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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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Cardoso S, de Alcântara Pessoa Filho P, Sousa F, Rodrigues Azzoni A. Arginine and di-arginine ligands for plasmid DNA purification using negative chromatography. Sep Purif Technol 2018. [DOI: 10.1016/j.seppur.2018.03.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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3
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Dias AM, Roque AC. The future of protein scaffolds as affinity reagents for purification. Biotechnol Bioeng 2016; 114:481-491. [DOI: 10.1002/bit.26090] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Ana M.G.C. Dias
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Campus Caparica Caparica 2829-516 Portugal
| | - Ana C.A. Roque
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Campus Caparica Caparica 2829-516 Portugal
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Selective purification of supercoiled p53-encoding pDNA with l-methionine–agarose matrix. Anal Biochem 2014; 459:61-9. [DOI: 10.1016/j.ab.2014.05.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/05/2014] [Accepted: 05/15/2014] [Indexed: 12/24/2022]
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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: 3.0] [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]
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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: 1.1] [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]
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Vandeventer PE, Mejia J, Nadim A, Johal MS, Niemz A. DNA adsorption to and elution from silica surfaces: influence of amino acid buffers. J Phys Chem B 2013; 117:10742-9. [PMID: 23931415 DOI: 10.1021/jp405753m] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solid phase extraction and purification of DNA from complex samples typically requires chaotropic salts that can inhibit downstream polymerase amplification if carried into the elution buffer. Amino acid buffers may serve as a more compatible alternative for modulating the interaction between DNA and silica surfaces. We characterized DNA binding to silica surfaces, facilitated by representative amino acid buffers, and the subsequent elution of DNA from the silica surfaces. Through bulk depletion experiments, we found that more DNA adsorbs to silica particles out of positively compared to negatively charged amino acid buffers. Additionally, the type of the silica surface greatly influences the amount of DNA adsorbed and the final elution yield. Quartz crystal microbalance experiments with dissipation monitoring (QCM-D) revealed multiphasic DNA adsorption out of stronger adsorbing conditions such as arginine, glycine, and glutamine, with DNA more rigidly bound during the early stages of the adsorption process. The DNA film adsorbed out of glutamate was more flexible and uniform throughout the adsorption process. QCM-D characterization of DNA elution from the silica surface indicates an uptake in water mass during the initial stage of DNA elution for the stronger adsorbing conditions, which suggests that for these conditions the DNA film is partly dehydrated during the prior adsorption process. Overall, several positively charged and polar neutral amino acid buffers show promise as an alternative to methods based on chaotropic salts for solid phase DNA extraction.
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Affiliation(s)
- Peter E Vandeventer
- Keck Graduate Institute of Applied Life Sciences , 535 Watson Drive, Claremont, California 91711, United States
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Bonturi N, Radke VSCO, Bueno SMA, Freitas S, Azzoni AR, Miranda EA. Sodium citrate and potassium phosphate as alternative adsorption buffers in hydrophobic and aromatic thiophilic chromatographic purification of plasmid DNA from neutralized lysate. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 919-920:67-74. [DOI: 10.1016/j.jchromb.2013.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Revised: 12/26/2012] [Accepted: 01/13/2013] [Indexed: 11/30/2022]
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Gaspar VM, Cruz C, Queiroz JA, Pichon C, Correia IJ, Sousa F. Sensitive Detection of Peptide–Minicircle DNA Interactions by Surface Plasmon Resonance. Anal Chem 2013; 85:2304-11. [DOI: 10.1021/ac303288x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Vítor M. Gaspar
- CICS-UBI - Centro de Investigação
em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação
em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - João A. Queiroz
- CICS-UBI - Centro de Investigação
em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Chantal Pichon
- Centre de Biophysique Moléculaire
CNRS UPR4301, INSERM and University of Orléans, F-45071 Orléans cedex 2, France
| | - Ilídio J. Correia
- CICS-UBI - Centro de Investigação
em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Fani Sousa
- CICS-UBI - Centro de Investigação
em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
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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: 1.2] [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
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Gaspar VM, Correia IJ, Sousa Â, Silva F, Paquete CM, Queiroz JA, Sousa F. Nanoparticle mediated delivery of pure P53 supercoiled plasmid DNA for gene therapy. J Control Release 2011; 156:212-22. [DOI: 10.1016/j.jconrel.2011.08.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 08/03/2011] [Accepted: 08/05/2011] [Indexed: 12/31/2022]
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Leitner A, Sturm M, Lindner W. Tools for analyzing the phosphoproteome and other phosphorylated biomolecules: a review. Anal Chim Acta 2011; 703:19-30. [PMID: 21843671 DOI: 10.1016/j.aca.2011.07.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 07/07/2011] [Accepted: 07/10/2011] [Indexed: 11/28/2022]
Abstract
Enrichment, separation and mass spectrometric analysis of biomolecules carrying a phosphate group plays an important role in current analytical chemistry. Application areas range from the preparative enrichment of phospholipids for biotechnological purposes and the separation and purification of plasmid DNA or mRNA to the specific preconcentration of phosphoproteins and -peptides to facilitate their later identification and characterization by mass spectrometry. Most of the recent improvements in this field were triggered by the need for phosphopeptide enrichment technology for the analysis of cellular protein phosphorylation events with the help of liquid chromatography-mass spectrometry. The high sensitivity of mass spectrometry and the possibility to combine this technique with different separation modes in liquid chromatography have made it the method of choice for proteome analysis. However, in the case of phosphoprotein analysis, the low abundance of the resulting phosphopeptides and their low quality fragment spectra interfere with the identification of phosphorylation events. Recent developments in phosphopeptide enrichment and fragmentation technologies successfully helped to overcome these limitations. In this review, we will focus on sample preparation techniques in the field of phosphoproteomics, but also highlight recent advancements for the analysis of other phosphorylated biomolecules.
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Chen WH, Fu JY, Kourentzi K, Willson RC. Nucleic acid affinity of clustered-charge anion exchange adsorbents: Effects of ionic strength and ligand density. J Chromatogr A 2011; 1218:258-62. [DOI: 10.1016/j.chroma.2010.11.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 11/08/2010] [Accepted: 11/11/2010] [Indexed: 10/18/2022]
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Ongkudon CM, Ho J, Danquah MK. Mitigating the looming vaccine crisis: production and delivery of plasmid-based vaccines. Crit Rev Biotechnol 2010; 31:32-52. [DOI: 10.3109/07388551.2010.483460] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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16
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Sousa A, Sousa F, Prazeres DMF, Queiroz JA. Histidine affinity chromatography of homo-oligonucleotides. Role of multiple interactions on retention. Biomed Chromatogr 2009; 23:745-53. [PMID: 19296518 DOI: 10.1002/bmc.1179] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The recent application of histidine-agarose affinity supports in plasmid purification takes advantage of the biorecognition of nucleic acid bases by the histidine ligand. This consideration prompted the need for better understanding the interactions involved in affinity chromatography of plasmid DNA with the histidine-agarose support. In this work, we used synthetic homo-deoxyoligonucleotides with different sizes (1-30 nucleotides long), to explore the effect of several conditions like hydrophobic character of the individual bases, presence of secondary structures, temperature, pH and salt concentration on the mechanism of retention of nucleic acids to histidine-agarose support. One of the most striking results shows that histidine interacts preferentially with guanine, and the presence of secondary structures on polyA and polyG oligonucleotides has a significant influence on retention. Otherwise, the temperature manipulation has not shown a direct influence on oligonucleotide retention, only inducing conformational changes on secondary structures. Overall, the results obtained provide valuable information for the future development and implementation of histidine and other amino acids as ligands in chromatography for the purification of plasmid DNA and other nucleic acids, by improving the knowledge of the interactions involved as well as of the parameters influencing the retention.
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Affiliation(s)
- A Sousa
- CICS-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001 Covilhã, Portugal
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Sousa A, Sousa F, Queiroz JA. Selectivity of arginine chromatography in promoting different interactions using synthetic oligonucleotides as model. J Sep Sci 2009; 32:1665-72. [PMID: 19370734 DOI: 10.1002/jssc.200800690] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Arginine has been effectively used in several chromatography methodologies to improve recovery, resolution, and to suppress aggregation. Recently, arginine chromatography was used to fully separate supercoiled and open circular plasmid DNA isoforms. The specific recognition of supercoiled plasmid isoform by arginine was hypothesised to be due to the ability of arginine matrix to be involved in complex interactions that are partly dependent on the conformation of the DNA molecule. In light of these considerations a study was conducted to understand the several interactions that a DNA molecule can promote with the arginine support, in accordance with the chromatographic conditions established. Consequently, knowing the ideal conditions to promote the specific interactions, it could be possible to perform a more targeted and efficient purification. This work describes the chromatography of oligonucleotides with sizes up to 30 bases on the arginine-agarose gel. The effect of several conditions like hydrophobic character of the individual bases, molecular mass of the oligonucleotides, presence of secondary structures, temperature and elution buffer composition (salt and arginine supplemented buffer) was investigated. According to previous atomic data referent to possible interactions between amino acids and DNA nucleotides, arginine can preferentially interact with guanine by hydrogen bond, but other interactions (ionic interactions, van der Waals contacts, water mediated bonds) may also be present and become dominant depending on the conditions used. The results also revealed that the application of arginine in the elution buffer led to an effective elution of oligonucleotides from the arginine chromatographic support by a competition strategy. In general, it was suggested that the affinity interaction promoted by the arginine support is responsible for the specific recognition of particular oligonucleotide bases, involving multiple interactions.
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Affiliation(s)
- Angela Sousa
- Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
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Yamamoto S, Yoshimoto N, Tarmann C, Jungbauer A. Binding site and elution behavior of DNA and other large biomolecules in monolithic anion-exchange chromatography. J Chromatogr A 2009; 1216:2616-20. [PMID: 19201415 DOI: 10.1016/j.chroma.2009.01.060] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 01/19/2009] [Accepted: 01/20/2009] [Indexed: 11/15/2022]
Abstract
Our previous study has shown that there is a good correlation between the number of charges of DNA (from trimer to 50-mer) and the number of binding sites B in electrostatic interaction chromatography (ion-exchange chromatography, IEC). It was also found that high salt (NaCl) concentration is needed to elute large DNAs (>0.6M). In this paper we further performed experiments with large DNAs (up to 95-mer polyT and polyA) and charged liposome particles of different sizes (ca. 30, 50 and 100 nm) with a monolithic anion-exchange disk in order to understand the binding and elution mechanism of very large charged biomolecules or particles. The peak salt (NaCl) concentration increased with increasing DNA length. However, above 50-mer DNAs the value did not increase significantly with DNA length (ca. 0.65-0.70 M). For liposome particles of different sizes the peak salt concentration (ca. 0.62 M) was similar and slightly lower than that for large DNAs (ca. 0.65-0.70 M). The binding site values (ca. 25-30) are smaller than those for large DNAs. When arginine was used as a mobile phase modulator, the elution position of polyA and polyT became very close whereas in NaCl gradient elution polyT appeared after polyA eluted. This was mainly due to suppression of hydrophobic interaction by arginine.
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Affiliation(s)
- Shuichi Yamamoto
- Bio-Process Engineering Laboratory, School of Engineering and Graduate School of Medicine, Yamaguchi University, Tokiwadai, Ube 755-8611, Japan.
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Sousa F, Passarinha L, Queiroz J. Biomedical application of plasmid DNA in gene therapy: A new challenge for chromatography. Biotechnol Genet Eng Rev 2009. [DOI: 10.5661/bger-26-83] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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