1
|
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: 5] [Impact Index Per Article: 2.5] [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
|
2
|
Carapito R, Bernardo SC, Pereira MM, Neves MC, Freire MG, Sousa F. Multimodal ionic liquid-based chromatographic supports for an effective RNA purification. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2023.123676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
|
3
|
Minkner R, Boonyakida J, Park EY, Wätzig H. Oligonucleotide separation techniques for purification and analysis: What can we learn for today's tasks? Electrophoresis 2022; 43:2402-2427. [PMID: 36285667 DOI: 10.1002/elps.202200079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/09/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
Nucleic acids are the blueprint of life. They are not only the construction plan of the single cell or higher associations of them, but also necessary for function, communication and regulation. Due to the pandemic, the attention shifted in particular to their therapeutic potential as a vaccine. As pharmaceutical oligonucleotides are unique in terms of their stability and application, special delivery systems were also considered. Oligonucleotide production systems can vary and depend on the feasibility, availability, price and intended application. To achieve good purity, reliable results and match the strict specifications in the pharmaceutical industry, the separation of oligonucleotides is always essential. Besides the separation required for production, additional and specifically different separation techniques are needed for analysis to determine if the product complies with the designated specifications. After a short introduction to ribonucleic acids (RNAs), messenger RNA vaccines, and their production and delivery systems, an overview regarding separation techniques will be provided. This not only emphasises electrophoretic separations but also includes spin columns, extractions, precipitations, magnetic nanoparticles and several chromatographic separation principles, such as ion exchange chromatography, ion-pair reversed-phase, size exclusion and affinity.
Collapse
Affiliation(s)
- Robert Minkner
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jirayu Boonyakida
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan.,Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Enoch Y Park
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan.,Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hermann Wätzig
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| |
Collapse
|
4
|
Neves M, Pereira P, Pedro A, Martins J, Trindade T, Queiroz J, Freire M, Sousa F. Improved ionic-liquid-functionalized macroporous supports able to purify nucleic acids in one step. Mater Today Bio 2020; 8:100086. [PMID: 33319188 PMCID: PMC7723793 DOI: 10.1016/j.mtbio.2020.100086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/28/2020] [Accepted: 11/02/2020] [Indexed: 11/16/2022] Open
Abstract
Nucleic acids are relevant biopolymers in therapy and diagnosis, for which their purity and biological activity are of crucial relevance. However, these features are difficult to achieve by cost-effective methods. Herein, we report the functionalization of a macroporous chromatographic support functionalized with an ionic liquid (IL) with remarkable performance to purify nucleic acids. An initial screening with distinct IL chemical structures supported in silica was carried out, allowing to identify the IL 1-methyl-3-propylimidazolium chloride as the most promising ligand. A chromatographic macroporous matrix able to be used in preparative liquid chromatography was then functionalized and binding/elution studies were performed. The IL 1-methyl-3-propylimidazolium chloride acts as a multimodal ligand with a remarkable dynamic binding capacity. This macroporous support allows the (one-step) purification of nucleic acids, namely small RNAs, ribosomal RNA, and genomic DNA, from a bacterial lysate, and can be regenerated and reused without compromising its separation performance.
Collapse
Affiliation(s)
- M.C. Neves
- CICECO – Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - P. Pereira
- CICS-UBI – Health Sciences Research Centre, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - A.Q. Pedro
- CICECO – Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - J.C. Martins
- CICS-UBI – Health Sciences Research Centre, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - T. Trindade
- CICECO – Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - J.A. Queiroz
- CICS-UBI – Health Sciences Research Centre, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - M.G. Freire
- CICECO – Aveiro Institute of Materials, Chemistry Department, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - F. Sousa
- CICS-UBI – Health Sciences Research Centre, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| |
Collapse
|
5
|
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: 1.7] [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
|
6
|
Nwokeoji AO, Kilby PM, Portwood DE, Dickman MJ. RNASwift: A rapid, versatile RNA extraction method free from phenol and chloroform. Anal Biochem 2016; 512:36-46. [DOI: 10.1016/j.ab.2016.08.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 12/11/2022]
|
7
|
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: 12] [Impact Index Per Article: 1.3] [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
|
8
|
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: 1.4] [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]
|
9
|
Dye affinity cryogels for plasmid DNA purification. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2015; 56:318-24. [DOI: 10.1016/j.msec.2015.06.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 12/11/2014] [Accepted: 06/22/2015] [Indexed: 11/18/2022]
|
10
|
Pereira P, Sousa Â, Queiroz JA, Figueiras A, Sousa F. Pharmaceutical-grade pre-miR-29 purification using an agmatine monolithic support. J Chromatogr A 2014; 1368:173-82. [DOI: 10.1016/j.chroma.2014.09.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 09/14/2014] [Accepted: 09/27/2014] [Indexed: 02/08/2023]
|
11
|
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: 4.0] [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]
|
12
|
Purification of pre-miR-29 by a new O-phospho-l-tyrosine affinity chromatographic strategy optimized using design of experiments. J Chromatogr A 2014; 1343:119-27. [DOI: 10.1016/j.chroma.2014.03.071] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 03/14/2014] [Accepted: 03/27/2014] [Indexed: 01/01/2023]
|
13
|
Pereira P, Sousa Â, Queiroz J, Correia I, Figueiras A, Sousa F. Purification of pre-miR-29 by arginine-affinity chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 951-952:16-23. [DOI: 10.1016/j.jchromb.2014.01.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/12/2014] [Accepted: 01/14/2014] [Indexed: 11/26/2022]
|
14
|
Pereira P, Sousa Â, Queiroz J, Figueiras A, Sousa F. New approach for purification of pre-miR-29 using lysine-affinity chromatography. J Chromatogr A 2014; 1331:129-32. [DOI: 10.1016/j.chroma.2014.01.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/06/2014] [Accepted: 01/10/2014] [Indexed: 11/29/2022]
|
15
|
Caramelo-Nunes C, Almeida P, Marcos J, Tomaz C. Aromatic ligands for plasmid deoxyribonucleic acid chromatographic analysis and purification: An overview. J Chromatogr A 2014; 1327:1-13. [DOI: 10.1016/j.chroma.2013.12.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/19/2013] [Accepted: 12/20/2013] [Indexed: 12/25/2022]
|
16
|
New approach in RNA quantification using arginine-affinity chromatography: potential application in eukaryotic and chemically synthesized RNA. Anal Bioanal Chem 2013; 405:8849-58. [DOI: 10.1007/s00216-013-7334-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/20/2013] [Accepted: 08/30/2013] [Indexed: 10/26/2022]
|
17
|
Mahut M, Gargano A, Schuchnigg H, Lindner W, Lämmerhofer M. Chemoaffinity material for plasmid DNA analysis by high-performance liquid chromatography with condition-dependent switching between isoform and topoisomer selectivity. Anal Chem 2013; 85:2913-20. [PMID: 23391311 DOI: 10.1021/ac3034823] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plasmid DNA may exist in three isoforms, the linear, open-circular (oc, "nicked"), and covalently closed circular (ccc, "supercoiled") form. We have recently reported on the chromatographic separation of supercoiled plasmid topoisomers on cinchona-alkaloid modified silica-based stationary phases. Herein, we present a selectivity switching mechanism to achieve separation of isoforms and/or supercoiled topoisomers using the very same chromatographic column and system. While salt gradient elution facilitates topoisomer separation, the supercoiled species are eluting as a single peak upon elution by a mixed pH and organic modifier gradient, still well separated from the other isoforms. We have found that a mobile phase pH value near the pI of the zwitterionic adsorbent surface leads to full recovery of all plasmid DNA isoforms, which is a major issue when using anion exchange-based resins. Furthermore, the observed elution pattern, oc < linear < ccc, is constant upon changes of mobile phase composition, gradient slope, and plasmid size. The remarkable isoform selectivity found on quinine-based selectors is explained by van't Hoff plots, revealing a different binding mechanism between the supercoiled plasmid on one hand and the oc and linear isoforms on the other hand.
Collapse
Affiliation(s)
- Marek Mahut
- Institute of Analytical Chemistry, University of Vienna, Währinger Strasse 38, A-1090 Vienna, Austria
| | | | | | | | | |
Collapse
|
18
|
Martins R, Maia CJ, Queiroz JA, Sousa F. A new strategy for RNA isolation from eukaryotic cells using arginine affinity chromatography. J Sep Sci 2012; 35:3217-26. [DOI: 10.1002/jssc.201200338] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 05/28/2012] [Accepted: 06/02/2012] [Indexed: 12/17/2022]
Affiliation(s)
- Rita Martins
- CICS-UBI-Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
| | - Cláudio J. Maia
- CICS-UBI-Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
| | - João A. Queiroz
- CICS-UBI-Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
| | - Fani Sousa
- CICS-UBI-Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
| |
Collapse
|