Hydrophobic interaction chromatography of homo-oligonucleotides on derivatized Sepharose CL-6B. Application of the solvophobic theory

Dilemma on plasmid DNA purification: binding capacity vs selectivity

Plasmid DNA chromatography is a powerful field in constant development and evolution. The use of this technique is considered mandatory in the production of an efficient and safe formulation to be applied for plasmid-mediated gene therapy. Concerning this, the search for an ideal chromatographic support/ligand combination motivated scientist to pursue a continuous improvement on the plasmid chromatography performance, looking for a progression on the ligands and supports used. The present review explores the different approaches used over time to purify plasmid DNA, ambitioning both high recovery and high purity levels. Overall, it is presented a critical discussion relying on the relevance of the binding capacity versus selectivity of the supports.

Molecular recognition of oligonucleotides and plasmid DNA by l-methionine

The present study explores the effect of oligonucleotide composition on the mechanism of retention to l-methionine agarose support by chromatography and saturation transfer difference (STD)-nuclear magnetic resonance (NMR) techniques. All chromatographic experiments were performed using 1.5 M (NH4 )2 SO4 . The binding profiles obtained by chromatography show that oligonucleotides with thymine had the highest retention time. In general, the larger homo-oligonucleotides are more retained to the l-methionine agarose support. Moreover, the study with hetero-oligonucleotides confirms that the presence of guanine reduces the retention on the l-methionine chromatographic support. These results are in accord with STD-NMR experiments, which show that the strongest signals were observed for the methyl group of thymine, and no STD signals were observed for the guanosine protons. Finally, the retention behaviour of linear plasmid DNA (pDNA) with different sizes and base composition (2.7-kbp pUC19, 6.05-kbp pVAX1-LacZ, 7.4-kbp pVAX1-LacZgag and 14-kbp pcDNA-based plasmid) was also evaluated by chromatography. The results indicate that the underlying mechanism of retention involves not only hydrophobic interactions but also other elementary interactions responsible for the biorecognition of pDNA molecules by l-methionine ligands.

Analogue encoding of physicochemical properties of proteins in their cognate messenger RNAs

Being related by the genetic code, mRNAs and their cognate proteins exhibit mutually interdependent compositions, which implies the possibility of a direct connection between their general physicochemical properties. Here we probe the general potential of the cell to encode information about proteins in the average characteristics of their cognate mRNAs and decode it in a ribosome-independent manner. We show that average protein hydrophobicity, calculated from either sequences or 3D structures, can be encoded in an analogue fashion by many different average mRNA sequence properties with the only constraint being that pyrimidine and purine bases be clearly distinguishable on average. Moreover, average characteristics of mRNA sequences enable discrimination between cytosolic and membrane proteins even in the absence of topogenic signal-based mechanisms. Our results suggest that protein and mRNA localization may be partly determined by basic physicochemical rationales and interdependencies between the two biomolecules.

mRNA transport contributes to the proper localization of its cognate proteins. Here the authors report a correlation between the physicochemical properties of mRNAs and their cognate proteins, suggesting that these properties of mRNAs can predict the subcellular localization of their cognate proteins.

Analysis of nucleotides binding to chromatography supports provided by nuclear magnetic resonance spectroscopy

The epitope mapping of nucleotides bound to three chromatography supports is accomplished using saturation transfer difference (STD)-NMR spectroscopy. This experiment involves subtracting a spectrum in which the support was selectively saturated from one recorded without support saturation. In the difference spectrum only the signals of the ligands that bind to the support and received saturation transfer remain. The nucleotide protons in closer contact with the support have more intense signals due to a more efficient transfer of saturation. We investigate the effects on the binding to the nucleotides by the introduction of a spacer arm between l-histidine and Sepharose. Our NMR experiments evidence a clear contribution of the spacer to the interaction with all the nucleotides, increasing the mobility of the amino acid and giving different STD responses. This enhanced mobility originates the reinforcement of the interactions with the sugar moiety and phosphate group of 5'-CMP and 5'-TMP or the base of 5'-GMP and 5'-UMP. Hence, with this study we show that by using STD NMR technique on chromatographic systems it is possible to provide a fast, robust and efficient way of screening the atoms involved in the binding to the supports.

Histidine affinity chromatography of homo-oligonucleotides. Role of multiple interactions on retention

The recent application of histidine-agarose affinity supports in plasmid purification takes advantage of the biorecognition of nucleic acid bases by the histidine ligand. This consideration prompted the need for better understanding the interactions involved in affinity chromatography of plasmid DNA with the histidine-agarose support. In this work, we used synthetic homo-deoxyoligonucleotides with different sizes (1-30 nucleotides long), to explore the effect of several conditions like hydrophobic character of the individual bases, presence of secondary structures, temperature, pH and salt concentration on the mechanism of retention of nucleic acids to histidine-agarose support. One of the most striking results shows that histidine interacts preferentially with guanine, and the presence of secondary structures on polyA and polyG oligonucleotides has a significant influence on retention. Otherwise, the temperature manipulation has not shown a direct influence on oligonucleotide retention, only inducing conformational changes on secondary structures. Overall, the results obtained provide valuable information for the future development and implementation of histidine and other amino acids as ligands in chromatography for the purification of plasmid DNA and other nucleic acids, by improving the knowledge of the interactions involved as well as of the parameters influencing the retention.

Binding site and elution behavior of DNA and other large biomolecules in monolithic anion-exchange chromatography

Our previous study has shown that there is a good correlation between the number of charges of DNA (from trimer to 50-mer) and the number of binding sites B in electrostatic interaction chromatography (ion-exchange chromatography, IEC). It was also found that high salt (NaCl) concentration is needed to elute large DNAs (>0.6M). In this paper we further performed experiments with large DNAs (up to 95-mer polyT and polyA) and charged liposome particles of different sizes (ca. 30, 50 and 100 nm) with a monolithic anion-exchange disk in order to understand the binding and elution mechanism of very large charged biomolecules or particles. The peak salt (NaCl) concentration increased with increasing DNA length. However, above 50-mer DNAs the value did not increase significantly with DNA length (ca. 0.65-0.70 M). For liposome particles of different sizes the peak salt concentration (ca. 0.62 M) was similar and slightly lower than that for large DNAs (ca. 0.65-0.70 M). The binding site values (ca. 25-30) are smaller than those for large DNAs. When arginine was used as a mobile phase modulator, the elution position of polyA and polyT became very close whereas in NaCl gradient elution polyT appeared after polyA eluted. This was mainly due to suppression of hydrophobic interaction by arginine.

Sequence-specific purification of DNA oligomers in hydrophobic interaction chromatography using peptide nucleic acid amphiphiles: extended dynamic range

We present improvements on a previously reported method (Vernille JP, Schneider JW. 2004. Biotechnol Prog 20(6):1776-1782) to purify DNA oligomers by attachment of peptide nucleic acid amphiphiles (PNAA) to particular sequences on the oligomers, followed by their separation from unbound oligomers using hydrophobic interaction chromatography (HIC). Use of alkyl-modified HIC media (butyl and octyl sepharose) over phenyl-modified media (phenyl sepharose) reduced the elution time of unbound DNA while not affecting the elution time of the PNAA/DNA complex. Modifying the alkane tail length for PNAA from C(12) to C(18) increased slightly the retention of PNAA/DNA duplexes. By combining these two refinements, we show that sequence-specific purifications of DNA oligomers 60 bases in length or more can be achieved with high resolution, even when the PNAA alkane is attached to the center of the target strand. The insensitivity of the PNAA/DNA duplex binding to choice of HIC media appears to be due to a surface-induced aggregation phenomenon that does not occur in the case of untagged DNA. We also report on the use of batch HIC as an adequate predictor of elution profiles in linear gradient HIC, and its potential to considerably reduce purification times by applying step gradients.

Calorimetric investigation of the adsorption of nitrogen bases and nucleosides on a hydrophobic interaction sorbent

Heats of adsorption for nitrogen bases and nucleosides on Sepharose CL-6B, a hydrophobic interaction adsorbent, were collected through flow microcalorimetry in order to ascertain the thermodynamic driving force for adsorption in each case. It was determined that enthalpy changes associated with base stacking self-interactions can contribute significantly to the observed heats of adsorption. Accordingly, the observed heats were the net effect of the adsorbate/adsorbent interactions and the adsorbate stacking self-interactions. Since base stacking proceeds beyond the dimer stage, multi-layer adsorption of these compounds is possible, even at low solution concentrations.

Hydrophobic interaction chromatography of homo-oligonucleotides on derivatized sepharose CL-6B. Using and relating two different models for describing the effect of salt and temperature on retention

The effect of salt and temperature on the interaction of homo-oligonucleotides with a derivatized Sepharose CL-6B hydrophobic support has been explained by the application of two different models: the solvophobic theory and the preferential interaction analysis. It has been shown that the two approaches give adequate descriptions of the experimental results. The models were used in order to estimate, respectively the parameter C, which is proportional to the reduction in hydrophobic exposed surface area upon adsorption, and the number of water and salt ions released upon adsorption. It was concluded that the magnitude of these parameters can be strongly influenced by the temperature, the hydrophobicity of the bases of the nucleotides, the molecular mass of the oligonucleotides and the presence of secondary structures. Parameter C was quantitatively related with the number of water molecules and salt ions released upon adsorption. These parameters were found to correlate linearly in cases where structural changes with temperature are not significant.