Specific berenil-DNA interactions: an approach for separation of plasmid isoforms by pseudo-affinity chromatography |
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Authors: | Caramelo-Nunes C Tente T Almeida P Marcos J C Tomaz C T |
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Institution: | aCICS – UBI-Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;bDepartment of Chemistry, University of Beira Interior, 6201-001 Covilhã, Portugal;cCenter of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal |
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Abstract: | Small molecules, like some antibiotics and anticancer agents that bind DNA with high specificity, can represent a relevant alternative as ligands in affinity processes for plasmid DNA (pDNA) purification. In the current study, pDNA binding affinities of berberine, berenil, kanamycin, and neomycin were evaluated by a competitive displacement assay with ethidium bromide using a fluorimetric titration technique. The binding between pDNA and ethidium bromide was tested in different buffer conditions, varying the type and the salt concentration, and was performed in both the absence and presence of the studied compounds. The results showed that the minor groove binder berenil has the higher pDNA binding constant. Chromatographic experiments using a derivatized column with berenil as ligand showed a total retention of pDNA using 1.3 M ammonium sulfate in eluent buffer. A selective separation of supercoiled and open circular isoforms was achieved by further decreasing the salt concentration to 0.6 M and then to 0 M. These results suggest a promising application of berenil as ligand for specific purification of pDNA supercoiled isoform by pseudo-affinity chromatography. |
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Keywords: | Small DNA ligands Berenil Minor groove binder Intercalator Pseudo-affinity chromatography |
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