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Coll De Peña A, Gutterman-Johns E, Gautam GP, Rutberg J, Frej MB, Mehta DR, Shah S, Tripathi A. Assessment of pDNA isoforms using microfluidic electrophoresis. Electrophoresis 2024. [PMID: 38571381 DOI: 10.1002/elps.202300293] [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: 12/17/2023] [Revised: 03/11/2024] [Accepted: 03/15/2024] [Indexed: 04/05/2024]
Abstract
The recent rise in nucleic acid-based vaccines and therapies has resulted in an increased demand for plasmid DNA (pDNA). As a result, there is added pressure to streamline the manufacturing of these vectors, particularly their design and construction, which is currently considered a bottleneck. A significant challenge in optimizing pDNA production is the lack of high-throughput and rapid analytical methods to support the numerous samples produced during the iterative plasmid construction step and for batch-to-batch purity monitoring. pDNA is generally present as one of three isoforms: supercoiled, linear, or open circular. Depending on the ultimate use, the desired isoform may be supercoiled in the initial stages for cell transfection or linear in the case of mRNA synthesis. Here, we present a high-throughput microfluidic electrophoresis method capable of detecting the three pDNA isoforms and determining the size and concentration of the predominant supercoiled and linear isoforms from 2 to 7 kb. The limit of detection of the method is 0.1 ng/µL for the supercoiled and linear isoforms and 0.5 ng/µL for the open circular isoform, with a maximum loading capacity of 10-15 ng/µL. The turnaround time is 1 min/sample, and the volume requirement is 10 µL, making the method suitable for process optimization and batch-to-batch analysis. The results presented in this study will enhance the understanding of electrophoretic transport in microscale systems dependent on molecular conformations and potentially aid technological advances in diverse areas relevant to microfluidic devices.
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Affiliation(s)
- Adriana Coll De Peña
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island, USA
| | - Everett Gutterman-Johns
- Department of Molecular Biology, Cell Biology, and Biochemistry, Division of Biology and Medicine, Brown University, Providence, Rhode Island, USA
| | | | - Jenna Rutberg
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island, USA
| | - Menel Ben Frej
- Applied Genomics, Revvity, Hopkinton, Massachusetts, USA
| | - Dipti R Mehta
- Applied Genomics, Revvity, Hopkinton, Massachusetts, USA
| | - Shreyas Shah
- Applied Genomics, Revvity, Hopkinton, Massachusetts, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island, USA
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He Y, Orlet J, Cunio O, Thompson L, Jones MT. Sensitive and rapid analysis of plasmid DNA topology isoforms by capillary gel electrophoresis with laser induced fluorescence in uncoated capillary. Electrophoresis 2024. [PMID: 38415778 DOI: 10.1002/elps.202300212] [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: 09/23/2023] [Revised: 01/28/2024] [Accepted: 02/11/2024] [Indexed: 02/29/2024]
Abstract
The work describes the use of SYBR Gold to improve the detection sensitivity of plasmid DNA topoisomers by capillary gel electrophoresis with laser induced fluorescence in an uncoated capillary. The impact of different dyes, including ethidium bromide, SYBR Green and SYBR Gold, was compared based on detection and separation of DNA plasmid topoisomers. Use of SYBR Gold enabled improvement of detection sensitivity by 15-fold while maintaining good separation resolution of the different topoisomers. The baseline dropped with the use SYBR Gold but was overcome by the employment of a capillary with longer ineffective length (40 vs. 20 cm). Separation resolution and reproducibility were impacted by the concentration of SYBR Gold and hydroxypropyl methylcellulose. With the use of a short capillary (10 cm effective length and 50 cm total length), fast separations of supercoiled, linear, open circular, and other isoforms were accomplished within 8 min. Appropriate capillary cleaning with 0.1 M sodium hydroxide/0.1 M hydrochloric acid and capillary storage with 0.1 M hydrochloric acid ensured good separation reproducibility of 217 runs during an extended period of use.
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Affiliation(s)
- Yan He
- Analytical Research and Development, Pfizer Inc, Chesterfield, Missouri, USA
| | - John Orlet
- Analytical Research and Development, Pfizer Inc, Chesterfield, Missouri, USA
| | - Olivia Cunio
- Analytical Research and Development, Pfizer Inc, Chesterfield, Missouri, USA
| | - Lawrence Thompson
- Analytical Research and Development, Pfizer Inc, Chesterfield, Missouri, USA
| | - Michael T Jones
- Analytical Research and Development, Pfizer Inc, Chesterfield, Missouri, USA
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Holland LA, He Y, Guerrette JR, Crihfield CL, Bwanali L. Simple, rapid, and reproducible capillary gel electrophoresis separation and laser-induced fluorescence detection of DNA topoisomers with unmodified fused silica separation capillaries. Anal Bioanal Chem 2021; 414:713-720. [PMID: 34693472 DOI: 10.1007/s00216-021-03714-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/26/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
The topology of DNA is a critical quality attribute for plasmid-based pharmaceuticals, making quantification of trace levels of plasmid topoisomers an important analytical priority. An automated and cost-effective method based on capillary gel electrophoresis laser-induced fluorescence detection is described. The method outlined in this report is significant because it is easily implemented by any laboratory for which routine analyses of plasmid topology are critical for the development of new plasmid-based therapies as well as for quality control of gene therapies utilizing supercoiled DNA. Detection of topoisomers was achieved by incorporating ethidium bromide in the separation medium. The detector response was improved by 3 orders of magnitude by utilizing a 605-nm optical filter with a 15-nm bandwidth. Separations of linear, open circle, supercoiled, and multimer DNA plasmids ranging from 4.2 to 10.5 kbp were accomplished in under 6 min using an unmodified fused silica capillary (50-μm internal diameter). The background electrolyte was comprised of 0.5% gel, which was hydroxypropylmethyl cellulose, 1 mM ethylenediaminetetraacetic acid, and 50 mM N-(2-acetamido)-2-aminoethanesulfonic acid (pH of 6.25). The separations, which balanced the bulk electroosmotic flow, the electrophoretic mobility of the DNA, and gel sieving were dependent upon the pH of the electrolyte and the gel concentration. Reproducibility was dependent upon the procedure used to prepare the gel as well as other factors including the ethidium bromide concentration and capillary conditioning. A single unmodified capillary operated for more than 150 runs had an across-day migration time precision of 1% relative standard deviation and percent area precision of 10% relative standard deviation.
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Affiliation(s)
- Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
| | - Yan He
- Analytical Research and Development, 875 Chesterfield Parkway, PfizerChesterfield, MO, 63017, USA
| | - Jessica R Guerrette
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Cassandra L Crihfield
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.,Biohybrid Solutions, LLC, 320 William Pitt Way, Pittsburgh, PA, 15238, USA
| | - Lloyd Bwanali
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
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Mitchenall LA, Hipkin RE, Piperakis MM, Burton NP, Maxwell A. A rapid high-resolution method for resolving DNA topoisomers. BMC Res Notes 2018; 11:37. [PMID: 29338757 PMCID: PMC5771066 DOI: 10.1186/s13104-018-3147-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/09/2018] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE Agarose gel electrophoresis has been the mainstay technique for the analysis of DNA samples of moderate size. In addition to separating linear DNA molecules, it can also resolve different topological forms of plasmid DNAs, an application useful for the analysis of the reactions of DNA topoisomerases. However, gel electrophoresis is an intrinsically low-throughput technique and suffers from other potential disadvantages. We describe the application of the QIAxcel Advanced System, a high-throughput capillary electrophoresis system, to separate DNA topoisomers, and compare this technique with gel electrophoresis. RESULTS We prepared a range of topoisomers of plasmids pBR322 and pUC19, and a 339 bp DNA minicircle, and compared their separation by gel electrophoresis and the QIAxcel System. We found superior resolution with the QIAxcel System, and that quantitative analysis of topoisomer distributions was straightforward. We show that the QIAxcel system has advantages in terms of speed, resolution and cost, and can be applied to DNA circles of various sizes. It can readily be adapted for use in compound screening against topoisomerase targets.
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Affiliation(s)
- Lesley A. Mitchenall
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Rachel E. Hipkin
- Qiagen Ltd., Skelton House, Lloyd St. North, Manchester, M15 6SH UK
- Present Address: Fluidigm Ltd, 12 New Fetter Lane, London, EC4A 1JP UK
| | - Michael M. Piperakis
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present Address: University Centre, Blackburn College, University Close, Blackburn, Lancashire BB2 1LH UK
| | - Nicolas P. Burton
- Inspiralis Ltd, Innovation Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
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Ban E, Song EJ. Recent developments and applications of capillary electrophoresis with laser-induced fluorescence detection in biological samples. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 929:180-6. [DOI: 10.1016/j.jchromb.2013.04.028] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/18/2013] [Accepted: 04/20/2013] [Indexed: 12/15/2022]
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Silva F, Queiroz JA, Domingues FC. Evaluating metabolic stress and plasmid stability in plasmid DNA production by Escherichia coli. Biotechnol Adv 2012; 30:691-708. [DOI: 10.1016/j.biotechadv.2011.12.005] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 12/01/2011] [Accepted: 12/29/2011] [Indexed: 01/26/2023]
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