation(s)
- Mária Brunderová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Vojtěch Havlíček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic
| | - Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic.
- The Rosalind Franklin Institute, Harwell Campus, Didcot, Oxfordshire, UK.
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic.
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic.
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13
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Balke I, Silamikelis I, Radovica-Spalvina I, Zeltina V, Resevica G, Fridmanis D, Zeltins A. Ryegrass mottle virus complete genome determination and development of infectious cDNA by combining two methods- 3' RACE and RNA-Seq. PLoS One 2023; 18:e0287278. [PMID: 38051715 DOI: 10.1371/journal.pone.0287278] [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: 06/02/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023] Open
Abstract
Ryegrass mottle virus (RGMoV; genus: Sobemovirus) is a single-stranded positive RNA virus with a 30 nm viral particle size. It exhibits T = 3 symmetry with 180 coat protein (CP) subunits forming a viral structure. The RGMoV genome comprises five open reading frames that encode P1, Px, a membrane-anchored 3C-like serine protease, a viral genome-linked protein, P16, an RNA-dependent RNA polymerase, and CP. The RGMoV genome size varies, ranging from 4175 nt (MW411579.1) to 4253 nt (MW411579.1) in the deposited sequences. An earlier deposited RGMoV complete genome sequence of 4212 nt length (EF091714.1) was used to develop an infectious complementary DNA (icDNA) construct for in vitro gRNA transcription from the T7 promoter. However, viral infection was not induced when the transcribed gRNA was introduced into oat plants, indicating the potential absence of certain sequences in either the 5' or 3' untranslated regions (UTR) or both. The complete sequence of the 3' UTR was determined through 3' end RACE, while the 5' UTR was identified using high-throughput sequencing (HTS)-RNA-Seq to resolve the potential absences. Only the icDNA vector containing the newly identified UTR sequences proved infectious, resulting in typical viral infection symptoms and subsequent propagation of progeny viruses, exhibiting the ability to cause repeated infections in oat plants after at least one passage. The successful generation of icDNA highlighted the synergistic potential of utilizing both methods when a single approach failed. Furthermore, this study demonstrated the reliability of HTS as a method for determining the complete genome sequence of viral genomes.
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Affiliation(s)
- Ina Balke
- Plant Virus Protein Research Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ivars Silamikelis
- Bioinformatics Core Facility, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ilze Radovica-Spalvina
- Genome Centre, Genotyping and Sequencing Unit, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Vilija Zeltina
- Plant Virology Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Gunta Resevica
- Plant Virology Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Davids Fridmanis
- "Exotic" Site Microbiome and G-Protein Coupled Receptor Functional Research Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Andris Zeltins
- Plant Virology Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
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14
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Deo S, Desai K, Patare A, Wadapurkar R, Rade S, Mahudkar S, Sathe M, Srivastava S, Prasanna P, Singh A. Evaluation of self-amplifying mRNA platform for protein expression and genetic stability: Implication for mRNA therapies. Biochem Biophys Res Commun 2023; 680:108-118. [PMID: 37738900 DOI: 10.1016/j.bbrc.2023.09.016] [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: 06/20/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/24/2023]
Abstract
The consecutive launch of mRNA vaccines like mRNA-1273, BNT 162b2, and GEMCOVAC®-19 against COVID-19 has triggered the debate of long-term expression, safety, and genomic integration of the mRNA vaccine platforms. In the present study, we examined the longevity of antigenic protein expression of mRNA-614 and mRNA-S1LC based on self-amplifying mRNA (SAM) in Expi-293F™, HEK-293 T, and ARPE-19 cells. The protein expression was checked by sandwich-ELISA, FACS, luciferase activity assay, and Western blot. The transcribed antigenic mRNA was sequenced and found to be un-mutated. Additionally, no genomic integration of the reverse transcribed mRNA was observed even up to 7 days post-transfection as verified by PCR. Furthermore, we have generated high-quality 3D structures of non-structural proteins (nsPs) in silico and the genes encoding for the nsPs were cloned and expressed using the T7 system. Findings from the current study have strengthened the fact that the alphavirus-based SAM platform has the potential to become a modality in the upcoming years.
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Affiliation(s)
- Swarda Deo
- Gennova Biopharmaceuticals Ltd. ITBT Park, Hinjawadi Phase 2 Road, Hinjawadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Kaushik Desai
- Gennova Biopharmaceuticals Ltd. ITBT Park, Hinjawadi Phase 2 Road, Hinjawadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Aishwarya Patare
- Gennova Biopharmaceuticals Ltd. ITBT Park, Hinjawadi Phase 2 Road, Hinjawadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Rucha Wadapurkar
- Gennova Biopharmaceuticals Ltd. ITBT Park, Hinjawadi Phase 2 Road, Hinjawadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Saniya Rade
- Gennova Biopharmaceuticals Ltd. ITBT Park, Hinjawadi Phase 2 Road, Hinjawadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Siddhi Mahudkar
- Gennova Biopharmaceuticals Ltd. ITBT Park, Hinjawadi Phase 2 Road, Hinjawadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Madhura Sathe
- Gennova Biopharmaceuticals Ltd. ITBT Park, Hinjawadi Phase 2 Road, Hinjawadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Shalini Srivastava
- Gennova Biopharmaceuticals Ltd. ITBT Park, Hinjawadi Phase 2 Road, Hinjawadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Pragya Prasanna
- Gennova Biopharmaceuticals Ltd. ITBT Park, Hinjawadi Phase 2 Road, Hinjawadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Ajay Singh
- Gennova Biopharmaceuticals Ltd. ITBT Park, Hinjawadi Phase 2 Road, Hinjawadi Rajiv Gandhi Infotech Park, Hinjawadi, Pune, Maharashtra, 411057, India.
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15
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Ting WW, Ng IS. Tunable T7 Promoter Orthogonality on T7RNAP for cis-Aconitate Decarboxylase Evolution via Base Editor and Screening from Itaconic Acid Biosensor. ACS Synth Biol 2023; 12:3020-3029. [PMID: 37750409 PMCID: PMC10595973 DOI: 10.1021/acssynbio.3c00344] [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: 06/05/2023] [Indexed: 09/27/2023]
Abstract
The deaminase-fused T7 RNA polymerase (T7RNAP) presents a promising toolkit for in vivo target-specific enzyme evolution, offering the unique advantage of simultaneous DNA modification and screening. Previous studies have reported the mutation efficiency of base editors relying on different resources. In contrast, the mechanism underlying the T7RNAP/T7 system is well-understood. Therefore, this study aimed to establish a new platform, termed dT7-Muta, by tuning the binding efficiency between T7RNAP and the T7 promoter for gene mutagenesis. The strategy for proof-of-concept involves alterations in the fluorescence distribution through dT7-Muta and screening of the mutants via flow cytometry. The cis-aconitate decarboxylase from Aspergillus terreus (AtCadA) was evolved and screened via an itaconate-induced biosensor as proof-of-function of enzyme evolution. First, the degenerated codons were designed within the binding and initial region of T7 promoters (dT7s), including upstream (U), central (C), and downstream (D) regions. Three strength variants of dT7 promoter from each design, i.e., strong (S), medium (M), and weak (W), were used for evaluation. Mutation using dT7s of varying strength resulted in a broader fluorescence distribution in sfGFP mutants from the promoters CW and DS. On the other hand, broader fluorescence distribution was observed in the AtCadA mutants from the original promoter T7, UW, and DS, with the highest fluorescence and itaconic acid titer at 860 a.u. and 0.51 g/L, respectively. The present platform introduces a novel aspect of the deaminase-based mutagenesis, emphasizing the potential of altering the binding efficiency between T7RNAP and the T7 promoter for further efforts in enzyme evolution.
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Affiliation(s)
- Wan-Wen Ting
- Department of Chemical
Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - I-Son Ng
- Department of Chemical
Engineering, National Cheng Kung University, Tainan 70101, Taiwan
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16
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Lee H, Xie T, Yu X, Schaffter SW, Schulman R. Plug-and-play protein biosensors using aptamer-regulated in vitro transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552680. [PMID: 37645783 PMCID: PMC10461910 DOI: 10.1101/2023.08.10.552680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Molecular biosensors that accurately measure protein concentrations without external equipment are critical for solving numerous problems in diagnostics and therapeutics. Modularly transducing the binding of protein antibodies, protein switches or aptamers into a useful output remains challenging. Here, we develop a biosensing platform based on aptamer-regulated transcription in which aptamers integrated into transcription templates serve as inputs to molecular circuits that can be programmed to a produce a variety of responses. We modularly design molecular biosensors using this platform by swapping aptamer domains for specific proteins and downstream domains that encode different RNA transcripts. By coupling aptamer-regulated transcription with diverse transduction circuits, we rapidly construct analog protein biosensors or digital protein biosensors with detection ranges that can be tuned over two orders of magnitude. Aptamer-regulated transcription is a straightforward and inexpensive approach for constructing programmable protein biosensors suitable for diverse research and diagnostic applications.
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Affiliation(s)
- Heonjoon Lee
- Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21218
| | - Tian Xie
- Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Xinjie Yu
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | | | - Rebecca Schulman
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
- Computer Science, Johns Hopkins University, Baltimore, MD 21218
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17
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Kang DD, Li H, Dong Y. Advancements of in vitro transcribed mRNA (IVT mRNA) to enable translation into the clinics. Adv Drug Deliv Rev 2023; 199:114961. [PMID: 37321375 PMCID: PMC10264168 DOI: 10.1016/j.addr.2023.114961] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
The accelerated progress and approval of two mRNA-based vaccines to address the SARS-CoV-2 virus were unprecedented. This record-setting feat was made possible through the solid foundation of research on in vitro transcribed mRNA (IVT mRNA) which could be utilized as a therapeutic modality. Through decades of thorough research to overcome barriers to implementation, mRNA-based vaccines or therapeutics offer many advantages to rapidly address a broad range of applications including infectious diseases, cancers, and gene editing. Here, we describe the advances that have supported the adoption of IVT mRNA in the clinics, including optimization of the IVT mRNA structural components, synthesis, and lastly concluding with different classes of IVT RNA. Continuing interest in driving IVT mRNA technology will enable a safer and more efficacious therapeutic modality to address emerging and existing diseases.
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Affiliation(s)
- Diana D Kang
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Haoyuan Li
- Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Yizhou Dong
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Department of Biomedical Engineering, The Center for Clinical and Translational Science, The Comprehensive Cancer Center; Dorothy M. Davis Heart & Lung Research Institute, Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, United States; Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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18
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Dousis A, Ravichandran K, Hobert EM, Moore MJ, Rabideau AE. An engineered T7 RNA polymerase that produces mRNA free of immunostimulatory byproducts. Nat Biotechnol 2023; 41:560-568. [PMID: 36357718 PMCID: PMC10110463 DOI: 10.1038/s41587-022-01525-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 09/22/2022] [Indexed: 11/12/2022]
Abstract
In vitro transcription (IVT) is a DNA-templated process for synthesizing long RNA transcripts, including messenger RNA (mRNA). For many research and commercial applications, IVT of mRNA is typically performed using bacteriophage T7 RNA polymerase (T7 RNAP) owing to its ability to produce full-length RNA transcripts with high fidelity; however, T7 RNAP can also produce immunostimulatory byproducts such as double-stranded RNA that can affect protein expression. Such byproducts require complex purification processes, using methods such as reversed-phase high-performance liquid chromatography, to yield safe and effective mRNA-based medicines. To minimize the need for downstream purification processes, we rationally and computationally engineered a double mutant of T7 RNAP that produces substantially less immunostimulatory RNA during IVT compared with wild-type T7 RNAP. The resulting mutant allows for a simplified production process with similar mRNA potency, lower immunostimulatory content and quicker manufacturing time compared with wild-type T7 RNAP. Herein, we describe the computational design and development of this improved T7 RNAP variant.
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Affiliation(s)
- Athanasios Dousis
- Moderna, Inc., Cambridge, MA, USA
- Tessera Therapeutics, Somerville, MA, USA
| | | | - Elissa M Hobert
- Moderna, Inc., Cambridge, MA, USA
- Laronde, Cambridge, MA, USA
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19
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Deich C, Cash B, Sato W, Sharon J, Aufdembrink L, Gaut NJ, Heili J, Stokes K, Engelhart AE, Adamala KP. T7Max transcription system. J Biol Eng 2023; 17:4. [PMID: 36691081 PMCID: PMC9872363 DOI: 10.1186/s13036-023-00323-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 01/04/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Efficient cell-free protein expression from linear DNA templates has remained a challenge primarily due to template degradation. In addition, the yields of transcription in cell-free systems lag behind transcriptional efficiency of live cells. Most commonly used in vitro translation systems utilize T7 RNA polymerase, which is also the enzyme included in many commercial kits. RESULTS Here we present characterization of a variant of T7 RNA polymerase promoter that acts to significantly increase the yields of gene expression within in vitro systems. We have demonstrated that T7Max increases the yield of translation in many types of commonly used in vitro protein expression systems. We also demonstrated increased protein expression yields from linear templates, allowing the use of T7Max driven expression from linear templates. CONCLUSIONS The modified promoter, termed T7Max, recruits standard T7 RNA polymerase, so no protein engineering is needed to take advantage of this method. This technique could be used with any T7 RNA polymerase- based in vitro protein expression system.
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Affiliation(s)
- Christopher Deich
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Brock Cash
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Wakana Sato
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Judee Sharon
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Lauren Aufdembrink
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Nathaniel J Gaut
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Joseph Heili
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Kaitlin Stokes
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Aaron E Engelhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
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20
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Zabolotskii AI, Kozlovskiy SV, Katrukha AG. The Influence of the Nucleotide Composition of Genes and Gene Regulatory Elements on the Efficiency of Protein Expression in Escherichia coli. BIOCHEMISTRY (MOSCOW) 2023; 88:S176-S191. [PMID: 37069120 DOI: 10.1134/s0006297923140109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Recombinant proteins expressed in Escherichia coli are widely used in biochemical research and industrial processes. At the same time, achieving higher protein expression levels and correct protein folding still remains the key problem, since optimization of nutrient media, growth conditions, and methods for induction of protein synthesis do not always lead to the desired result. Often, low protein expression is determined by the sequences of the expressed genes and their regulatory regions. The genetic code is degenerated; 18 out of 20 amino acids are encoded by more than one codon. Choosing between synonymous codons in the coding sequence can significantly affect the level of protein expression and protein folding due to the influence of the gene nucleotide composition on the probability of formation of secondary mRNA structures that affect the ribosome binding at the translation initiation phase, as well as the ribosome movement along the mRNA during elongation, which, in turn, influences the mRNA degradation and the folding of the nascent protein. The nucleotide composition of the mRNA untranslated regions, in particular the promoter and Shine-Dalgarno sequences, also affects the efficiency of mRNA transcription, translation, and degradation. In this review, we describe the genetic principles that determine the efficiency of protein production in Escherichia coli.
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Affiliation(s)
- Artur I Zabolotskii
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | | | - Alexey G Katrukha
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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21
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Avcilar-Kucukgoze I, Kashina AS. Preparation of tRNA Arg for Arginylation Assay by In Vitro Transcription. Methods Mol Biol 2023; 2620:93-99. [PMID: 37010753 DOI: 10.1007/978-1-0716-2942-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
This chapter describes the preparation of tRNAArg by in vitro transcription. tRNA produced by this method can be efficiently utilized for in vitro arginylation assays, following aminoacylation with Arg-tRNA synthetase, either directly during the arginylation reaction or separately to produce the purified preparation of Arg-tRNAArg. tRNA charging is described in other chapters of this book.
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Affiliation(s)
- Irem Avcilar-Kucukgoze
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anna S Kashina
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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22
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Senda N, Enomoto T, Kihara K, Yamashiro N, Takagi N, Kiga D, Nishida H. Development of an expression-tunable multiple protein synthesis system in cell-free reactions using T7-promoter-variant series. SYNTHETIC BIOLOGY (OXFORD, ENGLAND) 2022; 7:ysac029. [PMID: 36591595 PMCID: PMC9791696 DOI: 10.1093/synbio/ysac029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 11/01/2022] [Accepted: 11/24/2022] [Indexed: 11/27/2022]
Abstract
New materials with a low environmental load are expected to be generated through synthetic biology. To widely utilize this technology, it is important to create cells with designed biological functions and to control the expression of multiple enzymes. In this study, we constructed a cell-free evaluation system for multiple protein expression, in which synthesis is controlled by T7 promoter variants. The expression of a single protein using the T7 promoter variants showed the expected variety in expression levels, as previously reported. We then examined the expression levels of multiple proteins that are simultaneously produced in a single well to determine whether they can be predicted from the promoter activity values, which were defined from the isolated protein expression levels. When the sum of messenger ribonucleic acid (mRNA) species is small, the experimental protein expression levels can be predicted from the promoter activities (graphical abstract (a)) due to low competition for ribosomes. In other words, by using combinations of T7 promoter variants, we successfully developed a cell-free multiple protein synthesis system with tunable expression. In the presence of large amounts of mRNA, competition for ribosomes becomes an issue (graphical abstract (b)). Accordingly, the translation level of each protein cannot be directly predicted from the promoter activities and is biased by the strength of the ribosome binding site (RBS); a weaker RBS is more affected by competition. Our study provides information regarding the regulated expression of multiple enzymes in synthetic biology.
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Affiliation(s)
| | - Toshihiko Enomoto
- Department of Electrical Engineering and Bioscience, Waseda University, Shinjuku, Tokyo, Japan
| | - Kenta Kihara
- Department of Electrical Engineering and Bioscience, Waseda University, Shinjuku, Tokyo, Japan
| | - Naoki Yamashiro
- Department of Electrical Engineering and Bioscience, Waseda University, Shinjuku, Tokyo, Japan
| | - Naosato Takagi
- Department of Electrical Engineering and Bioscience, Waseda University, Shinjuku, Tokyo, Japan
| | - Daisuke Kiga
- Department of Electrical Engineering and Bioscience, Waseda University, Shinjuku, Tokyo, Japan
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23
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Pourseif MM, Masoudi-Sobhanzadeh Y, Azari E, Parvizpour S, Barar J, Ansari R, Omidi Y. Self-amplifying mRNA vaccines: Mode of action, design, development and optimization. Drug Discov Today 2022; 27:103341. [PMID: 35988718 DOI: 10.1016/j.drudis.2022.103341] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 07/14/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022]
Abstract
The mRNA-based vaccines are quality-by-design (QbD) immunotherapies that provide safe, tunable, scalable, streamlined and potent treatment possibilities against different types of diseases. The self-amplifying mRNA (saRNA) vaccines, as a highly advantageous class of mRNA vaccines, are inspired by the intracellular self-multiplication nature of some positive-sense RNA viruses. Such vaccine platforms provide a relatively increased expression level of vaccine antigen(s) together with self-adjuvanticity properties. Lined with the QbD saRNA vaccines, essential optimizations improve the stability, safety, and immunogenicity of the vaccine constructs. Here, we elaborate on the concepts and mode-of-action of mRNA and saRNA vaccines, articulate the potential limitations or technical bottlenecks, and explain possible solutions or optimization methods in the process of their design and development.
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Affiliation(s)
- Mohammad M Pourseif
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yosef Masoudi-Sobhanzadeh
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Erfan Azari
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Rais Ansari
- Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Fort Lauderdale, Florida, USA
| | - Yadollah Omidi
- Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Fort Lauderdale, Florida, USA.
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24
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Qin W, Li L, Yang F, Wang S, Yang GY. High-throughput iSpinach fluorescent aptamer-based real-time monitoring of in vitro transcription. BIORESOUR BIOPROCESS 2022; 9:112. [PMID: 38647769 PMCID: PMC10991154 DOI: 10.1186/s40643-022-00598-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
In vitro transcription (IVT) is an essential technique for RNA synthesis. Methods for the accurate and rapid screening of IVT conditions will facilitate RNA polymerase engineering, promoter optimization, and screening for new transcription inhibitor drugs. However, traditional polyacrylamide gel electrophoresis (PAGE) and high-performance liquid chromatography methods are labor intensive, time consuming and not compatible with real-time analysis. Here, we developed an inexpensive, high-throughput, and real-time detection method for the monitoring of in vitro RNA synthesis called iSpinach aptamer-based monitoring of Transcription Activity in Real-time (STAR). STAR has a detection speed at least 100 times faster than conventional PAGE method and provides comparable results in the analysis of in vitro RNA synthesis reactions. It also can be used as an easy and quantitative method to detect the catalytic activity of T7 RNA polymerase. To further demonstrate the utility of STAR, it was applied to optimize the initially transcribed region of the green fluorescent protein gene and the 3T4T variants demonstrated significantly enhanced transcription output, with at least 1.7-fold and 2.8-fold greater output than the wild-type DNA template and common transcription template, respectively. STAR may provide a valuable tool for many biotechnical applications related to the transcription process, which may pave the way for the development of better RNA-related enzymes and new drugs.
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Affiliation(s)
- Weitong Qin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liang Li
- Hzymes Biotechnology Co. Ltd, Hubei, 430010, China
| | - Fan Yang
- Hzymes Biotechnology Co. Ltd, Hubei, 430010, China
| | - Siyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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25
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Reed MA, Gerasimova YV. Single-tube isothermal label-free fluorescent sensor for pathogen detection based on genetic signatures. Front Chem 2022; 10:951279. [PMID: 36118306 PMCID: PMC9475119 DOI: 10.3389/fchem.2022.951279] [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: 05/23/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
We report on a single-tube biosensor for real-time detection of bacterial pathogens with multiplex capabilities. The biosensor consists of two DNA probes, which bind to the complementary fragment of a bacterial RNA to form a three-way junction (3WJ) nucleic acid structure. One of the probes encodes a fluorescent light-up RNA aptamer under T7 promoter. It allows for generation of multiple aptamer copies due to elongation and transcription of the 3WJ structure in the presence of the complementary target. The aptamer coordinates and thereby enhances fluorescence of a cognate fluorogenic dye, allowing for fluorescent detection of the RNA target. Multiple aptamer copies can be produced from a single target-dependent 3WJ structure allowing for amplification and visual observation of the signal. The limit of detection depended on the assay time and was found to be 1.7 nM or 0.6 nM for 30-min or 60-min assay, respectively, when N-methylmesoporphyrin IX (NMM) was used as a fluorescent indicator. The sensor is excellent in analyzing folded RNA targets and differentiating between closely related sequences due to the multicomponent character of the target-interrogating probe. Response to unamplified samples of total bacterial RNA from Mycobacterium tuberculosis complex or Escherichia coli was observed with excellent selectivity within 30 min under isothermal conditions at 50°C in a one-tube one-step assay. Several bacterial species can be detected in multiplex by utilizing biosensors with the template strands encoding different light-up aptamers. The isothermal one-tube-one-step format of the assay and the possibility to monitor the signal visually makes it amenable to use in a point-of-care scenario.
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26
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Miyachi R, Shimizu Y, Ichihashi N. Transfer RNA Synthesis-Coupled Translation and DNA Replication in a Reconstituted Transcription/Translation System. ACS Synth Biol 2022; 11:2791-2799. [PMID: 35848947 DOI: 10.1021/acssynbio.2c00163] [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: 11/28/2022]
Abstract
Transfer RNAs (tRNAs) are key molecules involved in translation. In vitro synthesis of tRNAs and their coupled translation are important challenges in the construction of a self-regenerative molecular system. Here, we first purified EF-Tu and ribosome components in a reconstituted translation system of Escherichia coli to remove residual tRNAs. Next, we expressed 15 types of tRNAs in the repurified translation system and performed translation of the reporter luciferase gene depending on the expression. Furthermore, we demonstrated DNA replication through expression of a tRNA encoded by DNA, mimicking information processing within the cell. Our findings highlight the feasibility of an in vitro self-reproductive system, in which tRNAs can be synthesized from replicating DNA.
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Affiliation(s)
- Ryota Miyachi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), Suita 565-0874, Osaka, Japan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.,Komaba Institute for Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan.,Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
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27
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Feyrer H, Gurdap CO, Marušič M, Schlagnitweit J, Petzold K. Enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR. PLoS One 2022; 17:e0264662. [PMID: 35802676 PMCID: PMC9269771 DOI: 10.1371/journal.pone.0264662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022] Open
Abstract
Solution NMR spectroscopy is a well-established tool with unique advantages for structural studies of RNA molecules. However, for large RNA sequences, the NMR resonances often overlap severely. A reliable way to perform resonance assignment and allow further analysis despite spectral crowding is the use of site-specific isotope labeling in sample preparation. While solid-phase oligonucleotide synthesis has several advantages, RNA length and availability of isotope-labeled building blocks are persistent issues. Purely enzymatic methods represent an alternative and have been presented in the literature. In this study, we report on a method in which we exploit the preference of T7 RNA polymerase for nucleotide monophosphates over triphosphates for the 5’ position, which allows 5’-labeling of RNA. Successive ligation to an unlabeled RNA strand generates a site-specifically labeled RNA. We show the successful production of such an RNA sample for NMR studies, report on experimental details and expected yields, and present the surprising finding of a previously hidden set of peaks which reveals conformational exchange in the RNA structure. This study highlights the feasibility of site-specific isotope-labeling of RNA with enzymatic methods.
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Affiliation(s)
- Hannes Feyrer
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Cenk Onur Gurdap
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Maja Marušič
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- Slovenian NMR Center, National Institute of Chemistry, Ljubljana, Slovenia
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- Centre de RMN à Très Hauts Champs de Lyon, UMR5082 CNRS/ENS-Lyon/Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- * E-mail:
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28
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D'Souza MH, Mrozowich T, Badmalia MD, Geeraert M, Frederickson A, Henrickson A, Demeler B, Wolfinger MT, Patel TR. Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats. Nucleic Acids Res 2022; 50:5881-5898. [PMID: 35639511 PMCID: PMC9177966 DOI: 10.1093/nar/gkac414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/26/2022] [Accepted: 05/09/2022] [Indexed: 12/05/2022] Open
Abstract
Human Long Intergenic Noncoding RNA-p21 (LincRNA-p21) is a regulatory noncoding RNA that plays an important role in promoting apoptosis. LincRNA-p21 is also critical in down-regulating many p53 target genes through its interaction with a p53 repressive complex. The interaction between LincRNA-p21 and the repressive complex is likely dependent on the RNA tertiary structure. Previous studies have determined the two-dimensional secondary structures of the sense and antisense human LincRNA-p21 AluSx1 IRs using SHAPE. However, there were no insights into its three-dimensional structure. Therefore, we in vitro transcribed the sense and antisense regions of LincRNA-p21 AluSx1 Inverted Repeats (IRs) and performed analytical ultracentrifugation, size exclusion chromatography, light scattering, and small angle X-ray scattering (SAXS) studies. Based on these studies, we determined low-resolution, three-dimensional structures of sense and antisense LincRNA-p21. By adapting previously known two-dimensional information, we calculated their sense and antisense high-resolution models and determined that they agree with the low-resolution structures determined using SAXS. Thus, our integrated approach provides insights into the structure of LincRNA-p21 Alu IRs. Our study also offers a viable pipeline for combining the secondary structure information with biophysical and computational studies to obtain high-resolution atomistic models for long noncoding RNAs.
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Affiliation(s)
- Michael H D'Souza
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Tyler Mrozowich
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Maulik D Badmalia
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Mitchell Geeraert
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Angela Frederickson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Borries Demeler
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada.,Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA.,NorthWest Biophysics Consortium, University of Lethbridge, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Michael T Wolfinger
- Bioinformatics and Computational Biology, Faculty of Computer Science, Währingerstrasse 29, 1090 Vienna, Austria.,Department of Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090 Vienna, Austria
| | - Trushar R Patel
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada.,Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada.,Li Ka Shing Institute of Virology and Discovery Lab, University of Alberta, Edmonton, AB T6G 2E1, Canada
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29
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ROSALIND: Rapid Detection of Chemical Contaminants with In Vitro Transcription Factor-Based Biosensors. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2433:325-342. [PMID: 34985754 DOI: 10.1007/978-1-0716-1998-8_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
ROSALIND (RNA Output Sensors Activated by Ligand Induction) is an in vitro biosensing system that detects small molecules using regulated transcription reactions. It consists of three key components: (1) RNA polymerases, (2) allosteric protein transcription factors, and (3) synthetic DNA transcription templates that together regulate the synthesis of a fluorescence-activating RNA aptamer. The system can detect a wide range of chemicals including antibiotics, small molecules, and metal ions. We have demonstrated that ROSALIND can be lyophilized and transported at ambient conditions for water testing on-site. Here, we describe how to set up a ROSALIND reaction for detecting various chemical contaminants in water using a model transcription factor as well as how to build a new ROSALIND sensor.
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30
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Schaffter SW, Strychalski EA. Cotranscriptionally encoded RNA strand displacement circuits. SCIENCE ADVANCES 2022; 8:eabl4354. [PMID: 35319994 PMCID: PMC8942360 DOI: 10.1126/sciadv.abl4354] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 02/01/2022] [Indexed: 05/21/2023]
Abstract
Engineered molecular circuits that process information in biological systems could address emerging human health and biomanufacturing needs. However, such circuits can be difficult to rationally design and scale. DNA-based strand displacement reactions have demonstrated the largest and most computationally powerful molecular circuits to date but are limited in biological systems due to the difficulty in genetically encoding components. Here, we develop scalable cotranscriptionally encoded RNA strand displacement (ctRSD) circuits that are rationally programmed via base pairing interactions. ctRSD circuits address the limitations of DNA-based strand displacement circuits by isothermally producing circuit components via transcription. We demonstrate circuit programmability in vitro by implementing logic and amplification elements, as well as multilayer cascades. Furthermore, we show that circuit kinetics are accurately predicted by a simple model of coupled transcription and strand displacement, enabling model-driven design. We envision ctRSD circuits will enable the rational design of powerful molecular circuits that operate in biological systems, including living cells.
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31
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Programming cell-free biosensors with DNA strand displacement circuits. Nat Chem Biol 2022; 18:385-393. [PMID: 35177837 PMCID: PMC8964419 DOI: 10.1038/s41589-021-00962-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 12/16/2021] [Indexed: 12/15/2022]
Abstract
Cell-free biosensors are powerful platforms for monitoring human and environmental health. Here, we expand their capabilities by interfacing them with toehold-mediated strand displacement circuits, a dynamic DNA nanotechnology that enables molecular computation through programmable interactions between nucleic acid strands. We develop design rules for interfacing a small molecule sensing platform called ROSALIND with toehold-mediated strand displacement to construct hybrid RNA–DNA circuits that allow fine-tuning of reaction kinetics. We use these design rules to build 12 different circuits that implement a range of logic functions (NOT, OR, AND, IMPLY, NOR, NIMPLY, NAND). Finally, we demonstrate a circuit that acts like an analog-to-digital converter to create a series of binary outputs that encode the concentration range of the molecule being detected. We believe this work establishes a pathway to create ‘smart’ diagnostics that use molecular computations to enhance the speed and utility of biosensors. ![]()
Equipping ROSALIND, a cell-free biosensing platform, with information processing circuits based on toehold-mediated DNA strand displacement enhances sensor performance and enables logic gate computation.
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32
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Kuret T, Sodin-Šemrl S, Leskošek B, Ferk P. Single Cell RNA Sequencing in Autoimmune Inflammatory Rheumatic Diseases: Current Applications, Challenges and a Step Toward Precision Medicine. Front Med (Lausanne) 2022; 8:822804. [PMID: 35118101 PMCID: PMC8804286 DOI: 10.3389/fmed.2021.822804] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 12/27/2021] [Indexed: 12/11/2022] Open
Abstract
Single cell RNA sequencing (scRNA-seq) represents a new large scale and high throughput technique allowing analysis of the whole transcriptome at the resolution of an individual cell. It has emerged as an imperative method in life science research, uncovering complex cellular networks and providing indices that will eventually lead to the development of more targeted and personalized therapies. The importance of scRNA-seq has been particularly highlighted through the analysis of complex biological systems, in which cellular heterogeneity is a key aspect, such as the immune system. Autoimmune inflammatory rheumatic diseases represent a group of disorders, associated with a dysregulated immune system and high patient heterogeneity in both pathophysiological and clinical aspects. This complicates the complete understanding of underlying pathological mechanisms, associated with limited therapeutic options available and their long-term inefficiency and even toxicity. There is an unmet need to investigate, in depth, the cellular and molecular mechanisms driving the pathogenesis of rheumatic diseases and drug resistance, identify novel therapeutic targets, as well as make a step forward in using stratified and informed therapeutic decisions, which could now be achieved with the use of single cell approaches. This review summarizes the current use of scRNA-seq in studying different rheumatic diseases, based on recent findings from published in vitro, in vivo, and clinical studies, as well as discusses the potential implementation of scRNA-seq in the development of precision medicine in rheumatology.
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Affiliation(s)
- Tadeja Kuret
- Faculty of Medicine, Institute of Cell Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Snežna Sodin-Šemrl
- Department of Rheumatology, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
| | - Brane Leskošek
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics/ELIXIR-SI Center, University of Ljubljana, Ljubljana, Slovenia
| | - Polonca Ferk
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics/ELIXIR-SI Center, University of Ljubljana, Ljubljana, Slovenia
- *Correspondence: Polonca Ferk
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33
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Recent advances in rotavirus reverse genetics and its utilization in basic research and vaccine development. Arch Virol 2021; 166:2369-2386. [PMID: 34216267 PMCID: PMC8254061 DOI: 10.1007/s00705-021-05142-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/27/2021] [Indexed: 11/29/2022]
Abstract
Rotaviruses are segmented double-stranded RNA viruses with a high frequency of gene reassortment, and they are a leading cause of global diarrheal deaths in children less than 5 years old. Two-thirds of rotavirus-associated deaths occur in low-income countries. Currently, the available vaccines in developing countries have lower efficacy in children than those in developed countries. Due to added safety concerns and the high cost of current vaccines, there is a need to develop cost-effective next-generation vaccines with improved safety and efficacy. The reverse genetics system (RGS) is a powerful tool for investigating viral protein functions and developing novel vaccines. Recently, an entirely plasmid-based RGS has been developed for several rotaviruses, and this technological advancement has significantly facilitated novel rotavirus research. Here, we review the recently developed RGS platform and discuss its application in studying infection biology, gene reassortment, and development of vaccines against rotavirus disease.
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