Tiago Matos

Specific recognition of supercoiled plasmid DNA in arginine affinity chromatography.

Arginine chromatography was used to fully separate supercoiled and open circular plasmid DNA (pDNA) isoforms. The results show that the arginine matrix promotes multiple interactions with pDNA, including not only electrostatic and hydrophobic but also biorecognition of nucleotide bases by the arginine ligand. The strong interactions occurring with DNA backbone provide stability, conducting to high effectiveness of arginine support to bind pDNA at low ionic strength. The specific interaction of arginine with sc pDNA could 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.

Plasmid DNA partitioning and separation using poly(ethylene glycol)/poly(acrylate)/salt aqueous two-phase systems.

Phase diagrams of poly(ethylene glycol)/polyacrylate/Na(2)SO(4) systems have been investigated with respect to polymer size and pH. Plasmid DNA from Escherichia coli can depending on pH and polymer molecular weight be directed to a poly(ethylene glycol) or to a polyacrylate-rich phase in an aqueous two-phase system formed by these polymers. Bovine serum albumin (BSA) and E. coli homogenate proteins can be directed opposite to the plasmid partitioning in these systems. Two bioseparation processes have been developed where in the final step the pDNA is partitioned to a salt-rich phase giving a total process yield of 60-70%. In one of them the pDNA is partitioned between the polyacrylate and PEG-phases in order to remove proteins. In a more simplified process the plasmid is partitioned to a PEG-phase and back-extracted into a Na(2)SO(4)-rich phase. The novel polyacrylate/PEG system allows a strong change of the partitioning between the phases with relatively small changes in composition or pH.

Plasmid DNA purification using a multimodal Chromatography resin

Multimodal chromatography is widely used for isolation of proteins because it often results in improved selectivity compared to conventional separation resins. The binding potential and chromatographic behavior of plasmid DNA have here been examined on a Capto Adhere resin. Capto Adhere is a recent multimodal chromatography material allowing molecular recognition between the ligand and target molecule, which is based on combined ionic and aromatic interactions. Capto Adhere proved to offer a very strong binding of nucleic acids. This property could be used to isolate plasmid DNA from a crude Escherichia coli extract. Using a stepwise NaCl gradient, pure plasmid DNA could be obtained without protein and endotoxin contaminations. The RNA fraction bound most strongly to the resin and could be eluted only at very high salt concentrations (2.0 M NaCl). The chromatographic separation behavior was very robust between pH values 6 and 9, and the dynamic binding capacity was estimated to 60 µg/ml resin. Copyright

Binding and elution behavior of small deoxyribonucleic acid fragments on a strong anion-exchanger multimodal chromatography resin.

The separation behavior of small single-stranded from double-stranded DNA molecules has been determined on a multimodal (mixed-mode) chromatography system. The resin used is a strong anion exchanger which also modulates hydrophobic recognition. The intrinsic differences between single- and double-stranded DNAs concerning charge, hydrophobicity and three-dimensional structure render this form of MMC suitable for separation of the different nucleic acid molecules. All DNAs tested bound strongly to the resin and they could be eluted with increasing NaCl concentrations. Each homopolymeric ssDNA sample resulted in a base-specific elution pattern when using a linear NaCl gradient. The elution order was poly(dA)<poly(dC)<poly(dG)<poly(dT) and this order was dependent on the secondary structure of the molecule. Such differences were not observed for small double-stranded DNAs. Due to the more hydrophobic nature of single-stranded DNA molecules they could be separated from double-stranded DNAs.

Fetal hemoglobin is much less prone to DNA cleavage compared to the adult protein

Hemoglobin (Hb) is well protected inside the red blood cells (RBCs). Upon hemolysis and when free in circulation, Hb can be involved in a range of radical generating reactions and may thereby attack several different biomolecules. In this study, we have examined the potential damaging effects of cell-free Hb on plasmid DNA (pDNA). Hb induced cleavage of supercoiled pDNA (sc pDNA) which was proportional to the concentration of Hb applied. Almost 70% of sc pDNA was converted to open circular or linear DNA using 10 µM of Hb in 12 h. Hb can be present in several different forms. The oxy (HbO2) and met forms are most reactive, while the carboxy-protein shows only low hydrolytic activity. Hemoglobin A (HbA) could easily induce complete pDNA cleavage while fetal hemoglobin (HbF) was three-fold less reactive. By inserting, a redox active cysteine residue on the surface of the alpha chain of HbF by site-directed mutagenesis, the DNA cleavage reaction was enhanced by 82%. Reactive oxygen species were not directly involved in the reaction since addition of superoxide dismutase and catalase did not prevent pDNA cleavage. The reactivity of Hb with pDNA can rather be associated with the formation of protein based radicals.

Nucleic acid and protein extraction from electropermeabilized E. coli cells on a microfluidic chip

Due to the extensive use of nucleic acid and protein analysis of bacterial samples, there is a need for simple and rapid extraction protocols for both plasmid DNA and RNA molecules as well as reporter proteins like the green fluorescent protein (GFP). In this report, an electropermeability technique has been developed which is based on exposing E. coli cells to low voltages to allow extraction of nucleic acids and proteins. The flow-through electropermeability chip used consists of a microfluidic channel with integrated gold electrodes that promote cell envelope channel formation at low applied voltages. This will allow small biomolecules with diameters less than 30 A to rapidly diffuse from the permeabilized cells to the surrounding solution. By controlling the applied voltage, partial and transient to complete cell opening can be obtained. By using DC voltages below 0.5 V, cell lysis can be avoided and the transiently formed pores can be closed again and the cells survive. This method has been used to extract RNA and GFP molecules under conditions of electropermeability. Plasmid DNA could be recovered when the applied voltage was increased to 2 V, thus causing complete cell lysis.

Preparative isolation of polymerase chain reaction products using mixed-mode chromatography

The polymerase chain reaction (PCR) has become one of the most useful techniques in molecular biology laboratories around the world. The purification of the target DNA product is often challenging, however, and most users are restricted to employing available commercial kits. The recent developments in mixed-mode chromatography have shown higher selectivity for a variety of nucleic acid-containing samples. Capto Adhere is a mixed-mode chromatography resin that offers a high-selectivity ligand and is here applied for the purification of amplified DNAs from PCR mixtures in a 10-min single step, with yields above 95%, high linearity, and high precision for different concentrations.