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Miller LM, Hawkins L, Jarrold MF. Compaction, Relaxation, and Linearization of Megadalton-Sized DNA Plasmids: DNA Structures Probed by CD-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1969-1975. [PMID: 39013154 DOI: 10.1021/jasms.4c00222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
High purity plasmid DNA is a raw material for recombinant protein production as well as an active ingredient in DNA vaccines. There are four primary plasmid structures that can be observed in a typical plasmid formulation: supercoiled, relaxed (circular), linearized, and condensed. Determining what structures are present in a sample is important, as the structure can affect activity; the supercoiled structure has the highest activity, and >90% supercoiled is desired for industry standards. Recently, charge detection mass spectrometry (CD-MS) was used to distinguish two of the structures, supercoiled and condensed, by measuring the charge deposited on the ions by positive mode electrospray. Here, CD-MS is used to probe the structures of DNA plasmids during compaction with polycations, and through enzymatic treatment to relax and linearize plasmids. We find that all four structural types for plasmid DNA have unique charging profiles that can be distinguished using CD-MS. The extent of mechanical shearing of the DNA plasmids during electrospray is strongly influenced by the structural type.
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Affiliation(s)
- Lohra M Miller
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Luke Hawkins
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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Pavlin N, Černigoj U, Bavčar M, Plesničar T, Mavri J, Zidar M, Bone M, Kralj Savič U, Sever T, Štrancar A. Analytical separation of plasmid DNA isoforms using anion exchanging chromatographic monoliths with 6 µm channels. Electrophoresis 2023; 44:1967-1977. [PMID: 37160710 DOI: 10.1002/elps.202300031] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 05/11/2023]
Abstract
High-performance liquid chromatography (HPLC)-based analytical assays are used to effectively monitor purity and quantity of plasmid DNA (pDNA) throughout the purification process. However, the phenomenon of physical entrapment of open circular (OC) isoforms pDNA inside narrow channels of chromatographic support decreases its accuracy and precision and the effect increases with pDNA size. The purpose of the study was to develop a chromatographic method for accurate analytical separation between isoforms of <16 kbp pDNA using weak anion exchanging monolithic column with large (6 µm) convective channels. Purified samples of 4.7 and 15.4 kbp large pDNA with known isoform composition were prepared and their isoforms separated in ascending salt gradient. Both OC and supercoiled (SC) isoforms were baseline separated at a flow rate below 0.5 mL min-1 in a guanidinium chloride (GdnCl) gradient with a ≥95% OC pDNA elution recovery. However, these chromatographic conditions increased 2 times the peak width for linear (LIN) pDNA isoform compared to the results using monoliths with 1.4 µm channel size. If other chaotropic agents, such as urea or thiocyanate (SCN), were added to Gdn ions, the elution volume for LIN isoform decreased. Optimization of combined GdnCl/GdnSCN gradient for pDNA elution resulted in a simple and robust chromatographic method, where OC-LIN and LIN-SC pDNA (up to 15 kbp size) were separated with resolution above 1.0 and above 2.0, respectively. The accessibility and general acceptance of anion exchange chromatography for pDNA analytics give the newly developed method a great potential for in-process control monitoring of pDNA production processes.
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Affiliation(s)
- Nejc Pavlin
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
| | - Urh Černigoj
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
| | - Mojca Bavčar
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
| | | | - Jan Mavri
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
| | - Martin Zidar
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
| | - Matevž Bone
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
| | | | - Tadej Sever
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
| | - Aleš Štrancar
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
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Kralj Š, Kodermac ŠM, Bergoč I, Kostelec T, Podgornik A, Štrancar A, Černigoj U. Effect of plasmid DNA isoforms on preparative anion exchange chromatography. Electrophoresis 2023; 44:1953-1966. [PMID: 37271857 DOI: 10.1002/elps.202300035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/08/2023] [Accepted: 05/23/2023] [Indexed: 06/06/2023]
Abstract
Increased need for plasmid DNA (pDNA) with sizes above 10 kbp (large pDNA) in gene therapy and vaccination brings the need for its large-scale production with high purity. Chromatographic purification of large pDNA is often challenging due to low process yields and column clogging, especially using anion-exchanging columns. The goal of our investigation was to evaluate the mass balance and pDNA isoform composition at column outlet for plasmids of different sizes in combination with weak anion exchange (AEX) monolith columns of varying channel size (2, 3 and 6 µm channel size). We have proven that open circular pDNA (OC pDNA) isoform is an important driver of reduced chromatographic performance in AEX chromatography. The main reason for the behaviour is the entrapment of OC pDNA in chromatographic supports with smaller channel sizes. Entrapment of individual isoforms was characterised for porous beads and convective monolithic columns. Convective entrapment of OC pDNA isoform was confirmed on both types of stationary phases. Porous beads in addition showed a reduced recovery of supercoiled pDNA (on an 11.6 kbp plasmid) caused by diffusional entrapment within the porous structure. Use of convective AEX monoliths or membranes with channel diameter >3.5 µm has been shown to increase yields and prevent irreversible pressure build-up and column clogging during purification of plasmids at least up to 16 kbp in size.
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Affiliation(s)
- Špela Kralj
- Sartorius BIA Separations d.o.o., Ajdovščina, Slovenia
| | | | - Ines Bergoč
- Sartorius BIA Separations d.o.o., Ajdovščina, Slovenia
| | | | - Aleš Podgornik
- Department of Chemical Engineering and Technical Safety, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
- COBIK, Ajdovščina, Slovenia
| | - Aleš Štrancar
- Sartorius BIA Separations d.o.o., Ajdovščina, Slovenia
| | - Urh Černigoj
- Sartorius BIA Separations d.o.o., Ajdovščina, Slovenia
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Černigoj U, Vidič J, Ferjančič A, Sinur U, Božič K, Mencin N, Martinčič Celjar A, Gagnon P, Štrancar A. Guanidine improves DEAE anion exchange-based analytical separation of plasmid DNA. Electrophoresis 2021; 42:2619-2625. [PMID: 34569093 DOI: 10.1002/elps.202100210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/04/2021] [Accepted: 09/17/2021] [Indexed: 11/10/2022]
Abstract
Elution of strong and weak anion exchangers with sodium chloride gradients is commonly employed for analysis of sample mixtures containing different isomers of plasmid DNA. Gradient elution of a weak anion exchanger (diethylaminoethyl) in the presence of guanidine hydrochloride (Gdn) roughly doubles resolution between open-circular (oc) and supercoiled (sc) isomers. It also improves resolution among sc, linear, and multimeric/aggregated forms. Sharper elution peaks with less tailing increase sensitivity about 30%. However, elution with an exclusively Gdn gradient to 900 mM causes more than 10% loss of plasmid. Elution with a sodium chloride gradient while maintaining Gdn at a level concentration of 300 mM achieves close to 100% recovery of sc plasmid while maintaining the separation improvements achieved by exclusively Gdn elution. Corresponding improvements in separation performance are not observed on a strong (quaternary amine) anion exchanger. Other chaotropic salts do not produce a favorable result on either exchanger, nor does the inclusion of surfactants or EDTA. Selectivity of the diethylaminoethyl-Gdn method is orthogonal to electrophoresis, but with better quantification than agarose electrophoresis, better quantitative accuracy than CE, and resolution approaching CE.
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Affiliation(s)
- Urh Černigoj
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
| | - Jana Vidič
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
| | - Ana Ferjančič
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
| | - Urša Sinur
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
| | - Klemen Božič
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
| | - Nina Mencin
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
| | | | - Pete Gagnon
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
| | - Aleš Štrancar
- BIA Separations d.o.o., a Sartorius company, Ajdovščina, Slovenia
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Černigoj U, Štrancar A. Scale-Up of Plasmid DNA Downstream Process Based on Chromatographic Monoliths. Methods Mol Biol 2021; 2197:167-192. [PMID: 32827137 DOI: 10.1007/978-1-0716-0872-2_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Purification of high-quality plasmid DNA in large quantities is a crucial step in its production for therapeutic use and is usually conducted by different chromatographic techniques. Large-scale preparations require the optimization of yield and homogeneity, while maximizing removal of contaminants and preserving molecular integrity. The advantages of Convective Interaction Media® (CIM®) monolith stationary phases, including low backpressure, fast separation of macromolecules, and flow-rate-independent resolution qualified them to be used effectively in separation of plasmid DNA on laboratory as well as on large scale. A development and scale-up of plasmid DNA downstream process based on chromatographic monoliths is described and discussed below. Special emphasis is put on the introduction of process analytical technology principles and tools for optimization and control of a downstream process.
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Podgornik A. Pressure drop in liquid chromatography. J Sep Sci 2018; 42:72-88. [DOI: 10.1002/jssc.201800882] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/13/2018] [Accepted: 11/06/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Aleš Podgornik
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Ljubljana Slovenia
- Center of Excellence for Biosensors; Instrumentation and Process Control - COBIK; Ajdovščina Slovenia
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Podgornik A, Hamachi M, Isakari Y, Yoshimoto N, Yamamoto S. Effect of pore size on performance of monolithic tube chromatography of large biomolecules. Electrophoresis 2017; 38:2892-2899. [DOI: 10.1002/elps.201700258] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/14/2017] [Accepted: 08/14/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Ales Podgornik
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Ljubljana Slovenia
- Center of Excellence; COBIK; Ajdovščina Slovenia
| | - Masataka Hamachi
- Bio-Process Engineering Laboratory, Graduate School of Medicine; Yamaguchi University; Ube Japan
| | - Yu Isakari
- Bio-Process Engineering Laboratory, Graduate School of Medicine; Yamaguchi University; Ube Japan
| | - Noriko Yoshimoto
- Bio-Process Engineering Laboratory, Graduate School of Medicine; Yamaguchi University; Ube Japan
- Biomedical Engineering Center (YUBEC); Yamaguchi University; Ube Japan
| | - Shuichi Yamamoto
- Bio-Process Engineering Laboratory, Graduate School of Medicine; Yamaguchi University; Ube Japan
- Biomedical Engineering Center (YUBEC); Yamaguchi University; Ube Japan
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Günal G, Kip Ç, Eda Öğüt S, İlhan H, Kibar G, Tuncel A. Comparative DNA isolation behaviours of silica and polymer based sorbents in batch fashion: monodisperse silica microspheres with bimodal pore size distribution as a new sorbent for DNA isolation. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2017; 46:178-184. [DOI: 10.1080/21691401.2017.1304404] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Gülçin Günal
- Bioengineering Division, Hacettepe University, Ankara, Turkey
| | - Çiğdem Kip
- Chemical Engineering Department, Hacettepe University, Ankara, Turkey
| | - S. Eda Öğüt
- Bioengineering Division, Hacettepe University, Ankara, Turkey
| | - Hasan İlhan
- Division of Nanotechnology and Nanomedicine, Hacettepe University, Ankara, Turkey
| | - Güneş Kibar
- Bioengineering Division, Hacettepe University, Ankara, Turkey
| | - Ali Tuncel
- Bioengineering Division, Hacettepe University, Ankara, Turkey
- Division of Nanotechnology and Nanomedicine, Hacettepe University, Ankara, Turkey
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Characterization of methacrylate chromatographic monoliths bearing affinity ligands. J Chromatogr A 2016; 1464:72-8. [DOI: 10.1016/j.chroma.2016.08.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/01/2016] [Accepted: 08/06/2016] [Indexed: 12/11/2022]
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Špec T, Peljhan S, Vidič J, Krajnc NL, Fonović M, Tavzes Č, Ropret P. CIM® monolith chromatography-enhanced ELISA detection of proteins in artists' paints: Ovalbumin as a case study. Microchem J 2016. [DOI: 10.1016/j.microc.2016.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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