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Ribeiro J, Luís MÂ, Rodrigues B, Santos FM, Mesquita J, Boto R, Tomaz CT. Cryogels and Monoliths: Promising Tools for Chromatographic Purification of Nucleic Acids. Gels 2024; 10:198. [PMID: 38534616 DOI: 10.3390/gels10030198] [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: 02/17/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The increasing demand for highly pure biopharmaceuticals has put significant pressure on the biotechnological industry to innovate in production and purification processes. Nucleic acid purification, crucial for gene therapy and vaccine production, presents challenges due to the unique physical and chemical properties of these molecules. Meeting regulatory standards necessitates large quantities of biotherapeutic agents of high purity. While conventional chromatography offers versatility and efficiency, it suffers from drawbacks like low flow rates and binding capacity, as well as high mass transfer resistance. Recent advancements in continuous beds, including monoliths and cryogel-based systems, have emerged as promising solutions to overcome these limitations. This review explores and evaluates the latest progress in chromatography utilizing monolithic and cryogenic supports for nucleic acid purification.
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Affiliation(s)
- João Ribeiro
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
- Department of Chemistry, University of Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal
| | - Marco  Luís
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
- Department of Chemistry, University of Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal
| | - Bruno Rodrigues
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
- Department of Chemistry, University of Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal
| | - Fátima Milhano Santos
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Calle Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Joana Mesquita
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
| | - Renato Boto
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
- Department of Chemistry, University of Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal
| | - Cândida Teixeira Tomaz
- CICS-UBI-Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
- Department of Chemistry, University of Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal
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Ferreira PL, Marie H, Berger T, Edelmann B, Rammo O, Sousa F. Evaluation of novel chromatographic prototypes for supercoiled plasmid DNA polishing. Front Bioeng Biotechnol 2024; 11:1296444. [PMID: 38249801 PMCID: PMC10797707 DOI: 10.3389/fbioe.2023.1296444] [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: 09/18/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024] Open
Abstract
Since the world first approved gene therapeutics, nucleic acid-based therapies have gained prominence. Several strategies for DNA-based therapy have been approved, and numerous clinical trials for plasmid DNA (pDNA)-based vaccines are currently in development. Due to the rising interest in pDNA for vaccination and gene therapy, plasmid manufacturing must become more effective. One of the most critical steps is downstream processing, involving isolation and purification procedures. To comply with the regulatory guidelines, pDNA must be available as a highly purified, homogeneous preparation of supercoiled pDNA (sc pDNA). This process undertakes several challenges, primarily due to the diversity of molecules derived from the producer organism. In this study, different resins were tested for the adsorption and selective polishing of sc pDNA. To identify optimal pDNA adsorption conditions, batch and column assays were performed with different resins while promoting electrostatic and hydrophobic interactions. The effect of ionic strength, pH, and contact time were evaluated and optimized. Additionally, static and dynamic binding capacities were determined for the selected resins. Analytical chromatography and agarose gel electrophoresis were used to assess the selectivity of the most promising resins toward sc pDNA isoform. Also, genomic DNA, endotoxins, and proteins were quantified to characterize the final sc pDNA quality. At the same time, the recovery and purity yields were evaluated by quantification of sc pDNA after the purification procedure. Overall, the results of the chromatographic assays using agmatine- and arginine-based resins have shown promising potential for sc pDNA polishing. Both resins demonstrated excellent binding capacity for pDNA, with agmatine outperforming arginine-based resin in terms of capacity. However, arginine-based resin exhibited a superior pDNA recovery yield, reaching a notable 52.2% recovery compared to 10.09% from agmatine. Furthermore, both resins exhibited high relative purity levels above 90% for the sc pDNA. The comprehensive characterization of the recovered sc pDNA also revealed a significant reduction in gDNA levels, reinforcing the potential of these prototypes for obtaining high-quality and pure sc pDNA. These findings highlight the promising applications of both resins in scalable pDNA purification processes for gene therapy and biopharmaceutical applications.
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Affiliation(s)
- Pedro L. Ferreira
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | | | - Tim Berger
- Merck Life Science KGaA, Darmstadt, Germany
| | | | | | - Fani Sousa
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
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Černigoj U, Vidič J, Ferjančič A, Sinur U, Božič K, Mencin N, Martinčič Celjar A, Gagnon P, Štrancar A. Guanidine improves DEAE anion exchange-based analytical separation of plasmid DNA. Electrophoresis 2021; 42:2619-2625. [PMID: 34569093 DOI: 10.1002/elps.202100210] [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: 07/06/2021] [Revised: 09/04/2021] [Accepted: 09/17/2021] [Indexed: 11/10/2022]
Abstract
Elution of strong and weak anion exchangers with sodium chloride gradients is commonly employed for analysis of sample mixtures containing different isomers of plasmid DNA. Gradient elution of a weak anion exchanger (diethylaminoethyl) in the presence of guanidine hydrochloride (Gdn) roughly doubles resolution between open-circular (oc) and supercoiled (sc) isomers. It also improves resolution among sc, linear, and multimeric/aggregated forms. Sharper elution peaks with less tailing increase sensitivity about 30%. However, elution with an exclusively Gdn gradient to 900 mM causes more than 10% loss of plasmid. Elution with a sodium chloride gradient while maintaining Gdn at a level concentration of 300 mM achieves close to 100% recovery of sc plasmid while maintaining the separation improvements achieved by exclusively Gdn elution. Corresponding improvements in separation performance are not observed on a strong (quaternary amine) anion exchanger. Other chaotropic salts do not produce a favorable result on either exchanger, nor does the inclusion of surfactants or EDTA. Selectivity of the diethylaminoethyl-Gdn method is orthogonal to electrophoresis, but with better quantification than agarose electrophoresis, better quantitative accuracy than CE, and resolution approaching CE.
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Affiliation(s)
- Urh Černigoj
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
| | - Jana Vidič
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
| | - Ana Ferjančič
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
| | - Urša Sinur
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
| | - Klemen Božič
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
| | - Nina Mencin
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
| | | | - Pete Gagnon
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
| | - Aleš Štrancar
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
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Valente JFA, Queiroz JA, Sousa F. Dilemma on plasmid DNA purification: binding capacity vs selectivity. J Chromatogr A 2020; 1637:461848. [PMID: 33421679 DOI: 10.1016/j.chroma.2020.461848] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 10/22/2022]
Abstract
Plasmid DNA chromatography is a powerful field in constant development and evolution. The use of this technique is considered mandatory in the production of an efficient and safe formulation to be applied for plasmid-mediated gene therapy. Concerning this, the search for an ideal chromatographic support/ligand combination motivated scientist to pursue a continuous improvement on the plasmid chromatography performance, looking for a progression on the ligands and supports used. The present review explores the different approaches used over time to purify plasmid DNA, ambitioning both high recovery and high purity levels. Overall, it is presented a critical discussion relying on the relevance of the binding capacity versus selectivity of the supports.
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Affiliation(s)
- J F A Valente
- CICS-UBI - Health Sciences Research Centre, Universidade da Beira Interior, Avenida Infante D. Henrique, 6200-506Covilhã, Portugal; CDRSP-IPLEIRIA - Centre for Rapid and Sustainable Product Development, Instituto Politécnico de Leiria, Rua de Portugal - Zona Industrial, 2430-028Marinha Grande, Portugal
| | - J A Queiroz
- CICS-UBI - Health Sciences Research Centre, Universidade da Beira Interior, Avenida Infante D. Henrique, 6200-506Covilhã, Portugal
| | - F Sousa
- CICS-UBI - Health Sciences Research Centre, Universidade da Beira Interior, Avenida Infante D. Henrique, 6200-506Covilhã, Portugal.
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Purification of supercoiled p53-encoding plasmid using an arginine-modified macroporous support. J Chromatogr A 2020; 1618:460890. [DOI: 10.1016/j.chroma.2020.460890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/02/2020] [Accepted: 01/13/2020] [Indexed: 12/19/2022]
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Santos T, Brito A, Boto R, Sousa P, Almeida P, Cruz C, Tomaz C. Influenza DNA vaccine purification using pHEMA cryogel support. Sep Purif Technol 2018. [DOI: 10.1016/j.seppur.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Abdulrahman A, Ghanem A. Recent advances in chromatographic purification of plasmid DNA for gene therapy and DNA vaccines: A review. Anal Chim Acta 2018; 1025:41-57. [PMID: 29801607 DOI: 10.1016/j.aca.2018.04.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 12/16/2022]
Abstract
The wide spread of infectious diseases have provoked the scientists to develop new types of vaccines. Among the different types of vaccines, the recently discovered plasmid DNA vaccines, have gained tremendous attentions in the last few decades as a modern approach of vaccination. The scientific interest in plasmid DNA vaccines is attributed to their prominent efficacy as they trigger not only the cellular immune response but also the humoral immune responses. Moreover, pDNA vaccines are easily to be stored, shipped and produced. However, the purification of the pDNA vaccines is a crucial step in their production and administration, which is usually conducted by different chromatographic techniques. This review summarizes the most recent chromatographic purification methods provided in the literature during the last five years following our last review in 2013, including affinity chromatography, hydrophobic interaction chromatography, ion exchange chromatography, multimodal chromatography, sample displacement chromatography and miscellaneous chromatographic methods.
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Affiliation(s)
- Ahmed Abdulrahman
- Chirality Program, Faculty of Science and Technology, University of Canberra, Australian Capital Territory (ACT), 2617, Australia
| | - Ashraf Ghanem
- Chirality Program, Faculty of Science and Technology, University of Canberra, Australian Capital Territory (ACT), 2617, Australia. http://www.chiralitygroup.com
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Acquah C, Danquah MK, Chan YW, Moy CKS, Ongkudon CM, Lau SY. Chromatographic characterisation of aptamer-modified poly(EDMA-co-GMA) monolithic disk format for protein binding and separation. SEP SCI TECHNOL 2018. [DOI: 10.1080/01496395.2018.1443139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Caleb Acquah
- Curtin Malaysia Research Institute, Curtin University, Miri, Malaysia
- Department of Chemical Engineering, Curtin University, Miri, Malaysia
| | - Michael K. Danquah
- Curtin Malaysia Research Institute, Curtin University, Miri, Malaysia
- Department of Chemical Engineering, Curtin University, Miri, Malaysia
| | - Yi Wei Chan
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - Charles K. S. Moy
- Department of Civil Engineering, Xi’an Jiaotong-Liverpool University, Suzhou, China
| | - Clarence M. Ongkudon
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - Sie Yon Lau
- Department of Chemical Engineering, Curtin University, Miri, Malaysia
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Raczyńska ED, Gal JF, Maria PC. The guanylated bioamine agmatine – A theoretical investigation of its structure and exceptional high basicity in the gas phase. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.03.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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