1
|
Aute R, Waghela N, Deshmukh MV. Key arginine residues in R2D2 dsRBD1 and dsRBD2 lead the siRNA recognition in Drosophila melanogaster RNAi pathway. Biophys Chem 2024; 310:107247. [PMID: 38663122 DOI: 10.1016/j.bpc.2024.107247] [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: 01/17/2024] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 05/23/2024]
Abstract
In Drosophila melanogaster, Dcr-2:R2D2 heterodimer binds to the 21 nucleotide siRNA duplex to form the R2D2/Dcr-2 Initiator (RDI) complex, which is critical for the initiation of siRNA-induced silencing complex (RISC) assembly. During RDI complex formation, R2D2, a protein that contains three dsRNA binding domains (dsRBD), senses two aspects of the siRNA: thermodynamically more stable end (asymmetry sensing) and the 5'-phosphate (5'-P) recognition. Despite several detailed studies to date, the molecular determinants arising from R2D2 for performing these two tasks remain elusive. In this study, we have performed structural, biophysical, and biochemical characterization of R2D2 dsRBDs. We found that the solution NMR-derived structure of R2D2 dsRBD1 yielded a canonical α1-β1-β2-β3-α2 fold, wherein two arginine salt bridges provide additional stability to the R2D2 dsRBD1. Furthermore, we show that R2D2 dsRBD1 interacts with thermodynamically asymmetric siRNA duplex independent of its 5'-phosphorylation state, whereas R2D2 dsRBD2 prefers to interact with 5'-P siRNA duplex. The mutation of key arginine residues, R53 and R101, in concatenated dsRBDs of R2D2 results in a significant loss of siRNA duplex recognition. Our study deciphers the active roles of R2D2 dsRBDs by showing that dsRBD1 initiates siRNA recognition, whereas dsRBD2 senses 5'-phosphate as an authentic mark on functional siRNA.
Collapse
Affiliation(s)
- Ramdas Aute
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nilam Waghela
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mandar V Deshmukh
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
2
|
Li Z, Bilic M, Nagar B. Isolation of short RNAs with homogeneous 3'-ends using quaternary-amine anion exchange chromatography. Biol Methods Protoc 2024; 9:bpae033. [PMID: 38855193 PMCID: PMC11162090 DOI: 10.1093/biomethods/bpae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/12/2024] [Accepted: 05/16/2024] [Indexed: 06/11/2024] Open
Abstract
Visualizing RNA-protein interactions through structural approaches requires the use of RNA molecules purified to homogeneity. We describe here a simple and effective method, free of acrylamide contamination and without using UV radiation, to separate in vitro synthesized, heterogeneous RNA transcripts (up to ∼15 nucleotides) at single-nucleotide resolution by quaternary-amine anion exchange chromatography. The quality of short RNAs isolated through this method is validated by gel electrophoresis, mass spectrometry, and crystallization with a protein-binding partner.
Collapse
Affiliation(s)
- Zixian Li
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montreal, QC H3G 0B1, Canada
| | - Mia Bilic
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montreal, QC H3G 0B1, Canada
| | - Bhushan Nagar
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montreal, QC H3G 0B1, Canada
| |
Collapse
|
3
|
Welbourne EN, Loveday KA, Nair A, Nourafkan E, Qu J, Cook K, Kis Z, Dickman MJ. Anion exchange HPLC monitoring of mRNA in vitro transcription reactions to support mRNA manufacturing process development. Front Mol Biosci 2024; 11:1250833. [PMID: 38516194 PMCID: PMC10955092 DOI: 10.3389/fmolb.2024.1250833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/15/2024] [Indexed: 03/23/2024] Open
Abstract
mRNA technology has recently demonstrated the ability to significantly change the timeline for developing and delivering a new vaccine from years to months. The potential of mRNA technology for rapid vaccine development has recently been highlighted by the successful development and approval of two mRNA vaccines for COVID-19. Importantly, this RNA-based approach holds promise for treatments beyond vaccines and infectious diseases, e.g., treatments for cancer, metabolic disorders, cardiovascular conditions, and autoimmune diseases. There is currently significant demand for the development of improved manufacturing processes for the production of mRNA therapeutics in an effort to increase their yield and quality. The development of suitable analytical methods for the analysis of mRNA therapeutics is critical to underpin manufacturing development and the characterisation of the drug product and drug substance. In this study we have developed a high-throughput, high-performance liquid chromatography (HPLC) workflow for the rapid analysis of mRNA generated using in vitro transcription (IVT). We have optimised anion exchange (AEX) HPLC for the analysis of mRNA directly from IVT. Chromatography was performed in under 6 min enabling separation of all of the key components in the IVT, including nucleoside triphosphates (NTPs), Cap analogue, plasmid DNA and mRNA product. Moreover, baseline separation of the NTPs was achieved, which facilitates accurate quantification of each NTP such that their consumption may be determined during IVT reactions. Furthermore, the HPLC method was used to rapidly assess the purification of the mRNA product, including removal of NTPs/Cap analogue and other contaminants after downstream purification, including solid phase extraction (SPE), oligo deoxythymidine (oligo-dT) affinity chromatography and tangential flow filtration (TFF). Using the developed method excellent precision was obtained with calibration curves for an external mRNA standard and NTPs giving correlation coefficients of 0.98 and 1.0 respectively. Intra- and inter-day studies on retention time stability of NTPs, showed a relative standard deviation ≤ 0.3% and ≤1.5% respectively. The mRNA retention time variability was ≤0.13%. This method was then utilised to monitor the progress of an IVT reaction for the production of Covid spike protein (C-Spike) mRNA to measure the increasing yield of mRNA alongside the consumption of NTPs during the reaction.
Collapse
Affiliation(s)
- Emma N. Welbourne
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Kate A. Loveday
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Adithya Nair
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Ehsan Nourafkan
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Jixin Qu
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Ken Cook
- ThermoFisher Scientific, Hemel Hempstead, United Kingdom
| | - Zoltán Kis
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
- Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - Mark J. Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| |
Collapse
|
4
|
Hengelbrock A, Schmidt A, Strube J. Digital Twin Fundamentals of mRNA In Vitro Transcription in Variable Scale Toward Autonomous Operation. ACS OMEGA 2024; 9:8204-8220. [PMID: 38405539 PMCID: PMC10882708 DOI: 10.1021/acsomega.3c08732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/27/2024]
Abstract
The COVID-19 pandemic caused the rapid development of mRNA (messenger ribonucleic acid) vaccines and new RNA-based therapeutic methods. However, the approval rate for candidates has the potential to be increased, with a significant number failing so far due to efficacy, safety, and manufacturing deficiencies, hindering equitable vaccine distribution during pandemics. This study focuses on optimizing the production of mRNA, a critical component of mRNA-based vaccines, using a scalable machine by investigating the key mechanisms of mRNA in vitro transcription. First, kinetic parameters for the mRNA production process were determined. The validity of the determination and the robustness of the model are demonstrated by predicting different reactions with and without substrate limitations as well as different transcripts. The optimized reaction conditions, including temperature, urea concentration, and concentration of reaction-enhancing additives, resulted in a 55% increase in mRNA yield with a 33% reduction in truncated mRNA. Additionally, the feasibility of a segmented flow approach allowed for high-throughput screening (HTS), enabling the production of 20 vaccine candidates within a short time frame, representing a 10-fold increase in productivity, compared to nonsegmented reactions limited by the residence time in the plug flow reactor. The findings presented for the first time here contribute to the development of a fully continuous and efficient manufacturing process for mRNA and other cell and gene therapy drugs/vaccine candidates as presented in our previous work, which discussed the integration of process analytical technologies and predictive process models in a Biopharma 4.0 facility to enable the production of clinical and large-scale doses, ensuring a rapid and resilient supply of critical therapeutics. The results in this study especially highlight that the same machine and equipment can be used for screening and manufacturing different drug candidates in continuous operation. By streamlining production and adhering to quality standards, this approach enhances the industry's ability to respond swiftly to pandemics and public health emergencies, addressing the urgent need for accessible and effective vaccines.
Collapse
Affiliation(s)
- Alina Hengelbrock
- Institute for Separation
and Process Technology, Clausthal University
of Technology, Clausthal-Zellerfeld 38678, Germany
| | - Axel Schmidt
- Institute for Separation
and Process Technology, Clausthal University
of Technology, Clausthal-Zellerfeld 38678, Germany
| | - Jochen Strube
- Institute for Separation
and Process Technology, Clausthal University
of Technology, Clausthal-Zellerfeld 38678, Germany
| |
Collapse
|
5
|
Feng X, Su Z, Cheng Y, Ma G, Zhang S. Messenger RNA chromatographic purification: advances and challenges. J Chromatogr A 2023; 1707:464321. [PMID: 37639849 DOI: 10.1016/j.chroma.2023.464321] [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: 07/26/2023] [Revised: 08/16/2023] [Accepted: 08/20/2023] [Indexed: 08/31/2023]
Abstract
Messenger RNA (mRNA) technologies have shown great potential in prophylactic vaccines and therapeutic medicines due to their adaptability, rapidity, efficacy, and safety. The purity of mRNA determines the efficacy and safety of mRNA drugs. Though chromatographic technologies are currently employed in mRNA purification, they are facing challenges, mainly arising from the large size, relatively simple chemical composition, instability, and high resemblance of by-products to the target mRNA. In this review, we will first make a comprehensive analysis of physiochemical properties differences between mRNA and proteins, then the major challenges facing in mRNA purification and general considerations are highlighted. A detailed summary of the state-of-arts in mRNA chromatographic purification will be provided, which are mainly classified into physicochemical property-based (size, charge, and hydrophobicity) and chemical structure-based (phosphate backbone, bases, cap structure, and poly A tail) technologies. Efforts in eliminating dsRNA byproducts via post in vitro transcript (IVT) purification and by manipulating the IVT process to reduce the generation of dsRNA are highlighted. Finally, a brief summary of the current status of chromatographic purification of the emerging circular mRNA (circRNA) is provided. We hope this review will provide some useful guidance for the Quality by Design (QbD) of mRNA downstream process development.
Collapse
Affiliation(s)
- Xue Feng
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinses Academy of Sciences, Beijing 100190, China; Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800, Australia; Monash Suzhou Research Institute, Monash University, SIP, Suzhou 215000, China
| | - Zhiguo Su
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinses Academy of Sciences, Beijing 100190, China
| | - Yuan Cheng
- Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800, Australia; Monash Suzhou Research Institute, Monash University, SIP, Suzhou 215000, China
| | - Guanghui Ma
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinses Academy of Sciences, Beijing 100190, China
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinses Academy of Sciences, Beijing 100190, China.
| |
Collapse
|
6
|
Pregeljc D, Skok J, Vodopivec T, Mencin N, Krušič A, Ličen J, Nemec KŠ, Štrancar A, Sekirnik R. Increasing yield of in vitro transcription reaction with at-line high pressure liquid chromatography monitoring. Biotechnol Bioeng 2023; 120:737-747. [PMID: 36471904 DOI: 10.1002/bit.28299] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 10/27/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
The COVID-19 pandemic triggered an unprecedented rate of development of messenger ribonucleic acid (mRNA) vaccines, which are produced by in vitro transcription reactions. The latter has been the focus of intense development to increase productivity and decrease cost. Optimization of in vitro transcription (IVT) depends on understanding the impact of individual reagents on the kinetics of mRNA production and the consumption of building blocks, which is hampered by slow, low-throughput, end-point analytics. We implemented a workflow based on rapid at-line high pressure liquid chromatography (HPLC) monitoring of consumption of nucleoside triphosphates (NTPs) with concomitant production of mRNA, with a sub-3 min read-out, allowing for adjustment of IVT reaction parameters with minimal time lag. IVT was converted to fed-batch resulting in doubling the reaction yield compared to batch IVT protocol, reaching 10 mg/ml for multiple constructs. When coupled with exonuclease digestion, HPLC analytics for quantification of mRNA was extended to monitoring capping efficiency of produced mRNA. When HPLC monitoring was applied to production of an anti-reverse cap analog (ARCA)-capped mRNA construct, which requires an approximate 4:1 ARCA:guanidine triphosphate ratio, the optimized fed-batch approach achieved productivity of 9 mg/ml with 79% capping. The study provides a methodological platform for optimization of factors influencing IVT reactions, converting the reaction from batch to fed-batch mode, determining reaction kinetics, which are critical for optimization of continuous addition of reagents, thus in principle enabling continuous manufacturing of mRNA.
Collapse
Affiliation(s)
- Domen Pregeljc
- BIA Separations d.o.o., a Sartorius Company, Ajdovščina, Slovenia
| | - Janja Skok
- BIA Separations d.o.o., a Sartorius Company, Ajdovščina, Slovenia
| | - Tina Vodopivec
- BIA Separations d.o.o., a Sartorius Company, Ajdovščina, Slovenia
| | - Nina Mencin
- BIA Separations d.o.o., a Sartorius Company, Ajdovščina, Slovenia
| | - Andreja Krušič
- BIA Separations d.o.o., a Sartorius Company, Ajdovščina, Slovenia
| | - Jure Ličen
- BIA Separations d.o.o., a Sartorius Company, Ajdovščina, Slovenia
| | - Kristina Š Nemec
- BIA Separations d.o.o., a Sartorius Company, Ajdovščina, Slovenia
| | - Aleš Štrancar
- BIA Separations d.o.o., a Sartorius Company, Ajdovščina, Slovenia
| | - Rok Sekirnik
- BIA Separations d.o.o., a Sartorius Company, Ajdovščina, Slovenia
| |
Collapse
|
7
|
Cui T, Fakhfakh K, Turney H, Güler-Gane G, Toloczko A, Hulley M, Turner R. Comprehensive studies on building a scalable downstream process for mRNAs to enable mRNA therapeutics. Biotechnol Prog 2023; 39:e3301. [PMID: 36101497 DOI: 10.1002/btpr.3301] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/21/2022] [Accepted: 09/01/2022] [Indexed: 11/12/2022]
Abstract
In recent years, mRNA-based therapeutics have been a fast-growing new class of biologics that can, in principle, encode any protein(s) directly in patients to treat various diseases. mRNA vaccines have been proven to work efficiently, have high potency, and can be rapidly developed and deployed, which is critical for a quick responses in the case of a pandemic. Such agile development is enabled by rapid synthesis of RNA in vitro using recombinant enzymes rather than relying on lengthy and complex cell culture processes. mRNA exhibits physical and chemical properties differing from protein-based therapeutics. It is highly negatively charged and the hydroxyl group makes mRNA less stable and more susceptible to hydrolysis and nucleophilic cleavage. This novel work shares comprehensive studies carried out to compare the performance of various mRNA purification strategies by considering its scalability and critical quality attributes. In addition, the paper provides insights on how to establish a scalable mRNA purification process that consists of ultrafiltration/diafiltration and chromatography steps with good recoveries. Alternative Oligo(dT) based columns were further explored aiming to improve total process recovery. With Oligo(dT) as a capture step, overall recoveries of 70% can be achieved for mRNAs studied here that encode anti-influenza immunoglobulin G monoclonal antibodies.
Collapse
Affiliation(s)
- Tingting Cui
- Purification Process Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge, UK
| | - Kareem Fakhfakh
- Purification Process Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge, UK
| | - Hannah Turney
- Purification Process Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge, UK
| | - Gülin Güler-Gane
- Biologics Engineering, Early Oncology, BioPharmaceuticals R&D, Cambridge, UK
| | - Aleksandra Toloczko
- Biologics Engineering, Early Oncology, BioPharmaceuticals R&D, Cambridge, UK
| | - Martyn Hulley
- Purification Process Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge, UK
| | - Richard Turner
- Purification Process Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge, UK
| |
Collapse
|
8
|
Minnaert AK, Vanluchene H, Verbeke R, Lentacker I, De Smedt SC, Raemdonck K, Sanders NN, Remaut K. Strategies for controlling the innate immune activity of conventional and self-amplifying mRNA therapeutics: Getting the message across. Adv Drug Deliv Rev 2021; 176:113900. [PMID: 34324884 PMCID: PMC8325057 DOI: 10.1016/j.addr.2021.113900] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023]
Abstract
The recent approval of messenger RNA (mRNA)-based vaccines to combat the SARS-CoV-2 pandemic highlights the potential of both conventional mRNA and self-amplifying mRNA (saRNA) as a flexible immunotherapy platform to treat infectious diseases. Besides the antigen it encodes, mRNA itself has an immune-stimulating activity that can contribute to vaccine efficacy. This self-adjuvant effect, however, will interfere with mRNA translation and may influence the desired therapeutic outcome. To further exploit its potential as a versatile therapeutic platform, it will be crucial to control mRNA's innate immune-stimulating properties. In this regard, we describe the mechanisms behind the innate immune recognition of mRNA and provide an extensive overview of strategies to control its innate immune-stimulating activity. These strategies range from modifications to the mRNA backbone itself, optimization of production and purification processes to the combination with innate immune inhibitors. Furthermore, we discuss the delicate balance of the self-adjuvant effect in mRNA vaccination strategies, which can be both beneficial and detrimental to the therapeutic outcome.
Collapse
Affiliation(s)
- An-Katrien Minnaert
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| | - Helena Vanluchene
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| | - Rein Verbeke
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| | - Ine Lentacker
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| | - Stefaan C De Smedt
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| | - Koen Raemdonck
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| | - Niek N Sanders
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| | - Katrien Remaut
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| |
Collapse
|
9
|
Karlsson H, Baronti L, Petzold K. A robust and versatile method for production and purification of large-scale RNA samples for structural biology. RNA (NEW YORK, N.Y.) 2020; 26:1023-1037. [PMID: 32354720 PMCID: PMC7373988 DOI: 10.1261/rna.075697.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/25/2020] [Indexed: 05/16/2023]
Abstract
Recent findings in genome-wide transcriptomics revealed that RNAs are involved in almost every biological process, across all domains of life. The characterization of native RNAs of unknown function and structure is particularly challenging due to their typical low abundance in the cell and the inherent sensitivity toward ubiquitous RNA degrading enzymes. Therefore, robust in vitro synthesis and extensive work-up methods are often needed to obtain samples amenable for biochemical, biophysical, and structural studies. Here, we present a protocol that combines the most recent advances in T7 in vitro transcription methodology with reverse phase ion pairing and ion exchange HPLC purification of RNAs for the production of yield-optimized large-scale samples. The method is easy to follow, robust and suitable for users with little or no experience within the field of biochemistry or chromatography. The complete execution of this method, for example, for production of isotopically labeled NMR samples, can be performed in less than a week.
Collapse
Affiliation(s)
- Hampus Karlsson
- Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, SE-104 35 Stockholm, Sweden
| | - Lorenzo Baronti
- Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, SE-104 35 Stockholm, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, SE-104 35 Stockholm, Sweden
| |
Collapse
|
10
|
Catani M, De Luca C, Medeiros Garcia Alcântara J, Manfredini N, Perrone D, Marchesi E, Weldon R, Müller-Späth T, Cavazzini A, Morbidelli M, Sponchioni M. Oligonucleotides: Current Trends and Innovative Applications in the Synthesis, Characterization, and Purification. Biotechnol J 2020; 15:e1900226. [PMID: 32298041 DOI: 10.1002/biot.201900226] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/17/2020] [Indexed: 12/12/2022]
Abstract
Oligonucleotides (ONs) are gaining increasing importance as a promising novel class of biopharmaceuticals. Thanks to their fundamental role in gene regulation, they can be used to develop custom-made drugs (also called N-to-1) able to act on the gene expression at pre-translational level. With recent approvals of ON-based therapeutics by the Food and Drug Administration (FDA), a growing demand for high-quality chemically modified ONs is emerging and their market is expected to impressively prosper in the near future. To satisfy this growing market demand, a scalable and economically sustainable ON production is needed. In this paper, the state of the art of the whole ON production process is illustrated with the aim of highlighting the most promising routes toward the auspicated market-size production. In particular, the most recent advancements in both the upstream stage, mainly based on solid-phase synthesis and recombinant technology, and the downstream one, focusing on chromatographic techniques, are reviewed. Since ON production is projected to expand to the large scale, automatized multicolumn countercurrent technologies will reasonably be required soon to replace the current ones based on batch single-column operations. This consideration is supported by a recent cutting-edge application of continuous chromatography for the ON purification.
Collapse
Affiliation(s)
- Martina Catani
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - Chiara De Luca
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - João Medeiros Garcia Alcântara
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta,", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| | - Nicolò Manfredini
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta,", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| | - Daniela Perrone
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - Elena Marchesi
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - Richard Weldon
- ChromaCon AG, Technoparkstrasse 1, Zürich, 8005, Switzerland
| | | | - Alberto Cavazzini
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - Massimo Morbidelli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta,", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| | - Mattia Sponchioni
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta,", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| |
Collapse
|
11
|
Théobald-Dietrich A, de Wijn R, Rollet K, Bluhm A, Rudinger-Thirion J, Paulus C, Lorber B, Thureau A, Frugier M, Sauter C. Structural Analysis of RNA by Small-Angle X-ray Scattering. Methods Mol Biol 2020; 2113:189-215. [PMID: 32006316 DOI: 10.1007/978-1-0716-0278-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Over the past two decades small-angle X-ray scattering (SAXS) has become a popular method to characterize solutions of biomolecules including ribonucleic acid (RNA). In an integrative structural approach, SAXS is complementary to crystallography, NMR, and electron microscopy and provides information about RNA architecture and dynamics. This chapter highlights the practical advantages of combining size-exclusion chromatography and SAXS at synchrotron facilities. It is illustrated by practical case studies of samples ranging from single hairpins and tRNA to a large IRES. The emphasis is also put on sample preparation which is a critical step of SAXS analysis and on optimized protocols for in vitro RNA synthesis ensuring the production of mg amount of pure and homogeneous molecules.
Collapse
Affiliation(s)
- Anne Théobald-Dietrich
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Raphaël de Wijn
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Kévin Rollet
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Alexandra Bluhm
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Joëlle Rudinger-Thirion
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Caroline Paulus
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Bernard Lorber
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | | | - Magali Frugier
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Claude Sauter
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France.
| |
Collapse
|
12
|
Kanwal F, Chen T, Zhang Y, Simair A, Lu C. A Modified In Vitro Transcription Approach to Improve RNA Synthesis and Ribozyme Cleavage Efficiency. Mol Biotechnol 2019; 61:469-476. [PMID: 30868354 DOI: 10.1007/s12033-019-00167-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA elements such as catalytic RNA, riboswitch, microRNA, and long non-coding RNA perform a major role in cellular processes. A complete understanding of cellular processes is impossible without knowing the structure-function relationship of participating RNA molecules that ultimately requires large quantities of pure RNAs. Thus, structural/functional analyses of emerging RNAs necessitate revised protocols for improved RNA quantity and quality. Here we present a modified in vitro transcription protocol to enhance ribozyme cleaving efficiency and RNA yield by working on two variables, i.e., incubation temperature and limiting GTPs. Following an improved RNA synthesis, the target RNA is purified from transcription mixture components through denaturing size-exclusion chromatography. The protocol confirms that cyclic elevated incubation temperatures during transcription and increased concentrations of GTPs improve the production rate of RNA. Our modified in vitro transcription method improves the ribozyme cleaving efficiency and targets RNA yield by four- to fivefold that can benefit almost any RNA-related study from protein-RNA interaction analysis to crystallography.
Collapse
Affiliation(s)
- Fariha Kanwal
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, DongHua University, 2999 North Ren Min Road, Shanghai, 201620, China
| | - Ting Chen
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, DongHua University, 2999 North Ren Min Road, Shanghai, 201620, China
| | - Yunlong Zhang
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, DongHua University, 2999 North Ren Min Road, Shanghai, 201620, China
| | - Altaf Simair
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, DongHua University, 2999 North Ren Min Road, Shanghai, 201620, China
| | - Changrui Lu
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, DongHua University, 2999 North Ren Min Road, Shanghai, 201620, China.
| |
Collapse
|
13
|
A review on native and denaturing purification methods for non-coding RNA (ncRNA). J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1120:71-79. [PMID: 31071581 DOI: 10.1016/j.jchromb.2019.04.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/20/2019] [Accepted: 04/15/2019] [Indexed: 12/20/2022]
Abstract
Recently, non-coding RNA (ncRNA) became the centerpiece of human genome research. Modern ncRNA-based research has revolutionized disease diagnosis and therapeutics. However, decoding structural/functional information of ncRNA requires large amount of pure RNA, and hence effective RNA preparation and purification protocols. This review focuses on purification schemes of synthetic oligonucleotides, particularly liquid chromatographic (LC) techniques as improved alternatives to urea-polyacrylamide gel electrophoresis (urea-PAGE) purification. Moreover, the review summarizes the shortcomings of urea-PAGE purification method and details the chromatographic purification such as affinity, ion-exchange (IE) or size-exclusion (SE) chromatography. Specifically, we discuss denaturing and native RNA purification schemes with newest developments. In short, the review evaluates nucleic acid purification schemes required for various structural analyses.
Collapse
|
14
|
Application of steric exclusion chromatography on monoliths for separation and purification of RNA molecules. J Chromatogr A 2018; 1574:50-59. [PMID: 30195858 DOI: 10.1016/j.chroma.2018.08.063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/22/2018] [Accepted: 08/31/2018] [Indexed: 11/23/2022]
Abstract
Steric exclusion chromatography (SXC) is a method for separation of large target solutes based on their association with a hydrophilic stationary phase through mutual steric exclusion of polyethylene glycol (PEG). Selectivity in SXC is determined by the size or shape (or both) of the solutes alongside the size and concentration of PEG molecules. Elution is achieved by decreasing the PEG concentration. In this study, SXC applicability for the separation and purification of single-stranded (ss) and double-stranded (ds) RNA molecules was evaluated for the first time. The retention of ssRNA and dsRNA molecules of different lengths on convective interaction media (CIM) monolithic columns was systematically studied under variable PEG-6000 and NaCl concentrations. We determined that over 90% of long ssRNAs (700-6374 nucleotides) and long dsRNAs (500-6374 base pairs) are retained on the stationary phase in 15% PEG-6000 and ≥0.4 M NaCl. dsDNA and dsRNA molecules of the same length were partially separated by SXC. Separation of RNA molecules below 100 nucleotides from longer RNA species is easily achieved by SXC. Furthermore, SXC has the potential to separate dsRNAs from ssRNAs of the same length. We also demonstrated that SXC is suitable for the enrichment of ssRNA (PRR1 bacteriophage) and dsRNA (Phi6 bacteriophage) viral genomes from contaminating cellular RNA species. In summary, SXC on CIM monolithic columns is an appropriate tool for rapid RNA separation and concentration.
Collapse
|
15
|
Synthesis and characterization of Ag+-decorated poly(glycidyl methacrylate) microparticle design for the adsorption of nucleic acids. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1081-1082:1-7. [DOI: 10.1016/j.jchromb.2018.02.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 02/05/2018] [Accepted: 02/15/2018] [Indexed: 11/18/2022]
|
16
|
Kwon H, Kim M, Seo Y, Moon YS, Lee HJ, Lee K, Lee H. Emergence of synthetic mRNA: In vitro synthesis of mRNA and its applications in regenerative medicine. Biomaterials 2017; 156:172-193. [PMID: 29197748 DOI: 10.1016/j.biomaterials.2017.11.034] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/25/2017] [Accepted: 11/21/2017] [Indexed: 12/15/2022]
Abstract
The field of gene therapy has evolved over the past two decades after the first introduction of nucleic acid drugs, such as plasmid DNA (pDNA). With the development of in vitro transcription (IVT) methods, synthetic mRNA has become an emerging class of gene therapy. IVT mRNA has several advantages over conventional pDNA for the expression of target proteins. mRNA does not require nuclear localization to mediate protein translation. The intracellular process for protein expression is much simpler and there is no potential risk of insertion mutagenesis. Having these advantages, the level of protein expression is far enhanced as comparable to that of viral expression systems. This makes IVT mRNA a powerful alternative gene expression system for various applications in regenerative medicine. In this review, we highlight the synthesis and preparation of IVT mRNA and its therapeutic applications. The article includes the design and preparation of IVT mRNA, chemical modification of IVT mRNA, and therapeutic applications of IVT mRNA in cellular reprogramming, stem cell engineering, and protein replacement therapy. Finally, future perspectives and challenges of IVT mRNA are discussed.
Collapse
Affiliation(s)
- Hyokyoung Kwon
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Minjeong Kim
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yunmi Seo
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yae Seul Moon
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hwa Jeong Lee
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Kyuri Lee
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Hyukjin Lee
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea.
| |
Collapse
|
17
|
Chen J, Wassarman KM, Feng S, Leon K, Feklistov A, Winkelman JT, Li Z, Walz T, Campbell EA, Darst SA. 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase. Mol Cell 2017; 68:388-397.e6. [PMID: 28988932 DOI: 10.1016/j.molcel.2017.09.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/11/2017] [Accepted: 09/05/2017] [Indexed: 01/25/2023]
Abstract
Noncoding RNAs (ncRNAs) regulate gene expression in all organisms. Bacterial 6S RNAs globally regulate transcription by binding RNA polymerase (RNAP) holoenzyme and competing with promoter DNA. Escherichia coli (Eco) 6S RNA interacts specifically with the housekeeping σ70-holoenzyme (Eσ70) and plays a key role in the transcriptional reprogramming upon shifts between exponential and stationary phase. Inhibition is relieved upon 6S RNA-templated RNA synthesis. We report here the 3.8 Å resolution structure of a complex between 6S RNA and Eσ70 determined by single-particle cryo-electron microscopy and validation of the structure using footprinting and crosslinking approaches. Duplex RNA segments have A-form C3' endo sugar puckers but widened major groove widths, giving the RNA an overall architecture that mimics B-form promoter DNA. Our results help explain the specificity of Eco 6S RNA for Eσ70 and show how an ncRNA can mimic B-form DNA to directly regulate transcription by the DNA-dependent RNAP.
Collapse
Affiliation(s)
- James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Karen M Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Shili Feng
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Katherine Leon
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Andrey Feklistov
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Jared T Winkelman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zongli Li
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
18
|
Koubek J, Chang YC, Yang SYC, Huang JJT. Trigger Factor-Induced Nascent Chain Dynamics Changes Suggest Two Different Chaperone-Nascent Chain Interactions during Translation. J Mol Biol 2017; 429:1733-1745. [PMID: 28385637 DOI: 10.1016/j.jmb.2017.03.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/30/2017] [Accepted: 03/30/2017] [Indexed: 11/25/2022]
Abstract
Protein biogenesis is poorly understood due to the ribosome that perturbs measurement attempted on the ribosome-bound nascent chain (RNC). Investigating nascent chain dynamics may provide invaluable insight into the co-translational processes such as structure formation or interaction with a chaperone [e.g., the bacterial trigger factor (TF)]. In this study, we aim to establish a platform for studying nascent chain dynamics by exploring the local environment near the fluorescent dye on site-specifically labeled RNCs with time-resolved fluorescence anisotropy. To prepare a quantitative model of fluorescence depolarization, we utilized intrinsically disordered protein bound to ribosome, which helped us couple the sub-nanosecond depolarization with the motion of the nascent chain backbone. This was consistent with zinc-finger-domain-containing RNCs, where the extent of sub-nanosecond motion decreased upon the addition of zinc when the fluorophore was in close proximity of the domain. After the characterization of disordered nascent chain dynamics, we investigated the synthesis of a model cytosolic protein, Entner-Doudoroff aldolase, labeled at different sites during various stages of translation. Depending on the stage of translation, the addition of the TF to the nascent chain led to two different responses in the nascent chain dynamics serendipitously, suggesting steric hindrance between the nascent chain and the chaperone as a mechanism for TF dissociation from the ribosome during translation. Overall, our study demonstrates the possible use of site-specific labeling and time-resolved anisotropy to gain insight on chaperone binding event at various stages of translation and hints on TF co-translational mechanism.
Collapse
Affiliation(s)
- Jiří Koubek
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, 11529, R.O.C
| | - Yi-Che Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, 11529, R.O.C
| | | | | |
Collapse
|
19
|
Munoz AM, Yourik P, Rajagopal V, Nanda JS, Lorsch JR, Walker SE. Active yeast ribosome preparation using monolithic anion exchange chromatography. RNA Biol 2016; 14:188-196. [PMID: 27981882 PMCID: PMC5324736 DOI: 10.1080/15476286.2016.1270004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In vitro studies of translation provide critical mechanistic details, yet purification of large amounts of highly active eukaryotic ribosomes remains a challenge for biochemists and structural biologists. Here, we present an optimized method for preparation of highly active yeast ribosomes that could easily be adapted for purification of ribosomes from other species. The use of a nitrogen mill for cell lysis coupled with chromatographic purification of the ribosomes results in 10-fold-increased yield and less variability compared with the traditional approach, which relies on sedimentation through sucrose cushions. We demonstrate that these ribosomes are equivalent to those made using the traditional method in a host of in vitro assays, and that utilization of this new method will consistently produce high yields of active yeast ribosomes.
Collapse
Affiliation(s)
- Antonio M Munoz
- a Laboratory on the Mechanism and Regulation of Protein Synthesis, The Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda , MD , USA
| | - Paul Yourik
- a Laboratory on the Mechanism and Regulation of Protein Synthesis, The Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda , MD , USA
| | | | - Jagpreet S Nanda
- a Laboratory on the Mechanism and Regulation of Protein Synthesis, The Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda , MD , USA
| | - Jon R Lorsch
- a Laboratory on the Mechanism and Regulation of Protein Synthesis, The Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda , MD , USA
| | - Sarah E Walker
- a Laboratory on the Mechanism and Regulation of Protein Synthesis, The Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda , MD , USA.,c Department of Biological Sciences , The State University of New York at Buffalo , Buffalo , NY , USA
| |
Collapse
|
20
|
Pereira P, Queiroz JA, Figueiras A, Sousa F. Current progress on microRNAs-based therapeutics in neurodegenerative diseases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27882692 DOI: 10.1002/wrna.1409] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/07/2016] [Accepted: 10/17/2016] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs)-based therapy has recently emerged as a promising strategy in the treatments of neurodegenerative diseases. Thus, in this review, the most recent and important challenges and advances on the development of miRNA therapeutics for brain targeting are discussed. In particular, this review highlights current knowledge and progress in the field of manufacturing, recovery, isolation, purification, and analysis of these therapeutic oligonucleotides. Finally, the available miRNA delivery systems are reviewed and an analysis is presented in what concerns to the current challenges that have to be addressed to ensure their specificity and efficacy. Overall, it is intended to provide a perspective on the future of miRNA-based therapeutics, focusing the biotechnological approach to obtain miRNAs. WIREs RNA 2017, 8:e1409. doi: 10.1002/wrna.1409 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Patrícia Pereira
- CICS-UBI - Health Sciences Research Centre, Universidade da Beira Interior, Covilhã, Portugal
| | - João A Queiroz
- CICS-UBI - Health Sciences Research Centre, Universidade da Beira Interior, Covilhã, Portugal
| | - Ana Figueiras
- CICS-UBI - Health Sciences Research Centre, Universidade da Beira Interior, Covilhã, Portugal.,REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy, Universidade de Coimbra, Coimbra, Portugal
| | - Fani Sousa
- CICS-UBI - Health Sciences Research Centre, Universidade da Beira Interior, Covilhã, Portugal
| |
Collapse
|
21
|
Yadav DK, Lukavsky PJ. NMR solution structure determination of large RNA-protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 97:57-81. [PMID: 27888840 DOI: 10.1016/j.pnmrs.2016.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/04/2016] [Accepted: 10/04/2016] [Indexed: 06/06/2023]
Abstract
Structure determination of RNA-protein complexes is essential for our understanding of the multiple layers of RNA-mediated posttranscriptional regulation of gene expression. Over the past 20years, NMR spectroscopy became a key tool for structural studies of RNA-protein interactions. Here, we review the progress being made in NMR structure determination of large ribonucleoprotein assemblies. We discuss approaches for the design of RNA-protein complexes for NMR structural studies, established and emerging isotope and segmental labeling schemes suitable for large RNPs and how to gain distance restraints from NOEs, PREs and EPR and orientational information from RDCs and SAXS/SANS in such systems. The new combination of NMR measurements with MD simulations and its potential will also be discussed. Application and combination of these various methods for structure determination of large RNPs will be illustrated with three large RNA-protein complexes (>40kDa) and other interesting complexes determined in the past six and a half years.
Collapse
Affiliation(s)
- Deepak Kumar Yadav
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Peter J Lukavsky
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic.
| |
Collapse
|
22
|
Köse K, Erol K, Özgür E, Uzun L, Denizli A. PolyAdenine cryogels for fast and effective RNA purification. Colloids Surf B Biointerfaces 2016; 146:678-86. [PMID: 27434154 DOI: 10.1016/j.colsurfb.2016.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 06/24/2016] [Accepted: 07/02/2016] [Indexed: 11/26/2022]
Abstract
Cryogels are used effectively for many diverse applications in a variety of fields. The isolation or purification of RNA, one of the potential utilizations for cryogels, is crucial due to their vital roles such as encoding, decoding, transcription and translation, and gene expression. RNA principally exists within every living thing, but their tendency to denaturation easily is still the most challenging issue. Herein, we aimed to develop adenine incorporated polymeric cryogels as an alternative sorbent for cost-friendly and fast RNA purification with high capacity. For this goal, we synthesized the polymerizable derivative of adenine called as adenine methacrylate (AdeM) through the substitution reaction between adenine and methacryloyl chloride. Then, 2-hydroxyethyl methacrylate (HEMA)-based cryogels were prepared in a partially frozen aqueous medium by copolymerization of monomers, AdeM, and HEMA. The cryogels were characterized by using Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), surface area measurements, thermogravimetric analysis (TGA), and swelling tests. RNA adsorption experiments were performed via batch system while varying different conditions including pH, initial RNA concentration, temperature, and interaction time. We achieved high RNA adsorption capacity of cryogels, with the swelling ratio around 510%, as 11.86mg/g. The cryogels might be reused at least five times without significant decrease in adsorption capacity.
Collapse
Affiliation(s)
- Kazım Köse
- Hacettepe University, Department of Chemistry, Ankara, Turkey; Hitit University, Scientific Technical Research and Application Center, Çorum, Turkey
| | - Kadir Erol
- Hacettepe University, Department of Chemistry, Ankara, Turkey; Hitit University, Department of Chemistry, Çorum, Turkey
| | - Erdoğan Özgür
- Hacettepe University, Department of Chemistry, Ankara, Turkey
| | - Lokman Uzun
- Hacettepe University, Department of Chemistry, Ankara, Turkey.
| | - Adil Denizli
- Hacettepe University, Department of Chemistry, Ankara, Turkey
| |
Collapse
|
23
|
Köse K, Uzun L. PolyGuanine methacrylate cryogels for ribonucleic acid purification. J Sep Sci 2016; 39:1998-2005. [PMID: 27004613 DOI: 10.1002/jssc.201600199] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/04/2016] [Accepted: 03/04/2016] [Indexed: 11/10/2022]
Abstract
The isolation and purification of ribonucleic acid have attracted attention recently for the understanding of the functions in detail because of the necessity for the treatment of genetic diseases. In this study, guanine-incorporated polymeric cryogels were developed to obtain highly purified ribonucleic acid. The satisfactory purification performance was achieved with the guanine-incorporated poly (2-hydroxyethyl methacrylate-guanine methacrylate) cryogels. The most crucial advantages to use guanine as a functional monomer are to obtain a real natural interaction between guanine on the polymeric material and cytosine on the ribonucleic acid. Moreover, using cryogel with a highly porous structure and high swelling ratio provide advantages of getting more water within the structure to get more analyte to interact. The characterization of cryogels has proved the success of the synthesis and the perfect natural interaction to be taken place between the ligand (guanine methacrylate) and the cytosine in the ribonucleic acid molecules. Although the pores within the structure of cryogels are small, they provide efficient and fast adsorption. The chromatographic separation performance was investigated for different conditions (pH, temperature etc.). The desorption ratio and reusability were also analyzed at the end of the five adsorption-desorption cycles with no significant changes.
Collapse
Affiliation(s)
- Kazım Köse
- Department of Chemistry, Hacettepe University, Ankara, Turkey.,Scientific Technical Research and Application Center, Hitit University, Çorum, Turkey
| | - Lokman Uzun
- Department of Chemistry, Hacettepe University, Ankara, Turkey
| |
Collapse
|
24
|
Affinity approaches in RNAi-based therapeutics purification. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:45-56. [DOI: 10.1016/j.jchromb.2016.01.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 01/05/2016] [Accepted: 01/12/2016] [Indexed: 02/07/2023]
|
25
|
Efficient large-scale preparation and purification of short single-stranded RNA oligonucleotides. Biotechniques 2016; 60:75-83. [PMID: 26842352 DOI: 10.2144/000114383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 12/12/2015] [Indexed: 11/23/2022] Open
Abstract
Sequence-specific RNA recognition by RNA-binding proteins plays a crucial role in the post-translational regulation of gene expression. Biophysical and biochemical studies help to unravel the principles of sequence-specific RNA recognition, but the methods used require large amounts of single-stranded RNA (ssRNA). Here we present a fast and robust method for large-scale preparation and purification of short ssRNA oligonucleotides for biochemical, biophysical, and structural studies. We designed an efficiently folding, self-cleaving hammerhead (HH) ribozyme to prepare ssRNA oligonucleotides. Hammerhead ribozyme RNAs self-cleave with over 95% efficiency during in vitro transcription as a function of magnesium concentration to produce high yields of the desired ssRNA products. The resulting ssRNAs can be purified from crude transcription reactions by denaturing anion-exchange chromatography and then desalted by weak anion-exchange chromatography using volatile ammonium bicarbonate buffer solutions. The ssRNA oligonucleotides produced this way are homogenous, as judged by mass spectrometry (MS), and are suitable for biochemical and biophysical studies. Moreover, for high-resolution NMR structure determination of RNA-protein complexes, our protocol enables efficient preparation of ssRNA oligonucleotides with various isotope-labeling schemes which are not commercially available.
Collapse
|
26
|
Koubek J, Chen YR, Cheng RP, Huang JJT. Nonorthogonal tRNA(cys)(Amber) for protein and nascent chain labeling. RNA (NEW YORK, N.Y.) 2015; 21:1672-82. [PMID: 26194135 PMCID: PMC4536326 DOI: 10.1261/rna.051805.115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/08/2015] [Indexed: 05/14/2023]
Abstract
In vitro-transcribed suppressor tRNAs are commonly used in site-specific fluorescence labeling for protein and ribosome-bound nascent chains (RNCs) studies. Here, we describe the production of nonorthogonal Bacillus subtilis tRNA(cys)(Amber) from Escherichia coli, a process that is superior to in vitro transcription in terms of yield, ease of manipulation, and tRNA stability. As cysteinyl-tRNA synthetase was previously shown to aminoacylate tRNA(cys)(Amber) with lower efficiency, multiple tRNA synthetase mutants were designed to optimize aminoacylation. Aminoacylated tRNA was conjugated to a fluorophore to produce BODIPY FL-cysteinyl-tRNA(cys)(Amber), which was used to generate ribosome-bound nascent chains of different lengths with the fluorophore incorporated at various predetermined sites. This tRNA tool may be beneficial in the site-specific labeling of full-length proteins as well as RNCs for biophysical and biological research.
Collapse
MESH Headings
- Amino Acyl-tRNA Synthetases/genetics
- Amino Acyl-tRNA Synthetases/metabolism
- Bacillus subtilis/genetics
- Cell-Free System
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Fluorescent Dyes/chemistry
- In Vitro Techniques
- Models, Molecular
- Protein Biosynthesis
- RNA Stability
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Transfer, Cys/biosynthesis
- RNA, Transfer, Cys/chemistry
- RNA, Transfer, Cys/genetics
- Transfer RNA Aminoacylation
Collapse
Affiliation(s)
- Jiří Koubek
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Nankang, Taipei 11529, Taiwan Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Richard Ping Cheng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | | |
Collapse
|
27
|
Cantero-Camacho Á, Gallego J. The conserved 3'X terminal domain of hepatitis C virus genomic RNA forms a two-stem structure that promotes viral RNA dimerization. Nucleic Acids Res 2015; 43:8529-39. [PMID: 26240378 PMCID: PMC4787799 DOI: 10.1093/nar/gkv786] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/21/2015] [Indexed: 02/06/2023] Open
Abstract
The 3′X domain of hepatitis C virus is a strongly conserved structure located at the 3′ terminus of the viral genomic RNA. This domain modulates the replication and translation processes of the virus in conjunction with an upstream 5BSL3.2 stem–loop, and contains a palindromic sequence that facilitates RNA dimerization. Based on nuclear magnetic resonance spectroscopy and gel electrophoresis, we report here that domain 3′X adopts a structure composed of two stem–loops, and not three hairpins or a mixture of folds, as previously proposed. This structure exposes unpaired terminal nucleotides after a double-helical stem and palindromic bases in an apical loop, favoring genomic RNA replication and self-association. At higher ionic strength the domain forms homodimers comprising an intermolecular duplex of 110 nucleotides. The 3′X sequences can alternatively form heterodimers with 5BSL3.2. This contact, reported to favor translation, likely involves local melting of one of the 3′X stem–loops.
Collapse
Affiliation(s)
- Ángel Cantero-Camacho
- Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - José Gallego
- Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001 Valencia, Spain
| |
Collapse
|
28
|
Cai WM, Chionh YH, Hia F, Gu C, Kellner S, McBee ME, Ng CS, Pang YLJ, Prestwich EG, Lim KS, Babu IR, Begley TJ, Dedon PC. A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications. Methods Enzymol 2015; 560:29-71. [PMID: 26253965 DOI: 10.1016/bs.mie.2015.03.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Here we describe an analytical platform for systems-level quantitative analysis of modified ribonucleosides in any RNA species, with a focus on stress-induced reprogramming of tRNA as part of a system of translational control of cell stress response. This chapter emphasizes strategies and caveats for each of the seven steps of the platform workflow: (1) RNA isolation, (2) RNA purification, (3) RNA hydrolysis to individual ribonucleosides, (4) chromatographic resolution of ribonucleosides, (5) identification of the full set of modified ribonucleosides, (6) mass spectrometric quantification of ribonucleosides, (6) interrogation of ribonucleoside datasets, and (7) mapping the location of stress-sensitive modifications in individual tRNA molecules. We have focused on the critical determinants of analytical sensitivity, specificity, precision, and accuracy in an effort to ensure the most biologically meaningful data on mechanisms of translational control of cell stress response. The methods described here should find wide use in virtually any analysis involving RNA modifications.
Collapse
Affiliation(s)
- Weiling Maggie Cai
- Department of Microbiology, National University of Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore
| | - Yok Hian Chionh
- Department of Microbiology, National University of Singapore, Singapore; Singapore-MIT Alliance for Research and Technology, Singapore
| | - Fabian Hia
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Chen Gu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Megan E McBee
- Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Chee Sheng Ng
- Singapore-MIT Alliance for Research and Technology, Singapore; School of Biological Sciences, Nanyang Technological Institute, Singapore
| | - Yan Ling Joy Pang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Erin G Prestwich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kok Seong Lim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - I Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Thomas J Begley
- College of Nanoscale Engineering and Science, State University of New York, Albany, New York, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
| |
Collapse
|
29
|
Vallazza B, Petri S, Poleganov MA, Eberle F, Kuhn AN, Sahin U. Recombinant messenger RNA technology and its application in cancer immunotherapy, transcript replacement therapies, pluripotent stem cell induction, and beyond. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:471-99. [DOI: 10.1002/wrna.1288] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/23/2015] [Accepted: 04/28/2015] [Indexed: 12/24/2022]
Affiliation(s)
| | | | | | | | | | - Ugur Sahin
- BioNTech RNA Pharmaceuticals GmbH; Mainz Germany
- TRON gGmbH; Mainz Germany
| |
Collapse
|
30
|
Martins R, Queiroz J, Sousa F. Ribonucleic acid purification. J Chromatogr A 2014; 1355:1-14. [DOI: 10.1016/j.chroma.2014.05.075] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 05/23/2014] [Accepted: 05/27/2014] [Indexed: 11/24/2022]
|
31
|
Flores JK, Walshe JL, Ataide SF. RNA and RNA–Protein Complex Crystallography and its Challenges. Aust J Chem 2014. [DOI: 10.1071/ch14319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
RNA biology has changed completely in the past decade with the discovery of non-coding RNAs. Unfortunately, obtaining mechanistic information about these RNAs alone or in cellular complexes with proteins has been a major problem. X-ray crystallography of RNA and RNA–protein complexes has suffered from the major problems encountered in preparing and purifying them in large quantity. Here, we review the available techniques and methods in vitro and in vivo used to prepare and purify RNA and RNA–protein complex for crystallographic studies. We also discuss the future directions necessary to explore the vast number of RNA species waiting for their atomic-resolution structure to be determined.
Collapse
|