New monolith technology for automated anion-exchange purification of nucleic acids.

Synthetic nucleic acid analysis often employs pellicular anion-exchange (AE) chromatography because it supports very high efficiency separations while offering means to control secondary structure, retention and resolution by readily modifiable chromatographic conditions. However, these pellicular anion-exchange (pAE) phases do not offer capacity sufficient for lab-scale oligonucleotide (ON) purification. In contrast, monolithic phases produce fast separations at capacities exceeding their pellicular counterparts, but do not exhibit capacities typical of fully porous, bead-based, anion-exchangers. In order to further increase monolith capacity and obtain the selectivity and mass transfer characteristics of pellicular phases, a surface-functionalized monolith was coated with pAE nanobeads (latexes) usually employed on the pellicular DNAPac phase. The nanobead-coated monolith exhibited chromatographic behaviors typical of polymer AE phases. Based on this observation the monolithic substrate surface porosity and latex diameters were co-optimized to produce a hybrid monolith harboring capacity similar to that of fully porous bead-based phases and peak shape approaching that of the pAE phases. We tested the hybrid monolith on a variety of previously developed pAE capabilities including control of ON selectivity, resolution of derivatized ONs, the ability to resolve RNA ONs harboring aberrant linkages at different positions in a single sequence and separation of phosphorothioate diastereoisomers. We compared the yield and purity of an 8 mg ON sample purified on both the new hybrid monolith and a benchmark AE column based on fully porous monodisperse beads. This comparison included an assessment of the relative selectivities of both columns. Finally, we demonstrated the ability to couple AE ON separations with ESI-MS using an automated desalting protocol. This protocol is also useful for preparing ONs for other assays, such as enzyme treatments, that may be sensitive to high salt levels.

Identification of RNA linkage isomers by anion exchange purification with electrospray ionization mass spectrometry of automatically desalted phosphodiesterase-II digests.

Among the possible contaminants unique to RNA are linkage isomers that are difficult to identify by standard oligonucleotide analysis techniques. In a prior study, we used nonporous and monolithic polymer anion exchangers for purification and demonstrated a method to identify the presence of the linkage isomers. We also suggested a confirming technique employing phosphodiesterase-II (PDase-II), an enzyme incapable of cleaving 2'-5' linkages. We now present a method identifying the location of the linkage in the RNA isomer by anion exchange purification and electrospray ionization mass spectrometry (ESI-MS) of the digestion products. Because the ion-pair reversed-phase liquid chromatography (IP-RPLC) desalting methods we previously employed do not effectively separate oligonucleotides less than 6 bases from salt, we employed a direct reversed-phase method to automatically desalt the digestion products and then assessed the desalted digests by ESI-MS. The length and base composition of the fragments identified indicate that PDase-II cleaves up to and skips over the aberrant linkage and then resumes cleavage 1 or 2 bases to the 3' side of the 2'-5' linkage.

Detection of aberrant 2'-5' linkages in RNA by anion exchange.

Formation of aberrant 2'-5' linkages can unintentionally occur in chemical synthesis of RNA. These linkages may arise by phosphoryl migration during deprotection, release, or subsequent steps during manufacture of therapeutic RNA. Their presence has been linked to a number of biochemical activities, so their potential for contribution to "off-target" effects is significant. Assaying for their presence, to ensure safe and effective therapeutic activity, is not straightforward. Since these linkages do not alter the RNA mass or the ionic or hydrophobic character of the product, confirmation of their presence or absence is not readily addressable by conventional chromatographic, electrophoretic, or mass spectrometric techniques. Since 2'-5' linkages are known to alter RNA solution conformation, they may also alter stationary phase interactions. A method for identifying the presence of these aberrant linkages by pellicular anion-exchange HPLC is presented in this unit.

Control of oligonucleotide retention on a pH-stabilized strong anion exchange column.

Strong anion exchange columns are preferred for oligonucleotide analyses due to their ability to effectively control secondary structure and poly(G) interactions. Methacrylate-based anion exchange phases minimize hydrophobic interactions with oligonucleotides, but they also tend to hydrolyze under alkaline conditions. In this article, we report the use of an anion exchange column prepared from a new class of methacrylate monomers designed to improve hydrolytic stability. This column is used to show predictable adjustment of oligonucleotide retention by eluent pH and composition. Features of the new column include (i) large, predictable, pH-dependent retention shifts (varying with specific changes in 5' or 3' terminal bases with NaCl-based eluents); (ii) reduced retention when solvent is added to NaCl-based eluents; and (iii) suppression of much of the column's hydrophobic interactions when CH3CN is used with NaClO4-based eluents at a neutral pH (i.e., this eluent system separates oligonucleotides primarily in order of their length). These observations will aid the development of elution conditions for both size-dependent and base sequence-dependent (or base composition-dependent) separations.

Improvements to in-line desalting of oligosaccharides separated by high-pH anion exchange chromatography with pulsed amperometric detection.

High-pH anion exchange chromatography with pulsed amperometric detection (HPAEC/PAD) (1) is routinely used to separate neutral and charged oligosaccharides differing by branch, linkage, and positional isomerism. Oligosaccharides are eluted in 0.1 M NaOH with gradients of sodium acetate (up to 0.25 M). Analyses of HPAEC/PAD-purified oligosaccharides generally require neutralization and removal of eluent salts. To facilitate the process, we designed and produced a cation-exchange system to remove sodium ions (Na+) from the eluent after oligosaccharide detection [the Carbohydrate Membrane Desalter (CMD), with a volatile regenerant]. Exchange of >99.5% of eluent Na+ for hydronium ions (H3O+) within the CMD generates dilute acetic acid (removable by vacuum evaporation). The exchange process desalts up to 0.35 M Na+ at 1.0 ml/min. Oligosaccharides collected after on-line desalting, evaporated and resuspended in their original volume of deionized water contained < or = 350 muM residual Na+ when the eluting sodium concentration was 300 mM. This represents a desalting efficiency of >99.8%. Recovery of neutral and sialylated oligosaccharides under these conditions ranged from 75 to 100%. With the CMD system and postcollection evaporation, HPAEC/PAD can purify oligosaccharides ready for further characterization. As a proof test, oligosaccharides from a human monoclonal antibody were separated by HPAEC/PAD, desalted with the CMD system, dried, and analyzed by matrix-assisted laser desorption-ionization, time-of-flight mass spectrometry.

Active transport of benzoate in Pseudomonas putida.

Benzoate uptake in Pseudomonas putida is mediated by an active transport system capable of accumulating benzoate against a 150-fold concentration gradient when subsequent metabolism is blocked by mutation. Initial benzoate transport rates are inhibited by CCCP, sodium azide, arsenate and DCCD. Uptake is stimulated by including a respirable carbon source during preincubation of the bacteria. The initial uptake rate and the ATP pool levels are not correlated and no periplasmic components were found to bind benzoate. These observations indicate that benzoate uptake is energized by the membrane potential, rather than by ATP hydrolysis.

Gut reactions of radioactive nitrite after intratracheal administration in mice.

Intratracheal administration to mice of radioactive nitrite labeled with nitrogen-13 (13NO2-) (half-life, 9.96 minutes) in dosages that do not cause pharmacological perturbation reveals that oxidative and reductive reactions occur in different organs. Oxidation of 13NO2- to radioactive nitrate (13NO3-) predominates in the blood and liver. Reduction of 13NO2- occurs in those mice that harbor intestinal microflora; this reduction does not occur in germ-free mice. The intestinal reduction products include ammonium, glutamate, glutamine, and urea. With a detection limit of about 0.01 percent of the instilled nitrogen-13, no labeled nitrosamines were detected within 30 minutes. Reduced nitrogen-13 is transported out of the intensive into the circulatory system and appears in the urine along with 13NO3-. The biological half-period for 13NO2- destruction is about 7 minutes, and both oxidation and reduction products are formed.

Kinetic evaluation, using 13N, reveals two assimilatory nitrate transport systems in Klebsiella pneumoniae.

A kinetic evaluation of initial rates of nitrate transport at concentrations between 1 microM and 1 mM indicated the presence of two transport processes. Analysis of the contribution of each process to the total activity permitted the determination of kinetic constants (Km) of 4.9 microM and 4.2 mM for the high-and low-affinity systems, respectively. The ratio of the maximal velocity of the high-affinity system to that of an apparent low-affinity system was about 0.3. Both systems were inhibited by the presence of NH4+ in the transport assay. Growth in the presence of equimolar NO3- and NH4+ repressed the synthesis of both systems when compared with growth in NO3- alone.

Characterization of a benzoate permease mutant of Pseudomonas putida.

A spontaneous mutant of Pseudomonas putida (PRS 2017) has been isolated which is incapable of growth on benzoate, does not induce the enzymes of the catechol branch of the beta-ketoadipate pathway when grown in the presence of benzoate, cannot accumulate radioactively labeled benzoate, yet grows well with mandelate as sole source of carbon and energy. This strain apparently lacks a benzoate permease, which in the wild type shows a Km of about 0.1 mM for benzoate, is inducible, and is not under the control of the regulatory system which governs the induction of the enzymes of the catechol branch of the beta-ketoadapate pathway. The lesion in PRS2017 is apparently single site and maps near other genes governing benzoate dissimilation.