Binding and elution strategy for improved performance of arginine affinity chromatography in supercoiled plasmid DNA purification

Sousa, Fani; Prazeres, D.M.F.; Queiroz, João A.

doi:10.1002/bmc.1097

Cited by 24 publications

(15 citation statements)

References 23 publications

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“…Arginine-agarose support was recently used to effectively purify pDNA [17] (supercoiled and open circular) [9], and it was suggested that the binding mechanism involves phenomenological interactions like biorecognition between amino acids and pDNA [14], including, electrostatic interactions, hydrophobic interactions, (multiple) hydrogen bond interactions, dipole-dipole forces, cation-p interactions, etc. Since plasmids are negatively charged due to the phosphate groups in the DNA backbone, it is easy to predict a favourable electrostatic interaction between the plasmid phosphate groups and arginine ligands.…”

Section: Resultsmentioning

confidence: 99%

“…This amino acid also facilitates elution of bound proteins from various column resins, including Protein-A or dye affinity [35] columns and hydrophobic interaction columns [33]. More recently it was demonstrated that this competition strategy with arginine in elution buffer is capable of the total elution of pDNA indicating that the interaction of pDNA with the matrix was weakened by competition [9,14]. In this work, the elution of the oligonucleotides by addition of an arginine-supplemented buffer was tested.…”

Section: Arginine In Elution Buffermentioning

confidence: 95%

“…Amino acids ligands were used in AC of proteins [3], oligosaccharides [11] and endotoxins [12], and, very recently, for the first time, their application for pDNA purification was asserted [13,14]. In general, the positively charged amino acid arginine mediates the largest number of contacts in protein-nucleic acid interactions [10].…”

Section: Introductionmentioning

confidence: 99%

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Selectivity of arginine chromatography in promoting different interactions using synthetic oligonucleotides as model

Sousa

Queiroz³

2009

J of Separation Science

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Arginine has been effectively used in several chromatography methodologies to improve recovery, resolution, and to suppress aggregation. Recently, arginine chromatography was used to fully separate supercoiled and open circular plasmid DNA isoforms. The specific recognition of supercoiled plasmid isoform by arginine was hypothesised to be due to the ability of arginine matrix to be involved in complex interactions that are partly dependent on the conformation of the DNA molecule. In light of these considerations a study was conducted to understand the several interactions that a DNA molecule can promote with the arginine support, in accordance with the chromatographic conditions established. Consequently, knowing the ideal conditions to promote the specific interactions, it could be possible to perform a more targeted and efficient purification. This work describes the chromatography of oligonucleotides with sizes up to 30 bases on the arginine-agarose gel. The effect of several conditions like hydrophobic character of the individual bases, molecular mass of the oligonucleotides, presence of secondary structures, temperature and elution buffer composition (salt and arginine supplemented buffer) was investigated. According to previous atomic data referent to possible interactions between amino acids and DNA nucleotides, arginine can preferentially interact with guanine by hydrogen bond, but other interactions (ionic interactions, van der Waals contacts, water mediated bonds) may also be present and become dominant depending on the conditions used. The results also revealed that the application of arginine in the elution buffer led to an effective elution of oligonucleotides from the arginine chromatographic support by a competition strategy. In general, it was suggested that the affinity interaction promoted by the arginine support is responsible for the specific recognition of particular oligonucleotide bases, involving multiple interactions.

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Section: Resultsmentioning

confidence: 99%

Section: Arginine In Elution Buffermentioning

confidence: 95%

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Selectivity of arginine chromatography in promoting different interactions using synthetic oligonucleotides as model

Sousa

Queiroz³

2009

J of Separation Science

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“…7,9 Positively charged amino acids covalently conjugated to chromatography resin have been used to purify plasmid DNA through a combination of ion exchange and affinity chromatography. 9,11 …”

Section: Introductionmentioning

confidence: 99%

DNA Adsorption to and Elution from Silica Surfaces: Influence of Amino Acid Buffers

et al. 2013

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Solid phase extraction and purification of DNA from complex samples typically requires chaotropic salts that can inhibit downstream polymerase amplification if carried into the elution buffer. Amino acid buffers may serve as a more compatible alternative for modulating the interaction between DNA and silica surfaces. We characterized DNA binding to silica surfaces, facilitated by representative amino acid buffers, and the subsequent elution of DNA from the silica surfaces. Through bulk depletion experiments, we found that more DNA adsorbs to silica particles out of positively compared to negatively charged amino acid buffers. Additionally, the type of the silica surface greatly influences the amount of DNA adsorbed, and the final elution yield. Quartz crystal microbalance experiments with dissipation monitoring (QCM-D) revealed multiphasic DNA adsorption out of stronger adsorbing conditions such as arginine, glycine, and glutamine, with DNA more rigidly bound during the early stages of the adsorption process. The DNA film adsorbed out of glutamate was more flexible and uniform throughout the adsorption process. QCM-D characterization of DNA elution from the silica surface indicates an uptake in water mass during the initial stage of DNA elution for the stronger adsorbing conditions, which suggests that for these conditions the DNA film is partly dehydrated during the prior adsorption process. Overall, several positively charged and polar neutral amino acid buffers show promise as an alternative to methods based on chaotropic salts for solid phase DNA extraction.

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“…Within the group of pseudobiospecific ligands, we can find small ligands (e.g., thiophilic, metal chelating), which are quite general and lack selectivity for specific targets (Batalha et al, 2012;Pina et al, 2014), for example imac, amino acid ligands (Sousa et al, 2009(Sousa et al, , 2010(Sousa et al, , 2011 expression in eukaryotic cells systems, and purification mostly relies on resins with protein A, which increases their production cost (Skerra, 2007). Antibodies are less stable in very harsh differences in pH, use of organic solvents, and high salt concentrations can lead to denaturation (W€ orn and Pl€ uckthun, 2001).…”

Section: Pseudobiospecificmentioning

confidence: 99%

The future of protein scaffolds as affinity reagents for purification

Dias

Roque

2016

Biotech & Bioengineering

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Affinity purification is one of the most powerful separation techniques extensively employed both at laboratory and production scales. While antibodies still represent the gold standard affinity reagents, others derived from non-immunoglobulin scaffolds emerged as interesting alternatives in particular for affinity purification. The lower costs of production, fast ligand development, and high robustness are appealing advantages of non-immunoglobulin scaffolds. These have successfully been used in the affinity purification of relevant targets as antibodies, human serum albumin, transferrin, and other biomarkers, as reviewed in this work. Furthermore, a critical assessment on the strengths, weaknesses, opportunities, and threats related with the implementation of non-immunoglobulin scaffolds as ligands in affinity purification are discussed. Biotechnol. Bioeng. 2017;114: 481-491. © 2016 Wiley Periodicals, Inc.

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Binding and elution strategy for improved performance of arginine affinity chromatography in supercoiled plasmid DNA purification

Cited by 24 publications

References 23 publications

Selectivity of arginine chromatography in promoting different interactions using synthetic oligonucleotides as model

Selectivity of arginine chromatography in promoting different interactions using synthetic oligonucleotides as model

DNA Adsorption to and Elution from Silica Surfaces: Influence of Amino Acid Buffers

The future of protein scaffolds as affinity reagents for purification

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