1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Kalinichenko SV, Shepelev MV, Korobko IV. A gel-less isolation of untagged plasmid DNA insert from vector backbone in homogeneous format. Anal Biochem 2017; 521:28-30. [PMID: 28082218 DOI: 10.1016/j.ab.2017.01.006] [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: 10/27/2016] [Revised: 01/06/2017] [Accepted: 01/07/2017] [Indexed: 11/24/2022]
Abstract
Agarose gel electrophoresis with subsequent DNA extraction from gel is routinely used for DNA fragment isolation after plasmid DNA digestion. We describe a gel-less method for DNA fragment isolation after plasmid DNA digestion which is based on in-solution negative selection through depletion of vector backbone bearing LoxP sites by sorption on solid phase-immobilized mutated Cre recombinase. The method might be especially useful in preparation of DNA fragments for transgenic animal generation where residual agarose presence is a concern, and DNA fragments are frequently large in size and thus might be mechanically damaged during purification with conventional affinity-based gel extraction methods.
Collapse
Affiliation(s)
- Svetlana V Kalinichenko
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov street, Moscow 119334, Russia
| | - Mikhail V Shepelev
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov street, Moscow 119334, Russia
| | - Igor V Korobko
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov street, Moscow 119334, Russia.
| |
Collapse
|
3
|
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.
Collapse
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
| | | | | | | | | | | | | |
Collapse
|
4
|
Improved production of L-threonine in Escherichia coli by use of a DNA scaffold system. Appl Environ Microbiol 2012; 79:774-82. [PMID: 23160128 DOI: 10.1128/aem.02578-12] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite numerous approaches for the development of l-threonine-producing strains, strain development is still hampered by the intrinsic inefficiency of metabolic reactions caused by simple diffusion and random collisions of enzymes and metabolites. A scaffold system, which can promote the proximity of metabolic enzymes and increase the local concentration of intermediates, was reported to be one of the most promising solutions. Here, we report an improvement in l-threonine production in Escherichia coli using a DNA scaffold system, in which a zinc finger protein serves as an adapter for the site-specific binding of each enzyme involved in l-threonine production to a precisely ordered location on a DNA double helix to increase the proximity of enzymes and the local concentration of metabolites to maximize production. The optimized DNA scaffold system for l-threonine production significantly increased the efficiency of the threonine biosynthetic pathway in E. coli, substantially reducing the production time for l-threonine (by over 50%). In addition, this DNA scaffold system enhanced the growth rate of the host strain by reducing the intracellular concentration of toxic intermediates, such as homoserine. Our DNA scaffold system can be used as a platform technology for the construction and optimization of artificial metabolic pathways as well as for the production of many useful biomaterials.
Collapse
|
5
|
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
| |
Collapse
|
6
|
Han Y, You G, Pattenden LK, Forde GM. The harnessing of peptide–monolith constructs for single step plasmid DNA purification. Process Biochem 2010. [DOI: 10.1016/j.procbio.2009.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
7
|
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]
|
8
|
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]
|
9
|
Mayrhofer P, Blaesen M, Schleef M, Jechlinger W. Minicircle-DNA production by site specific recombination and protein-DNA interaction chromatography. J Gene Med 2008; 10:1253-69. [PMID: 18767031 DOI: 10.1002/jgm.1243] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Conventional plasmid-DNA (pDNA) used in gene therapy and vaccination can be subdivided into a bacterial backbone and a transcription unit. Bacterial backbone sequences are needed for pDNA production in bacteria. However, for gene transfer application, these sequences are dispensable, reduce the overall efficiency of the DNA agent and, most importantly, represent a biological safety risk. For example, the dissemination of antibiotic resistance genes, as well as the uncontrolled expression of backbone sequences, may have profound detrimental effects and unmethylated CpG motifs have been shown to contribute to silencing of episomal transgene expression. Therefore, an important goal in nonviral vector development is to produce supercoiled pDNA lacking bacterial backbone sequences. METHODS A method is described to provide circular, supercoiled minimal expression cassettes (minicircle-DNA) based on two processes: (i) an inducible, sequence specific, in vivo recombination process that is almost 100% efficient and (2) a novel affinity-based chromatographic purification approach for the isolation of the minicircle-DNA. RESULTS Quantitative real-time polymerase chain reaction analysis, capillary gel electrophoresis and restriction analysis of the recombination products, and the minicircle-DNA revealed a recombination efficiency greater than 99.5% and a purity of the isolated minicircle-DNA of more than 98.5%. CONCLUSIONS The results obtained in the present study demonstrate that the described technology facilitates the production of highly pure minicircle-DNA for direct application in gene therapy and vaccination. The process described is efficient, stable and suitable for further scale-up in industrial large-scale manufacturing.
Collapse
|
10
|
Sousa F, Prazeres DM, Queiroz JA. Affinity chromatography approaches to overcome the challenges of purifying plasmid DNA. Trends Biotechnol 2008; 26:518-25. [DOI: 10.1016/j.tibtech.2008.05.005] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Revised: 05/21/2008] [Accepted: 05/28/2008] [Indexed: 02/05/2023]
|
11
|
Barbosa H, Hine AV, Brocchini S, Slater NKH, Marcos JC. Affinity partitioning of plasmid DNA with a zinc finger protein. J Chromatogr A 2008; 1206:105-12. [PMID: 18760786 DOI: 10.1016/j.chroma.2008.07.095] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 07/22/2008] [Accepted: 07/23/2008] [Indexed: 10/21/2022]
Abstract
The affinity isolation of pre-purified plasmid DNA (pDNA) from model buffer solutions using native and poly(ethylene glycol) (PEG) derivatized zinc finger-GST (Glutathione-S-Transferase) fusion protein was examined in PEG-dextran (DEX) aqueous two-phase systems (ATPSs). In the absence of pDNA, partitioning of unbound PEGylated fusion protein into the PEG-rich phase was confirmed with 97.5% of the PEGylated fusion protein being detected in the PEG phase of a PEG 600-DEX 40 ATPS. This represents a 1322-fold increase in the protein partition coefficient in comparison to the non-PEGylated protein (Kc = 0.013). In the presence of pDNA containing a specific oligonucleotide recognition sequence, the zinc finger moiety of the PEGylated fusion protein bound to the plasmid and steered the complex to the PEG-rich phase. An increase in the proportion of pDNA that partitioned to the PEG-rich phase was observed as the concentration of PEGylated fusion protein was increased. Partitioning of the bound complex occurred to such an extent that no DNA was detected by the picogreen assay in the dextran phase. It was also possible to partition pDNA using a non-PEGylated (native) zinc finger-GST fusion protein in a PEG 1000-DEX 500 ATPS. In this case the native ligand accumulated mainly in the PEG phase. These results indicate good prospects for the design of new plasmid DNA purification methods using fusion proteins as affinity ligands.
Collapse
Affiliation(s)
- H Barbosa
- Department of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | | | | | | | | |
Collapse
|
12
|
Voß C. Downstream Processing of Plasmid DNA for Gene Therapy and Genetic Vaccination. Chem Eng Technol 2008. [DOI: 10.1002/ceat.200800069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
13
|
|
14
|
Forde GM. Preparation, analysis and use of an affinity adsorbent for the purification of GST fusion protein. Methods Mol Biol 2008; 421:125-136. [PMID: 18826052 DOI: 10.1007/978-1-59745-582-4_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Methods are presented for the preparation, ligand density analysis and use of an affinity adsorbent for the purification of a glutathione S-transferase (GST) fusion protein in packed and expanded bed chromatographic processes. The protein is composed of GST fused to a zinc finger transcription factor (ZnF). Glutathione, the affinity ligand for GST purification, is covalently immobilized to a solid-phase adsorbent (Streamline). The GST-ZnF fusion protein displays a dissociation constant of 0.6 x 10(-6) M to glutathione immobilized to Streamline. Ligand density optimization, fusion protein elution conditions (pH and glutathione concentration) and ligand orientation are briefly discussed.
Collapse
Affiliation(s)
- Gareth M Forde
- Department of Chemical Engineering, Monash University, Clayton, Victoria, Australia
| |
Collapse
|
15
|
Duarte SP, Fortes AG, Prazeres DMF, Marcos JC. Preparation of plasmid DNA polyplexes from alkaline lysates by a two-step aqueous two-phase extraction process. J Chromatogr A 2007; 1164:105-12. [PMID: 17632115 DOI: 10.1016/j.chroma.2007.06.061] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2007] [Revised: 06/24/2007] [Accepted: 06/26/2007] [Indexed: 10/23/2022]
Abstract
This work studied the possibility of using polyethyleimine (PEI) as an affinity ligand for the purification of plasmid DNA (pDNA) from alkaline lysates using aqueous two-phase systems (ATPSs). The goal was to find conditions under which this cationic polymer could steer the partition of pDNA to the phase where less impurities accumulate. In poly(ethylene glycol) (PEG)/ammonium sulphate systems, neither free nor PEGylated PEI (pPEI) were able to change the partition of pDNA. This is probably due to the high salt concentration present in these systems that impair the interaction between pDNA and PEI. In PEG 3350/dextran 110 systems, the desired effect could be observed but 0.2-0.5M ammonium sulphate had to be added to prevent the co-partition of RNA to the same phase. These results were used to develop a methodology to obtain polyplexes from alkaline lysates in a two-step ATPSs extraction process. In the first step, a PEG 600/ammonium sulphate system is used to remove most impurities to the top phase. The pDNA-containing bottom phase is then isolated and contacted with a second PEG 3350/dextran 110 system supplemented with a small amount of pPEI (0.2%). Plasmid yield was 100% and the final preparation had no RNA and only small amounts of contaminant protein. Additionally, pDNA was obtained in the form of 53nm-sized polyplexes which are likely to suit specific gene delivery applications.
Collapse
Affiliation(s)
- Sónia P Duarte
- Centro de Química, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | | | | | | |
Collapse
|
16
|
Lao UL, Kostal J, Mulchandani A, Chen W. Affinity purification of plasmid DNA by temperature-triggered precipitation. Nat Protoc 2007; 2:1263-8. [PMID: 17546022 DOI: 10.1038/nprot.2007.171] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol presents a new method to purify plasmid DNA using temperature-triggered precipitation. The principle is based on the specific DNA-binding affinity of a bacterial metalloregulatory (MerR) protein to its cognate DNA sequence and the temperature responsiveness of elastin-like protein (ELP). A bifunctional ELP-MerR fusion protein is created to enable the precipitation of plasmid DNA, designed to contain the MerR recognition sequence, by a simple temperature trigger. The protocol covers all stages of the process from the design of ELP-MerR fusion proteins and MerR-binding plasmids, to the isolation of plasmid DNA from Escherichia coli cultures after boiling lysis, the subsequent temperature-triggered precipitation of plasmid DNA-fusion protein complexes and final elution of plasmid DNA by mild heating. This protocol is well suited to laboratory research-scale applications, producing plasmid DNA of better purity and similar yield as one of the most commonly used laboratory methods, standard alkaline lysis (known as the midiprep procedure). The protocol takes approximately 30 min to obtain pure plasmid DNA from cell cultures using the temperature-triggered precipitation method.
Collapse
Affiliation(s)
- U Loi Lao
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Ave, Riverside, California 92507, USA
| | | | | | | |
Collapse
|
17
|
Darby RAJ, Forde GM, Slater NKH, Hine AV. Affinity purification of plasmid DNA directly from crude bacterial cell lysates. Biotechnol Bioeng 2007; 98:1103-8. [PMID: 17497740 DOI: 10.1002/bit.21492] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have shown previously that a sequence-specific DNA-binding protein based on the Lac repressor protein can isolate pre-purified DNA efficiently from simple buffer solution but our attempts to purify plasmids directly from crude starting materials were disappointing with impractically low DNA yields. We have optimized the procedure and present a simple affinity methodology whereby plasmid DNA is purified directly by mixing two crude cell lysates, one cell lysate containing the plasmid and the other the protein affinity ligand, without the need for treatment by RNaseA. After IMAC chromatography, high purity supercoiled DNA is recovered in good yields of 100-150 microg plasmid per 200 mL shake flask culture. Moreover, the resulting DNA is free from linear or open-circular plasmid DNA, genomic DNA, RNA, and protein, to the limits of our detection. Furthermore, we show that lyophilized affinity ligand can be stored at room temperature and re-hydrated for use when required.
Collapse
Affiliation(s)
- Richard A J Darby
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, United Kingdom
| | | | | | | |
Collapse
|
18
|
Abstract
The concept of curing diseases at the genetic level was already introduced in the 1970s, but only the evolution of molecular biology and tools for genetic manipulation brought the idea into labs and clinics during the last 16 years. Viral and non-viral vectors and delivery systems were developed to transfer therapeutic genes into the target cells. In the case of non-viral approaches plasmid DNA has become a very promising gene delivery vector because it can easily be genetically manipulated and produced by cultivation of plasmid harbouring Escherichia coli and subsequent downstream processing, thus making production easy in comparison to other gene delivery vectors. Another advantage in using plasmid DNA is the low risk of immunogenic reactions and oncogen activation that can arise while using viral vectors. This review describes the recent development in plasmid manufacturing ranging from bacterial cultivation in batch and fedbatch mode to produce plasmid-bearing E. coli over cell lysis and subsequent purification to storage, application, and process and quality control.
Collapse
Affiliation(s)
- Carsten Voss
- Fermentation Engineering, Faculty of Technology, Bielefeld University, Germany.
| |
Collapse
|
19
|
Forde GM, Ghose S, Slater NKH, Hine AV, Darby RAJ, Hitchcock AG. LacO-LacI interaction in affinity adsorption of plasmid DNA. Biotechnol Bioeng 2006; 95:67-75. [PMID: 16646090 DOI: 10.1002/bit.20955] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Current approaches for purifying plasmids from bacterial production systems exploit the physiochemical properties of nucleic acids in non-specific capture systems. In this study, an affinity system for plasmid DNA (pDNA) purification has been developed utilizing the interaction between the lac operon (lacO) sequence contained in the pDNA and a 64mer synthetic peptide representing the DNA-binding domain of the lac repressor protein, LacI. Two plasmids were evaluated, the native pUC19 and pUC19 with dual lacO3/lacOs operators (pUC19(lacO3/lacOs)), where the lacOs operator is perfectly symmetrical. The DNA-protein affinity interaction was evaluated by surface plasmon resonance using a Biacore system. The affinity capture of DNA in a chromatography system was evaluated using LacI peptide that had been immobilized to Streamline adsorbent. The KD-values for double stranded DNA (dsDNA) fragments containing lacO1 and lacO3 and lacOS and lacO3 were 5.7 +/- 0.3 x 10(-11) M and 4.1 +/- 0.2 x 10(-11) M respectively, which compare favorably with literature reports of 5 x 10(-10)-1 x 10(-9) M for native lacO1 and 1-1.2 x 10(-10) M for lacO1 in a saline buffer. Densitometric analysis of the gel bands from the affinity chromatography run clearly showed a significant preference for capture of the supercoiled fraction from the feed pDNA sample. The results indicate the feasibility of the affinity approach for pDNA capture and purification using native protein-DNA interaction.
Collapse
Affiliation(s)
- Gareth M Forde
- Department of Chemical Engineering, Cambridge Unit for Bioscience Engineering (CUBE), Pembroke Street, University of Cambridge, Cambridge CB2 3RA, UK
| | | | | | | | | | | |
Collapse
|
20
|
Abstract
In responding to future influenza pandemics and other infectious agents, plasmid DNA overcomes many of the limitations of conventional vaccine production approaches.
Collapse
Affiliation(s)
- Gareth M Forde
- Victorian Endowment for Science, Knowledge, and Innovation (VESKI), Department of Chemical Engineering, Monash University, Clayton, Melbourne, Australia, 3800.
| |
Collapse
|
21
|
Li Y, Dong XY, Sun Y. High-speed chromatographic purification of plasmid DNA with a customized biporous hydrophobic adsorbent. Biochem Eng J 2005. [DOI: 10.1016/j.bej.2005.06.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
22
|
Choi YS, Pack SP, Yoo YJ. Development of a Plasmid Display System using GAL4 DNA Binding Domain for the in Vitro Screening of Functional Proteins. Biotechnol Lett 2005; 27:1707-11. [PMID: 16247679 DOI: 10.1007/s10529-005-2735-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Accepted: 08/24/2005] [Indexed: 11/24/2022]
Abstract
A plasmid display system using GAL4 DNA binding domain (GAL4 DBD) was constructed to enrich the molecular diversity and in vitro selection of functional proteins. Model proteins used were enhanced green fluorescent protein (EGFP) and glutathione S-transferase (GST). The feasibility of this display system was examined using enrichment experiments of target protein from a model protein mixture and identifying the encoding genes by PCR, in which the model protein mixture includes GAL4 DBD/GST fusion protein, GAL4 DBD/EGFP fusion protein, and xylanase. Target proteins of GAL4 DBD/GST and GAL4 DBD/EGFP from the model protein mixture were efficiently isolated by the plasmid display, respectively. The results show that the display system is sufficiently sensitive to select a target protein from a protein mixture, and that it is possible to discover the functional proteins from large libraries using relatively simple approaches.
Collapse
Affiliation(s)
- Yoo Seong Choi
- School of Chemical and Biological Engineering, Seoul National University, 151-742, Seoul, Korea
| | | | | |
Collapse
|
23
|
Ferreira GNM. Chromatographic Approaches in the Purification of Plasmid DNA for Therapy and Vaccination. Chem Eng Technol 2005. [DOI: 10.1002/ceat.200500158] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
24
|
Abstract
The use of plasmid DNA in gene therapy and genetic vaccination has increased the need for scalable and sustainable production processes. One key challenge for bioprocess engineering is the separation of plasmid DNA from structurally related impurities. Affinity purification procedures allow a highly selective capturing of the target molecule. In this paper, we present the isolation of a his-tagged lac repressor, its non-covalent immobilisation to different matrices and binding of DNA, thus enabling us to screen for combinations of ligands and stationary phases by using a building block principle.
Collapse
Affiliation(s)
- Anja Hasche
- Department of Fermentation Engineering, Faculty of Technology, Bielefeld University, Universitaetsstrasse 25, P.O. Box 100131, D-33501 Bielefeld, Germany
| | | |
Collapse
|
25
|
Darby RAJ, Hine AV. LacI‐mediated sequence‐specific affinity purification of plasmid DNA for therapeutic applications. FASEB J 2005; 19:801-3. [PMID: 15760969 DOI: 10.1096/fj.04-2812fje] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Affinity purification of plasmid DNA is an attractive option for the biomanufacture of therapeutic plasmids, which are strictly controlled for levels of host protein, DNA, RNA, and endotoxin. Plasmid vectors are considered to be a safer alternative than viruses for gene therapy, but milligram quantities of DNA are required per dose. Previous affinity approaches have involved triplex DNA formation and a sequence-specific zinc finger protein. We present a more generically applicable protein-based approach, which exploits the lac operator, present in a wide diversity of plasmids, as a target sequence. We used a GFP/His-tagged LacI protein, which is precomplexed with the plasmid, and the resulting complex was immobilized on a solid support (TALON resin). Ensuing elution gives plasmid DNA, in good yield (>80% based on recovered starting material, 35-50% overall process), free from detectable RNA and protein and with minimal genomic DNA contamination. Such an affinity-based process should enhance plasmid purity and ultimately, after appropriate development, may simplify the biomanufacturing process of therapeutic plasmids.
Collapse
Affiliation(s)
- Richard A J Darby
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | | |
Collapse
|
26
|
Abstract
Liquid chromatography plays a central role in process-scale manufacturing of therapeutic plasmid DNA (pDNA) for gene therapy and DNA vaccination. Apart from its use as a preparative purification step, it is also very useful as an analytical tool to monitor and control pDNA quality during processing and in final formulations. This paper gives an overview of the use of pDNA chromatography. The specificity of pDNA purification and the consequent limitations to the performance of chromatography are described. Strategies currently used to overcome those limitations, as well as other possible solutions are presented. Applications of the different types of chromatography to the purification of therapeutic pDNA are reviewed, and the main advantages and disadvantages behind each technique highlighted.
Collapse
Affiliation(s)
- M M Diogo
- Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | | | | |
Collapse
|
27
|
Hughes MD, Zhang ZR, Sutherland AJ, Santos AF, Hine AV. Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing: identification of novel zinc finger proteins. Nucleic Acids Res 2005; 33:e32. [PMID: 15722478 PMCID: PMC549430 DOI: 10.1093/nar/gni031] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We have successfully linked protein library screening directly with the identification of active proteins, without the need for individual purification, display technologies or physical linkage between the protein and its encoding sequence. By using 'MAX' randomization we have rapidly constructed 60 overlapping gene libraries that encode zinc finger proteins, randomized variously at the three principal DNA-contacting residues. Expression and screening of the libraries against five possible target DNA sequences generated data points covering a potential 40,000 individual interactions. Comparative analysis of the resulting data enabled direct identification of active proteins. Accuracy of this library analysis methodology was confirmed by both in vitro and in vivo analyses of identified proteins to yield novel zinc finger proteins that bind to their target sequences with high affinity, as indicated by low nanomolar apparent dissociation constants.
Collapse
Affiliation(s)
- Marcus D. Hughes
- School of Life and Health Sciences, Aston UniversityAston Triangle, Birmingham B4 7ET, UK
- ProtaMAX Ltd55 Colmore Row, Birmingham B3 2AS, UK
| | - Zhan-Ren Zhang
- School of Life and Health Sciences, Aston UniversityAston Triangle, Birmingham B4 7ET, UK
| | - Andrew J. Sutherland
- Chemical Engineering and Applied Chemistry, School of Engineering & Applied Science, Aston UniversityAston Triangle, Birmingham B4 7ET, UK
| | - Albert F. Santos
- GE Healthcare, Cardiff LaboratoriesForest Farm, Whitchurch, Cardiff CF14 7YT, UK
| | - Anna V. Hine
- School of Life and Health Sciences, Aston UniversityAston Triangle, Birmingham B4 7ET, UK
- ProtaMAX Ltd55 Colmore Row, Birmingham B3 2AS, UK
- To whom correspondence should be addressed. Tel: +44 121 204 3961; Fax: +44 121 359 0733;
| |
Collapse
|
28
|
Kostal J, Mulchandani A, Chen W. Affinity purification of plasmid DNA by temperature-triggered precipitation. Biotechnol Bioeng 2004; 85:293-7. [PMID: 14748084 DOI: 10.1002/bit.10890] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This report describes a new plasmid DNA purification method, which takes advantage of the DNA-binding affinity and specificity of the bacterial metalloregulatory protein MerR, and of the temperature responsiveness of elastin-like proteins (ELPs). Upon increasing the temperature, ELP undergoes a reversible phase transition from water-soluble forms into aggregates, and this property was exploited for the precipitation of plasmid DNA containing the MerR recognition sequence by a simple temperature trigger. In one purification step, plasmid DNA was purified from E. coli cell lysates to a better purity than that prepared by a standard alkaline purification method, with no contaminating chromosomal DNA and cellular proteins. This protein-based approach, in combination with the reversible phase transition feature of ELP, makes the outlined method a promising candidate for large-scale purification of plasmid DNA for sensitive applications such as nonviral gene therapy or DNA vaccines.
Collapse
Affiliation(s)
- Jan Kostal
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, USA
| | | | | |
Collapse
|