Login Register Cart 0
Generic placeholder image

Current Protein & Peptide Science

Editor-in-Chief

ISSN (Print): 1389-2037
ISSN (Online): 1875-5550

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Review Article

Separation of Nucleic Acids Using Single- and Multimodal Chromatography

Author(s): Tiago Matos and Leif Bülow*

Volume 20, Issue 1, 2019

Page: [49 - 55] Pages: 7

DOI: 10.2174/1389203718666171024112556

Price: $65

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).

Keywords: Hydrophobic interactions, anion exchange, DNA, plasmid, multimodal, chromatography, elution.

« Previous Next »
Graphical Abstract

[1]
Kalisky, T.; Quake, S.R. Single-cell genomics. Nat. Methods, 2011, 8, 311-314.
[2]
Rubanyi, G.M. The future of human gene therapy. Mol. Aspects Med., 2001, 22, 113-142.
[3]
Prazeres, D.M.; Monteiro, G.A.; Ferreira, G.N.; Diogo, M.M.; Ribeiro, S.C.; Cabral, J.M. Purification of plasmids for gene therapy and DNA vaccination. Biotechnol. Annu. Rev., 2001, 7, 1-30.
[4]
Ferreira, G.N.; Monteiro, G.A.; Prazeres, D.M.; Cabral, J.M. Downstream processing of plasmid DNA for gene therapy and DNA vaccine applications. Trends Biotechnol., 2000, 18, 380-388.
[5]
Sousa, F.; Queiroz, J.A. Supercoiled plasmid quality assessment by analytical arginine-affinity chromatography. J. Chromatogr. A, 2011, 1218, 124-129.
[6]
Smith, C.R.; DePrince, R.B.; Dackor, J.; Weigl, D.; Griffith, J.; Persmark, M. Separation of topological forms of plasmid DNA by anion-exchange HPLC: shifts in elution order of linear DNA. J. Chromatogr. B ., 2007, 854, 121-127.
[7]
Hitchcock, A.G.; Sergeant, J.A.; Rahman, S.F.; Tharia, H.A.; Blom, H. Scale-up of a plasmid DNA purification process. Bioprocess Int., 2010, 8, 46-54.
[8]
Ferreira, G.N.M.; Cabral, J.M.S.; Prazeres, D.M.F. A comparison of gel filtration chromatographic supports for plasmid purification. Biotechnol. Tech., 1997, 11, 417-420.
[9]
Prazeres, D.M.; Schluep, T.; Cooney, C. Preparative purification of supercoiled plasmid DNA using anion-exchange chromatography. J. Chromatogr. A, 1998, 806, 31-45.
[10]
Eon-Duval, A.; Burke, G. Purification of pharmaceutical-grade plasmid DNA by anion-exchange chromatography in an RNase-free process. J. Chromatogr. B., 2004, 804, 327-335.
[11]
Diogo, M.M.; Queiroz, J.A.; Monteiro, G.A.; Martins, S.A.; Ferreira, G.N.; Prazeres, D.M. Purification of a cystic fibrosis plasmid vector for gene therapy using hydrophobic interaction chromatography. Biotechnol. Bioeng., 2000, 68, 576-583.
[12]
Caramelo-Nunes, C.; Tente, T.; Almeida, P.; Marcos, J.C.; Tomaz, C.T. Specific berenil-DNA interactions: an approach for separation of plasmid isoforms by pseudo-affinity chromatography. Anal. Biochem., 2011, 412, 153-158.
[13]
Sousa, A.; Sousa, F.; Queiroz, J.A. Differential interactions of plasmid DNA, RNA and genomic DNA with amino acid-based affinity matrices. J. Sep. Sci., 2010, 33, 2610-2618.
[14]
Sousa, F.; Prazeres, D.M.; Queiroz, J.A. Improvement of transfection efficiency by using supercoiled plasmid DNA purified with arginine affinity chromatography. J. Gene Med., 2009, 11, 79-88.
[15]
Zhong, L.; Scharer, J.; Moo-Young, M.; Fenner, D.; Crossley, L.; Honeyman, C.H.; Suen, S.Y.; Chou, C.P. Potential application of hydrogel-based strong anion-exchange membrane for plasmid DNA purification. J. Chromatogr. B., 2011, 879, 564-572.
[16]
Guerrero-German, P.; Prazeres, D.M.; Guzman, R.; Montesinos-Cisneros, R.M.; Tejeda-Mansir, A. Purification of plasmid DNA using tangential flow filtration and tandem anion-exchange membrane chromatography. Bioprocess Biosyst. Eng., 2009, 32, 615-623.
[17]
Johansson, H.O.; Matos, T.; Luz, J.S.; Feitosa, E.; Oliveira, C.C.; Pessoa, A. Jr, Bülow, L.; Tjerneld, F. Plasmid DNA partitioning and separation using poly(ethylene glycol)/poly(acrylate)/salt aqueous two-phase systems. J. Chromatogr. A, 2012, 1233, 30-35.
[18]
Ferreira, G.N.; Cabral, J.M.; Prazeres, D.M. Studies on the batch adsorption of plasmid DNA onto anion-exchange chromatographic supports. Biotechnol. Prog., 2000, 16, 416-424.
[19]
Levy, M.S.; O’Kennedy, R.D.; Ayazi-Shamlou, P.; Dunnill, P. Biochemical engineering approaches to the challenges of producing pure plasmid DNA. Trends Biotechnol., 2000, 18, 296-305.
[20]
Benčina, M.; Podgornik, A.; Štrancar, A. Characterization of methacrylate monoliths for purification of DNA molecules. J. Sep. Sci., 2004, 27, 801-810.
[21]
Nordborg, A.; Hilder, E.F. Recent advances in polymer monoliths for ion-exchange chromatography. Anal. Bioanal. Chem., 2009, 394, 71-84.
[22]
Sousa, A.; Bicho, D.; Tomaz, C.T.; Sousa, F.; Queiroz, J.A. Performance of a non-grafted monolithic support for purification of supercoiled plasmid DNA. J. Chromatogr. A, 2011, 1218, 1701-1706.
[23]
Shin, M.J.; Tan, L.; Jeong, M.H.; Kim, J-H.; Choe, W-S. Monolith-based immobilized metal affinity chromatography increases production efficiency for plasmid DNA purification. J. Chromatogr. A, 2011, 1218, 5273-5278.
[24]
Smrekar, V.; Smrekar, F.; Strancar, 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.
[25]
Černigoj, U.; Barut, M.; Podgornik, A.; Peterka, M.; Strancar, A. A multimodal histamine ligand for chromatographic purification of plasmid DNA. J. Chromatogr. A, 2013, 1281, 87-93.
[26]
Paril, C.; Horner, D.; Ganja, R.; Jungbauer, A. Adsorption of pDNA on microparticulate charged surface. J. Biotechnol., 2009, 141, 47-57.
[27]
Tiainen, P.; Galaev, I.; Larsson, P.O. Plasmid adsorption to anion-exchange matrices: comments on plasmid recovery. Biotechnol. J., 2007, 2, 726-735.
[28]
Tiainen, P.; Gustavsson, P-E.; Ljunglöf, A.; Larsson, P-O. Superporous agarose anion exchangers for plasmid isolation. J. Chromatogr. A, 2007, 1138, 84-94.
[29]
Tiainen, P.; Rokebul Anower, M.; Larsson, P.O. High-capacity composite adsorbents for nucleic acids. J. Chromatogr. A, 2011, 1218, 5235-5240.
[30]
Teeters, M.; Root, T.; Lightfoot, E. Adsorption and desorption behavior of plasmid DNA on ion-exchange membranes: effect of salt valence and compaction agents. J. Chromatogr. A, 2004, 1036, 73-78.
[31]
Huber, C.G. Micropellicular stationary phases for high-performance liquid chromatography of double-stranded DNA. J. Chromatogr. A, 1998, 806, 3-30.
[32]
Murphy, J.C.; Wibbenmeyer, J.A.; Fox, G.E.; Willson, R.C. Purification of plasmid DNA using selective precipitation by compaction agents. Nature, 1999, 17, 10-11.
[33]
Matos, T.; Queiroz, J.A.; Bülow, L. Plasmid DNA purification using a multimodal chromatography resin. J. Mol. Recognit., 2014, 27, 184-189.
[34]
Matos, T.; Queiroz, J.A.; Bülow, L. Binding and elution behavior of small deoxyribonucleic acid fragments on a strong anion-exchanger multimodal chromatography resin. J. Chromatogr. A, 2013, 1302, 40-44.
[35]
Ferreira, G.N.; Cabral, J.M.; Prazeres, D.M. Development of process flow sheets for the purification of supercoiled plasmids for gene therapy applications. Biotechnol. Prog., 1999, 15, 725-731.
[36]
Urthaler, J.; Schlegl, R.; Podgornik, A.; Strancar, A.; Jungbauer, A.; Necina, R. Application of monoliths for plasmid DNA purification. J. Chromatogr. A, 2005, 1065, 93-106.
[37]
Theodossiou, I.; Søndergaard, M.; Thomas, O.R. Design of expanded bed supports for the recovery of plasmid DNA by anion exchange adsorption. Bioseparation, 2001, 10, 31-44.
[38]
Westman, E.; Eriksson, S.; Laas, T.; Pernemalm, P.A.; Skold, S.E. Separation of DNA restriction fragments by ion-exchange chromatography on FPLC columns Mono P and Mono Q. Anal. Biochem., 1987, 166, 158-171.
[39]
Chen, W.H.; Fu, J.Y.; Kourentzi, K.; Willson, R.C. Nucleic acid affinity of clustered-charge anion exchange adsorbents: effects of ionic strength and ligand density. J. Chromatogr. A, 2011, 1218, 258-262.
[40]
Yamamoto, S.; Nakamura, M.; Tarmann, C.; Jungbauer, A. Retention studies of DNA on anion-exchange monolith chromatography binding site and elution behavior. J. Chromatogr. A, 2007, 1144, 155-160.
[41]
Yamamoto, S.; Yoshimoto, N.; Tarmann, C.; Jungbauer, A. Binding site and elution behavior of DNA and other large biomolecules in monolithic anion-exchange chromatography. J. Chromatogr. A, 2009, 1216, 2616-2620.
[42]
Arakawa, T.; Timasheff, S.N. Preferential interactions of proteins with salts in concentrated solutions. Biochemistry, 1982, 21, 6545-6552.
[43]
Melander, W.R.; Elrassi, Z.; Horváth, C. Interplay of hydrophobic and electrostatic interactions in biopolymer chromatography. J. Chromatogr. , 1989, 469, 3-27.
[44]
Melander, W.R.; Corradini, D.; Horváth, C. Salt-mediated retention of proteins in hydrophobic-interaction chromatography. J. Chromatogr. , 1984, 317, 67-85.
[45]
Melander, W.; Horváth, C. Chromatography on hydrophobic interactions of proteins : an interpretation in precipitation and of the lyotropic series. Arch. Biochem. Biophys., 1977, 183, 200-215.
[46]
Porath, J.; Sundberg, L.; Fornstedt, N.; Olsson, I. Salting-out in amphiphilic gels as a new approach to hydrophobic adsorption. Nature, 1973, 245, 465-466.
[47]
Porath, J. Salt-promoted adsorption: recent developments. J. Chromatogr. A, 1986, 376, 331-341.
[48]
Haimer, E.; Tscheliessnig, A.; Hahn, R.; Jungbauer, A. Hydrophobic interaction chromatography of proteins IV. Kinetics of protein spreading. J. Chromatogr. A, 2007, 1139, 84-94.
[49]
Diogo, M.M.; Queiroz, J.A.; Prazeres, D.M.F. Assessment of purity and quantification of plasmid DNA in process solutions using high-performance hydrophobic interaction chromatography. J. Chromatogr. A, 2003, 998, 109-117.
[50]
Stadler, J.; Lemmens, R.; Nyhammar, T. Plasmid DNA purification. J. Gene Med., 2004, 6, 54-66.
[51]
Diogo, M.M.; Queiroz, J.A.; Prazeres, D.M. Studies on the retention of plasmid DNA and Escherichia coli nucleic acids by hydrophobic interaction chromatography. Bioseparation, 2001, 10, 211-220.
[52]
Iuliano, S.; Fisher, J.R.; Chen, M.; Kelly, W.J. Rapid analysis of a plasmid by hydrophobic-interaction chromatography with a non-porous resin. J. Chromatogr. A, 2002, 972, 77-86.
[53]
Kallberg, K.; Johansson, H.O.; Bulow, L. Multimodal chromatography: an efficient tool in downstream processing of proteins. Biotechnol. J., 2012, 7, 1485-1495.
[54]
Yang, Y.; Geng, X. Mixed-mode chromatography and its applications to biopolymers. J. Chromatogr. A, 2011, 1218, 8813-8825.
[55]
Kopaciewicz, W.; Rounds, M.A.; Regnier, F.E. Stationary phase contributions to retention in high-performance anion-exchange protein chromatography: ligand density and mixed mode effects. J. Chromatogr. A, 1985, 318, 157-172.
[56]
Mclaughlin, L.W. Mixed-mode chromatography of nucleic acids. Chem. Rev., 1989, 89, 309-319.
[57]
Trammell, B.C.; Hillmyer, M.A.; Carr, P.W. A study of the Lewis Acid-Base interactions of Polybutadiene-Coated Zirconia. Anal. Chem., 2001, 73, 3323-3331.
[58]
Xindu, G.; Lili, W. Liquid chromatography of recombinant proteins and protein drugs. J. Chromatogr. B., 2008, 866, 133-153.
[59]
Burton, S.C.; Harding, D.R. Salt-independent adsorption chromatography: new broad-spectrum affinity methods for protein capture. J. Biochem. Biophys. Methods, 2001, 49, 275-287.
[60]
Cabanne, C. Efficient purification of recombinant proteins fused to maltose-binding protein by mixed-mode chromatography. J. Chromatogr. A, 2009, 1216, 4451-4456.
[61]
Kallberg, K.; Becker, K.; Bülow, L. Application of a pH responsive multimodal hydrophobic interaction chromatography medium for the analysis of glycosylated proteins. J. Chromatogr. A, 2011, 1218, 678-683.
[62]
Davies, N.H.; Euerby, M.R.; McCalley, D.V. A study of retention and overloading of basic compounds with mixed-mode reversed-phase/cation-exchange columns in high performance liquid chromatography. Biotechnol. Appl. Biochem., 2007, 1138, 65-72.
[63]
Zhao, G.; Dong, X.Y.; Sun, Y. Ligands for mixed-mode protein chromatography: Principles, characteristics and design. J. Biotechnol., 2009, 144, 3-11.
[64]
Johansson, B.L.; Belew, M.; Eriksson, S.; Glad, G.; Lind, O.; Maloisel, J.L.; Norrman, N. Preparation and characterization of prototypes for multi-modal separation media aimed for capture of negatively charged biomolecules at high salt conditions. J. Chromatogr. A, 2003, 1016, 21-33.
[65]
Eriksson, K.; Rodrigo, G.; Brekkan, E. MAb contaminant removal with a multimodal anion exchanger. Bioprocess Int., 2009, 7, 52-56.
[66]
Chen, J.; Tetrault, J.; Zhang, Y.; Wasserman, A.; Conley, G.; Dileo, M.; Haimes, E.; Nixon, A.E.; Ley, A. The distinctive separation attributes of mixed-mode resins and their application in monoclonal antibody downstream purification process. J. Chromatogr. A, 2010, 1217, 216-224.
[67]
Gagnon, P. IgG aggregate removal by charged-hydrophobic mixed mode chromatography. Curr. Pharm. Biotechnol., 2009, 10, 434-439.
[68]
Silva-Santos, A.R.; Alves, C.P.A.; Prazeres, D.M.F.; Azevedo, A.M. Separation of plasmid DNA topoisomers by multimodal chromatography. Anal. Biochem., 2016, 503, 68-70.
[69]
Liang, X.G.; Kuhn, H.; Frank-Kamenetskii, M.D. Monitoring single-stranded DNA secondary structure formation by determining the topological state of DNA catenanes. Biophys. J., 2006, 90, 2877-2889.
[70]
Langowski, J. Salt effects on internal motion of super helical and linear pUC8 DNA. Biophys. Chem., 1987, 27, 263-271.
[71]
Cardenas, M.; Schillén, K.; Pebalk, D.; Nylander, T.; Lindman, B. Interaction between DNA and charged colloids could be hydrophobically driven. Biomacromolecules, 2005, 6, 832-837.
[72]
Diogo, M.M.; Queiroz, J.A.; Prazeres, D.M.F. Studies on the retention of plasmid DNA and Escherichia coli nucleic acids by hydrophobic interaction chromatography. Bioseparation, 2001, 10, 211-220.
[73]
Matos, T.; Mohamed, E.T.; Queiroz, J.A.; Bülow, L. CaptoTM Resins for DNA purification: A minor difference in ligand composition greatly influences the separation of guanidyl containing fragments. Chromatographia, 2016, 79, 1277-1282.
[74]
Matos, T.; Silva, G.; Queiroz, J.A.; Bülow, L. Preparative isolation of polymerase chain reaction products using mixed-mode chromatography. Anal. Biochem., 2015, 489, 73-75.
[75]
Matos, T.; Johansson, H.O.; Queiroz, J.A.; Bülow, L. Isolation of PCR DNA fragments using aqueous two-phase systems. Sep. Purif. Technol., 2014, 122, 144-148.

Rights & Permissions Print Cite
Article Metrics
43
4
1
1
World Immunization Week
© 2024 Bentham Science Publishers | Privacy Policy