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Paiva WA, Alakwe SD, Marfai J, Jennison-Henderson MV, Achong RA, Duche T, Weeks AA, Robertson-Anderson RM, Oldenhuis NJ. From Bioreactor to Bulk Rheology: Achieving Scalable Production of Highly Concentrated Circular DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2405490. [PMID: 38935929 DOI: 10.1002/adma.202405490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/10/2024] [Indexed: 06/29/2024]
Abstract
DNA serves as a model system in polymer physics due to its ability to be obtained as a uniform polymer with controllable topology and nonequilibrium behavior. Currently, a major obstacle in the widespread adoption of DNA is obtaining it on a scale and cost basis that accommodates bulk rheology and high-throughput screening. To address this, recent advancements in bioreactor-based plasmid DNA production is coupled with anion exchange chromatography producing a unified approach to generating gram-scale quantities of monodisperse DNA. With this method, 1.1 grams of DNA is obtained per batch to generate solutions with concentrations up to 116 mg mL-1. This solution of uniform supercoiled and relaxed circular plasmid DNA, is roughly 69 times greater than the overlap concentration. The utility of this method is demonstrated by performing bulk rheology measurements at sample volumes up to 1 mL on DNA of different lengths, topologies, and concentrations. The measured elastic moduli are orders of magnitude larger than those previously reported for DNA and allowed for the construction of a time-concentration superposition curve that spans 12 decades of frequency. Ultimately, these results can provide important insights into the dynamics of ring polymers and the nature of highly condensed DNA dynamics.
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Affiliation(s)
- Wynter A Paiva
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Somkene D Alakwe
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Juexin Marfai
- Department of Physics and Biophysics, College of Arts and Sciences, University of San Diego, Shiley Center for Science and Technology, 5998 Alcala Park, San Diego, CA, 92110, USA
| | - Madigan V Jennison-Henderson
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Rachel A Achong
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Tinotenda Duche
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - April A Weeks
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Rae M Robertson-Anderson
- Department of Physics and Biophysics, College of Arts and Sciences, University of San Diego, Shiley Center for Science and Technology, 5998 Alcala Park, San Diego, CA, 92110, USA
| | - Nathan J Oldenhuis
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
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2
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Chavan D, Adolacion JRT, Crum M, Nandy S, Lee KH, Vu B, Kourentzi K, Sabo A, Willson RC. Isolation and Barcoding of Trace Pollen-free DNA for Authentication of Honey. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14084-14095. [PMID: 36279293 DOI: 10.1021/acs.jafc.2c04309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Adulteration and mislabeling of honey to mask its true origin have become a global concern. Pollen microscopy, the current gold standard for identifying honey's geographical and plant origins, is laborious, requires extensive training, and fails to identify filtered honey and honey spiked with pollen from a more favorable plant to disguise its origins. We successfully isolated pollen-free DNA from filtered honey using three types of adsorbents: (i) anti-dsDNA antibodies coupled to magnetic microspheres; (ii) anion-exchange adsorbent; and (iii) ceramic hydroxyapatite. The internal transcribed spacer 2 region of the captured pollen-free DNA was polymerase chain reaction-amplified and subjected to next-generation sequencing. Using an in-house bioinformatics pipeline, initial experiments showed that anion exchange had the greatest capacity to capture trace pollen-free DNA, and it was successfully applied to isolate DNA from five honey samples. Enrichment of trace pollen-free DNA from filtered honey samples opens a new approach for identifying the true origins of honey.
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Affiliation(s)
- Dimple Chavan
- Department of Biology and Biochemistry, University of Houston, Houston, Texas77204, United States
| | - Jay R T Adolacion
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas77204, United States
| | - Mary Crum
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas77204, United States
| | - Suman Nandy
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas77204, United States
| | - Kyung Hyun Lee
- Center for Clinical Research & Evidence-Based Medicine, The University of Texas Health Science Center at Houston, Houston, Texas77030, United States
| | - Binh Vu
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas77204, United States
| | - Katerina Kourentzi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas77204, United States
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas77030, United States
| | - Richard C Willson
- Department of Biology and Biochemistry, University of Houston, Houston, Texas77204, United States
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas77204, United States
- Escuela de Medicina y Ciencias de la Salud ITESM, Monterrey, Nuevo León64710, Mexico
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3
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Mikhail B, Dmitrijs M, Ivan M. A new device-mediated miniprep method. AMB Express 2022; 12:21. [PMID: 35192071 PMCID: PMC8863996 DOI: 10.1186/s13568-022-01360-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 11/30/2022] Open
Abstract
Small-scale plasmid DNA preparation or miniprep is a fundamental technique in estimation cloning experiments and is widely used for DNA methylation analysis in epigenetic research. Current plasmid DNA minipreps use the alkali-SDS-based method in a three-solution format and require spin column-based purification steps. This procedure requires the vortexing or pipetting of pelleted bacteria by centrifugation and manual mixing of the solutions. Here, we describe a centrifuge/mixer-based instrument with the ability to perform centrifugation, vibration, and rotor oscillation in order to perform all steps of plasmid DNA isolation by device only. We found that by applying rotor oscillation-driven mixing of solutions added in the lysis and neutralization steps, homogeneous mixing was achieved within 5 s at a rotor oscillation amplitude of 45° and oscillation frequency of 400 ± 30 rpm, yielding the maximal quantity and quality of plasmid DNA. No increase in host chromosome presence purified by this approach occurs for high-copy-number plasmids compared to manually performed miniprep, and indeed, there is a significant decrease in the presence of the chromosomal fraction in low-copy-number plasmids. The supercoiled form of plasmid DNA purified at a rotor oscillation amplitude of 45° does not turn into an open circular (OC) isoform when the plasmid is stored for 1 year at plus four degrees, in contrast to the plasmid purified with rotor oscillation amplitudes of 270°, 180° and 90°. The programmed time-work-efficient protocol of plasmid miniprep installed in the device gives the extreme simplicity of plasmid minipreps speeding up and facilitating the isolation of plasmid DNAs. New devise-mediated plasmid miniprep method (DM) performs all mixing steps without operator intervention. The DM method produces plasmid DNAs free of the dCCC form and significantly reduces the contamination with genomic DNA in the low-copy-number plasmid. DM miniprep plasmids are reliable templates for bisulfite PCR sequencing analysis.
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Alves CPA, Prazeres DMF, Monteiro GA. Minicircle Biopharmaceuticals–An Overview of Purification Strategies. FRONTIERS IN CHEMICAL ENGINEERING 2021. [DOI: 10.3389/fceng.2020.612594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Minicircles are non-viral delivery vectors with promising features for biopharmaceutical applications. These vectors are plasmid-derived circular DNA molecules that are obtained in vivo in Escherichia coli by the intramolecular recombination of a parental plasmid, which generates a minicircle containing the eukaryotic therapeutic cassette of interest and a miniplasmid containing the prokaryotic backbone. The production process results thus in a complex mixture, which hinders the isolation of minicircle molecules from other DNA molecules. Several strategies have been proposed over the years to meet the challenge of purifying and obtaining high quality minicircles in compliance with the regulatory guidelines for therapeutic use. In minicircle purification, the characteristics of the strain and parental plasmid used have a high impact and strongly affect the purification strategy that can be applied. This review summarizes the different methods developed so far, focusing not only on the purification method itself but also on its dependence on the upstream production strategy used.
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5
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Almeida AM, Costa D, Simões AR, Queiroz JA, Sousa F, Sousa Â. Enhancement of a biotechnological platform for the purification and delivery of a human papillomavirus supercoiled plasmid DNA vaccine. N Biotechnol 2020; 59:1-9. [PMID: 32622863 DOI: 10.1016/j.nbt.2020.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 03/30/2020] [Accepted: 04/13/2020] [Indexed: 01/21/2023]
Abstract
New biotechnological strategies are being explored, aimed at rapid and economic manufacture of large quantities of DNA vaccines with the required purity for therapeutic applications, as well as their correct delivery as biopharmaceuticals to target cells. This report describes the purification of supercoiled (sc) HPV-16 E6/E7 plasmid DNA (pDNA) vaccine from a bacterial lysate, using an arginine-based monolith, presenting a spacer arm in its configuration. To enhance the performance of the purification process, monolith modification with the spacer arm can improve accessibility of the arginine ligand. By using a low NaCl concentration at pH 7.0, a condition to eliminate the RNA impurity directly in the flow through was established. The pH increase to 7.5 allowed the elimination of non-functional pDNA isoforms, the sc pDNA being recovered by increasing the ionic strength. As well as a binding capacity of 2.53 mg/mL obtained with a pre-purified sc pDNA sample, the column also purified sc pDNA from high lysate loading, with capacities above 1 mg/mL. Due to the sample displacement phenomena, non-functional pDNA isoforms were eliminated throughout column loading, favoring the degree of purity of final sc pDNA of 93.3%-98.5%. Thereafter, purified sc pDNA was successfully encapsulated into CaCO3-gelatin nano-complexes. Delivery of the pDNA-carriers to THP-1 cells was assessed through pDNA cellular uptake evaluation and correct E6 expression was verified by mRNA and protein detection. A biotechnological platform was established for sc pDNA purification and delivery to dendritic cells, stimulating further in vivo studies.
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Affiliation(s)
- Ana M Almeida
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Diana Costa
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Ana R Simões
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - João A Queiroz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Fani Sousa
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Ângela Sousa
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal.
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6
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Lu XA, He T, Han Z, Ding Y, Zhao L, Liu G, De Smet F, Huang X, Chen D, Qi F, Zhao X. Production of lentiviral vectors in suspension cells using low proportion of supercoiled circular plasmid DNA. Cytotechnology 2020; 72:10.1007/s10616-020-00433-4. [PMID: 33123933 PMCID: PMC7695760 DOI: 10.1007/s10616-020-00433-4] [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: 03/18/2020] [Accepted: 10/16/2020] [Indexed: 10/23/2022] Open
Abstract
The supercoiled circular (SC) topology form of plasmid DNA has been regarded to be advantageous over open circular or linearized analogue in transfection and expression efficiency, and therefore are largely demanded in the biopharmaceutical manufacturing. However, production of high-purity SC plasmid DNA would result in high manufacturing cost. The effect of SC proportion in plasmid DNA on the quality of packaged lentiviral vectors has never been reported. In this study, we established an efficient system for production of high-titer lentiviral vectors using suspension HEK293SF cells in serum-free media, and the lentiviral titer was not associated with the proportion of SC plasmid DNA. Plasmids DNA with different proportion of SC, open-circular, and linearized forms were prepared using the thermal denaturation method, and were transfected to adherent HEK293T or suspension HEK293SF cells for packaging of lentiviral vectors. The titer of lentiviral vectors from HEK293T cells, but not from HEK293SF cells, was significantly impaired when the proportion of SC plasmid DNA decreased from 60-80% to 30-40%. Further decrease of SC plasmid proportion to 3% led to a dramatic reduction of lentiviral titer no matter the packaging cell line was. However, lentiviral vectors from HEK293SF cells still showed a high titer even when the proportion of SC plasmid DNA was 3%. This study demonstrated that extremely high proportion of SC plasmid DNA was not required for packaging of high-titer lentiviral vector in HEK293SF cells, at least under our manufacturing process.
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Affiliation(s)
- Xin-An Lu
- Immunochina Pharmaceuticals Co., Ltd, 100089, Beijing, China
| | - Ting He
- Immunochina Pharmaceuticals Co., Ltd, 100089, Beijing, China
| | - Zhihai Han
- Department of Pulmonary and Critical Care Medicine, The Sixth Medical Center of PLA General Hospital, 100048, Beijing, China
| | - Yanping Ding
- Immunochina Pharmaceuticals Co., Ltd, 100089, Beijing, China
| | - Liang Zhao
- Immunochina Pharmaceuticals Co., Ltd, 100089, Beijing, China
| | - Guanghua Liu
- Immunochina Pharmaceuticals Co., Ltd, 100089, Beijing, China
| | - Floris De Smet
- Sartorius Stedim North America Inc., 565 Johnson Avenue, Bohemia, New York, 11716, USA
| | - Xiaojun Huang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, No. 11 South Street of Xizhimen, Xicheng District, 100044, Beijing, China
| | - Danqing Chen
- Immunochina Pharmaceuticals Co., Ltd, 100089, Beijing, China
| | - Feifei Qi
- Immunochina Pharmaceuticals Co., Ltd, 100089, Beijing, China.
| | - Xiangyu Zhao
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, No. 11 South Street of Xizhimen, Xicheng District, 100044, Beijing, China.
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7
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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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8
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Silva-Santos AR, Alves CP, Monteiro G, Azevedo AM, Prazeres DMF. Multimodal chromatography of supercoiled minicircles: A closer look into DNA-ligand interactions. Sep Purif Technol 2019. [DOI: 10.1016/j.seppur.2018.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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9
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Cell Separation and Disruption, Product Recovery, and Purification. ESSENTIALS IN FERMENTATION TECHNOLOGY 2019. [DOI: 10.1007/978-3-030-16230-6_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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10
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Matos T, Bülow L. Separation of Nucleic Acids Using Single- and Multimodal Chromatography. Curr Protein Pept Sci 2018; 20:49-55. [DOI: 10.2174/1389203718666171024112556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/01/2017] [Accepted: 09/22/2017] [Indexed: 12/23/2022]
Abstract
The needs for purified nucleic acids for preparative and analytical applications have increased
constantly, demanding for the development of new and more efficient methods for their recovery and
isolation. DNA molecules harbour some intrinsic chemical properties that render them suitable for
chromatographic separations. These include a negatively charged phosphate backbone as well as a hydrophobic
character originating mainly from the major groove of DNA which exposes the base pairs on
the surface of the molecule. In addition, single stranded DNA often allows for a free exposure of the hydrophobic
aromatic bases. In this review, multimodal chromatography (MMC) has been evaluated as an
alternative tool for complex separations of nucleic acids. MMC embraces more than one kind of interaction
between the chromatographic ligand and the target molecules. These resins have often proved superior
to conventional single-mode chromatographic materials for DNA isolation, including, e.g., the purification
of plasmid DNA from crude cell lysates and for the preparation of DNA fragments before or
after a polymerase chain reaction (PCR).
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Affiliation(s)
- Tiago Matos
- Pure and Applied Biochemistry, Chemical Center, Lund University, Lund, Sweden
| | - Leif Bülow
- Pure and Applied Biochemistry, Chemical Center, Lund University, Lund, Sweden
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11
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Song Y, Li X, Fan JB, Kang H, Zhang X, Chen C, Liang X, Wang S. Interfacially Polymerized Particles with Heterostructured Nanopores for Glycopeptide Separation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1803299. [PMID: 30102426 DOI: 10.1002/adma.201803299] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/06/2018] [Indexed: 06/08/2023]
Abstract
Porous polymer materials are extensively used for biomolecule separation. However, conventional homogeneous porous polymer materials cannot efficiently separate specific low-abundance biomolecules from complex samples. Here, particles fabricated by emulsion interfacial polymerization featuring heterostructured nanopores with tunable size are reported, which can be used to realize low-abundance glycopeptide (GP) separation from complex biofluids. The heterostructured surface inside the nanopores allows solvent-dependent local adsorption of biomolecules onto hydrophilic or hydrophobic regions. Low-abundance hydrophilic GPs in complex biofluids can be efficiently separated via the hydrophilic region of nanopores in low-polarity solvent after the hydrophobic region removes high-abundance hydrophobic proteins and non-glycopeptides in high-polarity solvent. It is expected that these particles with heterostructured nanopores can be used for separation of nucleic acids, saccharides, and proteins, and downstream clinical diagnosis.
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Affiliation(s)
- Yongyang Song
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, CAS Center for Excellence in Nanoscience, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xiuling Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Jun-Bing Fan
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, CAS Center for Excellence in Nanoscience, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Hongjian Kang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xiaofei Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Cheng Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xinmiao Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Shutao Wang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, CAS Center for Excellence in Nanoscience, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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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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13
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Santos T, Proença Z, Queiroz J, Tomaz C, Cruz C. Plasmid purification by using a new naphthalene tripodal support. Sep Purif Technol 2017. [DOI: 10.1016/j.seppur.2017.06.072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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14
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15
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Köse K, Erol K, Emniyet AA, Köse DA, Avcı GA, Uzun L. Fe(II)-Co(II) Double Salt Incorporated Magnetic Hydrophobic Microparticles for Invertase Adsorption. Appl Biochem Biotechnol 2015; 177:1025-39. [DOI: 10.1007/s12010-015-1794-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 08/02/2015] [Indexed: 11/24/2022]
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17
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Grandhi TSP, Mallik A, Lin KN, Miryala B, Potta T, Tian Y, Rege K. Aminoglycoside antibiotic-derived anion-exchange microbeads for plasmid DNA binding and in situ DNA capture. ACS APPLIED MATERIALS & INTERFACES 2014; 6:18577-89. [PMID: 25314226 DOI: 10.1021/am503240q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Plasmid DNA (pDNA) therapeutics are being investigated for gene therapy and DNA vaccines against diseases including cancer, cystic fibrosis and AIDS. In addition, several applications in modern biotechnology require pDNA for transient protein production. Here, we describe the synthesis, characterization, and evaluation of microbeads ("Amikabeads") derived from the aminoglycoside antibiotic amikacin for pDNA binding and in situ DNA capture from mammalian cells. The parental aminoglycoside-derived microbeads (Amikabeads-P) acted as anion-exchange materials, and demonstrated high capacities for binding pDNA. Binding of pDNA was significantly enhanced following quaternization of the amines on the microbeads (Amikabeads-Q). Amikabeads were further employed for the disruption and extraction of DNA from mammalian cells, indicating their utility for in situ DNA capture. Our results indicate that Amikabeads are a novel material, with multiple reactive groups for further conjugation, and can have several applications in plasmid DNA biotechnology.
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Affiliation(s)
- Taraka Sai Pavan Grandhi
- Harrington Biomedical Engineering, School of Biological and Health Systems Engineering ‡Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University , Tempe, Arizona 85287, United States
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18
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Üzek R, Özkara S, Güngüneş H, Uzun L, Şenel S. Magnetic Nanoparticles for Plasmid DNA Purification through Hydrophobic Interaction Chromatography. SEP SCI TECHNOL 2014. [DOI: 10.1080/01496395.2014.905958] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Bai JS, Bai S, Shi QH, Sun Y. Purification of supercoiled plasmid DNA from clarified bacterial lysate by arginine-affinity chromatography: Effects of spacer arms and ligand density. J Sep Sci 2014; 37:1386-95. [DOI: 10.1002/jssc.201400092] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Jin-Shan Bai
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin China
| | - Shu Bai
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin China
| | - Qing-Hong Shi
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin China
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin China
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20
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Separation and purification of linear covalently closed deoxyribonucleic acid by Q-anion exchange membrane chromatography. J Chromatogr A 2014; 1339:214-8. [DOI: 10.1016/j.chroma.2014.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 03/04/2014] [Accepted: 03/04/2014] [Indexed: 01/11/2023]
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21
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Raksha S, Tan WS, Hamid M, Ramanan RN, Tey BT. A Single-Step Purification of the Glycoprotein of Nipah Virus Produced in Insect Cells using an Anion Exchange Chromatography Method. SEP SCI TECHNOL 2014. [DOI: 10.1080/01496395.2013.838265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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22
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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: 0.7] [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]
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Soares A, Queiroz JA, Sousa F, Sousa A. Purification of human papillomavirus 16 E6/E7 plasmid deoxyribonucleic acid-based vaccine using an arginine modified monolithic support. J Chromatogr A 2013; 1320:72-9. [PMID: 24210303 DOI: 10.1016/j.chroma.2013.10.053] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/11/2013] [Accepted: 10/15/2013] [Indexed: 12/28/2022]
Abstract
The development of efficient plasmid DNA (pDNA) purification processes has fostered therapeutic applications like gene therapy and DNA vaccination. In fact, monolithic supports have emerged as interesting approaches to purify pDNA due to their excellent mass transfer properties and high binding capacity for large biomolecules. The present study describes a method that combines the high selectivity of arginine affinity ligands with the versatility of monoliths to efficiently purify the supercoiled (sc) plasmid HPV-16 E6/E7. Quality control tests indicated that the level of impurities (proteins, endotoxins, gDNA and RNA) in the final plasmid sample was in accordance with the guidelines proposed by regulatory agencies. Breakthrough experiments were designed to compare the dynamic binding capacity of pDNA in the conventional arginine-agarose matrix with the modified monolithic support. The arginine monolith capacity was substantially higher than the conventional arginine-agarose matrix at 10% of breakthrough under the flow rate and pDNA concentration used. Overall, given that the pDNA final product complies with regulatory specifications, this combined support can be the key to obtain an adequate non-viral vaccine against a HPV infection.
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Affiliation(s)
- A Soares
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
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24
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Gabor B, Černigoj U, Barut M, Štrancar A. Reversible entrapment of plasmid deoxyribonucleic acid on different chromatographic supports. J Chromatogr A 2013; 1311:106-14. [DOI: 10.1016/j.chroma.2013.08.075] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 08/02/2013] [Accepted: 08/19/2013] [Indexed: 12/11/2022]
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25
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van der Heijden I, Gomez-Eerland R, van den Berg JH, Oosterhuis K, Schumacher TN, Haanen JBAG, Beijnen JH, Nuijen B. Transposon leads to contamination of clinical pDNA vaccine. Vaccine 2013; 31:3274-80. [PMID: 23707695 DOI: 10.1016/j.vaccine.2013.05.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 05/02/2013] [Accepted: 05/08/2013] [Indexed: 11/17/2022]
Abstract
We report an unexpected contamination during clinical manufacture of a Human Papilomavirus (HPV) 16 E6 encoding plasmid DNA (pDNA) vaccine, with a transposon originating from the Escherichia coli DH5 host cell genome. During processing, presence of this transposable element, insertion sequence 2 (IS2) in the plasmid vector was not noticed until quality control of the bulk pDNA vaccine when results of restriction digestion, sequencing, and CGE analysis were clearly indicative for the presence of a contaminant. Due to the very low level of contamination, only an insert-specific PCR method was capable of tracing back the presence of the transposon in the source pDNA and master cell bank (MCB). Based on the presence of an uncontrolled contamination with unknown clinical relevance, the product was rejected for clinical use. In order to prevent costly rejection of clinical material, both in-process controls and quality control methods must be sensitive enough to detect such a contamination as early as possible, i.e. preferably during plasmid DNA source generation, MCB production and ultimately during upstream processing. However, as we have shown that contamination early in the process development pipeline (source pDNA, MCB) can be present below limits of detection of generally applied analytical methods, the introduction of "engineered" or transposon-free host cells seems the only 100% effective solution to avoid contamination with movable elements and should be considered when searching for a suitable host cell-vector combination.
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Affiliation(s)
- I van der Heijden
- Department of Pharmacy & Pharmacology, Slotervaart Hospital/The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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26
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Smrekar V, Smrekar F, Štrancar A, Podgornik A. Single step plasmid DNA purification using methacrylate monolith bearing combination of ion-exchange and hydrophobic groups. J Chromatogr A 2013; 1276:58-64. [DOI: 10.1016/j.chroma.2012.12.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 12/12/2012] [Accepted: 12/16/2012] [Indexed: 01/31/2023]
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27
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Üzek R, Uzun L, Şenel S, Denizli A. Nanospines incorporation into the structure of the hydrophobic cryogels via novel cryogelation method: An alternative sorbent for plasmid DNA purification. Colloids Surf B Biointerfaces 2013; 102:243-50. [DOI: 10.1016/j.colsurfb.2012.08.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 08/09/2012] [Accepted: 08/14/2012] [Indexed: 10/28/2022]
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28
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Bo H, Wang J, Chen Q, Shen H, Wu F, Shao H, Huang S. Using a single hydrophobic-interaction chromatography to purify pharmaceutical-grade supercoiled plasmid DNA from other isoforms. PHARMACEUTICAL BIOLOGY 2013; 51:42-48. [PMID: 23013372 DOI: 10.3109/13880209.2012.703678] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
CONTEXT The recent developments in non-viral gene therapy and DNA vaccine have fostered the development of efficient plasmid DNA (pDNA) purification processes. OBJECTIVES This work aimed to establish a cost-effective purification process for the large-scale production of plasmid DNA for gene therapy and DNA vaccine. MATERIALS AND METHODS E. coli DH5α harboring pCDNA3.1-GFP (7200 base pairs) was used as a model plasmid. Hydrophobic-interaction chromatography (HIC) was employed to purify supercoiled plasmid DNA (sc pDNA). RESULTS With this method, not only host contaminants, but also open circular plasmid DNA (oc pDNA) could be removed from sc pDNA. Anion-exchange HPLC analysis proved that the recovery of HIC could reach 75%. The plasmid DNA exhibited high purity with supercoiled percentage of 98 ± 1.2% and undetectable residual endotoxins, genomic DNA, RNA and protein. The purity of pDNA had nothing to do with the flow rate in the range at least up to 400 cm/h. Liposomes transfection experiment prove that the purified pDNA in this article had higher transfection efficiency than the control pDNA. DISCUSSION AND CONCLUSION In the present work, we confirmed the possibility of separation of sc pDNA from oc pDNA and other host contaminants using a single HIC chromatography.
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Affiliation(s)
- Huaben Bo
- Institute of Genetic Engineering, Southern Medical University, Guangzhou, PR China
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29
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Wright JL, Jordan M, Wurm FM. Extraction of plasmid DNA using reactor scale alkaline lysis and selective precipitation for scalable transient transfection. Cytotechnology 2012; 35:165-73. [PMID: 22358855 DOI: 10.1023/a:1013106032341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
DNA extracted and purified for vaccination, gene therapy or transfection of cultured cells has to meet different criteria. We describe herein, a scalable process for the primary extraction of plasmid DNA suitable for transient expression of recombinant protein. We focus on the scale up of alkaline lysis for the extraction of plasmid DNA from Escherichia coli, and use a simple stirred tank reactor system to achieve this. By adding a series of three precipitations (including a selective precipitation step with ammonium acetate) we enrich very quickly the plasmid DNA content in the extract. The process has been thus far used to extract up to 100 mg of plasmid from 1.5 l of clarified lysate, corresponding to an E.coli bioreactor fermentation of 3 l.
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Affiliation(s)
- J L Wright
- Laboratory of Cellular Biotechnology, Swiss Federal Institute of Technology Lausanne, 1015, Lausanne, Switzerland
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30
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Sousa Â, Sousa F, Queiroz JA. Advances in chromatographic supports for pharmaceutical-grade plasmid DNA purification. J Sep Sci 2012; 35:3046-58. [DOI: 10.1002/jssc.201200307] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 05/28/2012] [Accepted: 06/02/2012] [Indexed: 01/04/2023]
Affiliation(s)
- Ângela Sousa
- 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
| | - João A. Queiroz
- CICS-UBI - Centro de Investigação em Ciências da Saúde; Universidade da Beira Interior; Covilhã Portugal
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31
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Selective isolation of G-quadruplexes by affinity chromatography. J Chromatogr A 2012; 1246:62-8. [PMID: 22398385 DOI: 10.1016/j.chroma.2012.02.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 02/06/2012] [Accepted: 02/09/2012] [Indexed: 01/13/2023]
Abstract
G-quadruplex (G4) is a characteristic secondary structure of nucleic acids containing repetitive tandem guanines. G4-forming sequences are found prevalent in the human genome by bioinformatics analysis. Accumulating evidence has suggested that G4s are involved in many biological processes. Selective isolation of G4s would be an effective tool in the study of G4s. In this paper, we prepared four affinity matrixes using hemin or a perylene derivative (N,N'-Bis-(2-(amino)ethyl)-3,4,9,10-perylenetetracarboxylic acid diimide, Pery01) as ligand, and investigated the retention behaviors of different G4s on these matrixes. Our experimental results suggest that the π-π stacking interaction between ligand and G-tetrad plays a key role in the selective isolation of G4s, whereas the electrostatic interaction between DNA and matrix causes the nonspecific binding. One matrix prepared by immobilizing Pery01 on polyglycidylmethacrylate (PGMA) beads through an aminocaproic acid spacer exhibits good selectivity for parallel structure G4s and has been successfully used to directly isolate a spiked parallel G4 from plasma.
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32
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Isolation and purification of recombinant proteins, antibodies and plasmid DNA with hydroxyapatite chromatography. Biotechnol J 2011; 7:90-102. [DOI: 10.1002/biot.201100015] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 09/27/2011] [Accepted: 11/04/2011] [Indexed: 11/07/2022]
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33
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Yagi H, Ebara M, Yamamoto K, Aoyagi T. Effect of grafted smart polymer architectures on interaction with hydrophobic molecules in newly developed induction heating chromatography system. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2011. [DOI: 10.1016/j.msec.2011.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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34
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Zhong L, Srirangan K, Scharer J, Moo-Young M, Fenner D, Crossley L, Howie Honeyman C, Suen SY, Perry Chou C. Developing an RNase-free bioprocess to produce pharmaceutical-grade plasmid DNA using selective precipitation and membrane chromatography. Sep Purif Technol 2011. [DOI: 10.1016/j.seppur.2011.09.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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35
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36
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Shin MJ, Tan L, Jeong MH, Kim JH, Choe WS. Monolith-based immobilized metal affinity chromatography increases production efficiency for plasmid DNA purification. J Chromatogr A 2011; 1218:5273-8. [DOI: 10.1016/j.chroma.2011.06.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 06/03/2011] [Accepted: 06/08/2011] [Indexed: 11/24/2022]
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37
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Schmidts T, Dobler D, von den Hoff S, Schlupp P, Garn H, Runkel F. Protective effect of drug delivery systems against the enzymatic degradation of dermally applied DNAzyme. Int J Pharm 2011; 410:75-82. [DOI: 10.1016/j.ijpharm.2011.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 03/09/2011] [Accepted: 03/13/2011] [Indexed: 11/26/2022]
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38
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Cheng L, Sun X, Yi X, Zhang Y. Large-scale plasmid preparation for transient gene expression. Biotechnol Lett 2011; 33:1559-64. [PMID: 21476094 DOI: 10.1007/s10529-011-0612-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 03/28/2011] [Indexed: 11/24/2022]
Abstract
Large-scale transient gene expression of recombinant protein in mammalian cells requires a great amount of plasmid. An economical method for large-scale plasmid preparation, based on fed-batch fermentation and an improved plasmid extraction process, has been established. Fed-batch growth of E. coli was carried out in 5 l bioreactor by controlling the glucose concentration below 1 g l(-1) after the feeding was started. Plasmid yields of 490 and 580 mg l(-1) were achieved with two strains of E. coli cells bearing pCEP4-EGFP and pID-EG respectively, representing 24.5- and 26-fold increases over those of the batch culture in shake-flask. To improve the procedure for large-scale preparation of plasmid DNA, addition of RNase to resuspension buffer and ultrafiltration of clarified lysate were adopted, and the quality of the resultant plasmid was comparable to that of commercial kit as disclosed in the small-scale transient transfection. This plasmid production process has great potential in the large scale transient gene expression which needs a large quantity of plasmid DNA.
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Affiliation(s)
- Lu Cheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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39
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Noirclerc-Savoye M, Gallet B, Bernaudat F, Vernet T. Large scale purification of linear plasmid DNA for efficient high throughput cloning. Biotechnol J 2010; 5:978-85. [PMID: 20845387 DOI: 10.1002/biot.201000132] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this report we describe a rapid, simple, and efficient method for large-scale purification of linear plasmid DNA to answer demand from high-throughput gene cloning. The process is based on the separation of the linear vector from small DNA fragments by anion exchange chromatography. Gene cloning experiments by restriction/ligation or the In-Fusion technique confirmed the high quality of the linearized vector as 100% of the genes were successfully cloned.
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40
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Li H, Bo H, Wang J, Shao H, Huang S. Separation of supercoiled from open circular forms of plasmid DNA, and biological activity detection. Cytotechnology 2010; 63:7-12. [PMID: 21120691 DOI: 10.1007/s10616-010-9322-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 11/13/2010] [Indexed: 11/29/2022] Open
Abstract
To establish a cost-effective purification process for the large-scale production of plasmid DNA for gene therapy and DNA vaccination, a single anion-exchange chromatography (AEC) step was employed to purify supercoiled plasmid DNA (sc pDNA) from other isoforms and Escherichia coli impurities present in a clarified lysate. Two different size and conformation plasmids were used as model targets, and showed similar elution behavior in this chromatographic operation, in which sc pDNA was effectively separated from open circle plasmid DNA (oc pDNA) in a salt gradient. The process delivered high-purity pDNA of homogeneity of 95 ± 1.1% and almost undetectable levels of endotoxins, genomic DNA, RNA and protein, at a yield of 65 ± 8%. Furthermore, the transfection efficiency (29 ± 0.4%) was significantly higher than that (20 ± 0.1%) of a pDNA control. The present study confirms the possibility of using a single AEC step to purify sc pDNA from other isoforms and host contaminants present in a clarified E. coli lysate.
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Affiliation(s)
- Huangjin Li
- School of Life Science and Bio-Pharmaceutical, Guangdong Pharmaceutical University, 510006, Guangzhou, China
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41
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Process optimisation for anion exchange monolithic chromatography of 4.2kbp plasmid vaccine (pcDNA3F). J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:2719-25. [DOI: 10.1016/j.jchromb.2010.08.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 08/11/2010] [Accepted: 08/12/2010] [Indexed: 11/22/2022]
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42
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Ebrahimpour M, Jahanshahi M, Hosenian AH. Adsorption Strategy of Plasmid DNA Nanoparticulate: Preparative Purification by a Simple Custom Expanded Bed Column. Chromatographia 2010. [DOI: 10.1365/s10337-010-1676-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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43
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Rege K, Heng M. Miniaturized parallel screens to identify chromatographic steps required for recombinant protein purification. Nat Protoc 2010; 5:408-17. [DOI: 10.1038/nprot.2009.149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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44
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Smrekar F, Podgornik A, Ciringer M, Kontrec S, Raspor P, Štrancar A, Peterka M. Preparation of pharmaceutical-grade plasmid DNA using methacrylate monolithic columns. Vaccine 2010; 28:2039-45. [DOI: 10.1016/j.vaccine.2009.10.061] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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45
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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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46
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Butler MD, Kluck B, Bentley T. DNA spike studies for demonstrating improved clearance on chromatographic media. J Chromatogr A 2009; 1216:6938-45. [PMID: 19733359 DOI: 10.1016/j.chroma.2009.08.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 08/16/2009] [Accepted: 08/18/2009] [Indexed: 11/28/2022]
Abstract
DNA spike clearance methods were used to demonstrate improved clearance factors on anion exchange and hydrophobic interaction columns used in the production of human therapeutic proteins. DNA clearance at large-scale was first measured for a monoclonal antibody expressed in Chinese Hamster Ovary (CHO) cells and an antibody fragment expressed in Escherichia coli. Small-scale spike experiments were then performed on individual chromatographic steps using host-specific DNA paired with TaqMan PCR assay methods. This approach has advantages of improved specificity, sensitivity, cost and throughput compared to other types of spike clearance methods. The anion exchange column used in the monoclonal antibody process was shown to have very high capacity for CHO DNA, resulting in greater than 7.1 log reduction. The anion exchange and hydrophobic interaction columns used in the antibody fragment process were shown to have high E. coli DNA clearance capability, with greater than 5.1 and 5.3 logs clearance, respectively. Compared to the large-scale process, higher log reduction values were achieved in small-scale spike clearance studies by challenging the chromatographic steps with load DNA levels 2-5 logs higher than the large-scale process levels. Using highly specific and sensitive spike clearance methods, we demonstrated consistently high DNA clearance factors for each of the production processes that meet industry and regulatory standards for human therapeutics. The method is applicable to a broad range of industrial scale processes where demonstration of the robustness of DNA clearance is necessary to support development or licensure of biopharmaceutical products.
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47
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Adsorption of pDNA on microparticulate charged surface. J Biotechnol 2009; 141:47-57. [DOI: 10.1016/j.jbiotec.2009.02.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Revised: 02/09/2009] [Accepted: 02/12/2009] [Indexed: 11/18/2022]
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48
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Sousa F, Prazeres DMF, Queiroz JA. Binding and elution strategy for improved performance of arginine affinity chromatography in supercoiled plasmid DNA purification. Biomed Chromatogr 2009; 23:160-5. [DOI: 10.1002/bmc.1097] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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49
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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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50
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Danquah MK, Liu S, Ho J, Forde GM, Wang L, Coppel RL. Rapid production of a plasmid DNA encoding a malaria vaccine candidate via amino-functionalized poly(GMA-co-EDMA) monolith. AIChE J 2008. [DOI: 10.1002/aic.11595] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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