Buffer Constituents Research Articles

PH-dependent reaction triggering in PmHMGR crystals for time-resolved crystallography

Serial crystallography and time-resolved data collection can readily be employed to investigate the catalytic mechanism of Pseudomonas mevalonii 3-hydroxy-3-methylglutaryl (HMG)-coenzyme-A (CoA) reductase (PmHMGR) by changing the environmental conditions in the crystal and so manipulating the reaction rate. This enzyme uses a complex mechanism to convert mevalonate to HMG-CoA using the co-substrate CoA and cofactor NAD+. The multi-step reaction mechanism involves an exchange of bound NAD+ and large conformational changes by a 50-residue subdomain. The enzymatic reaction can be run in both forward and reverse directions in solution and is catalytically active in the crystal for multiple reaction steps. Initially, the enzyme was found to be inactive in the crystal starting with bound mevalonate, CoA, and NAD+. To observe the reaction from this direction, we examined the effects of crystallization buffer constituents and pH on enzyme turnover, discovering a strong inhibition in the crystallization buffer and a controllable increase in enzyme turnover as a function of pH. The inhibition is dependent on ionic concentration of the crystallization precipitant ammonium sulfate but independent of its ionic composition. Crystallographic studies show that the observed inhibition only affects the oxidation of mevalonate but not the subsequent reactions of the intermediate mevaldehyde. Calculations of the pKa values for the enzyme active site residues suggest that the effect of pH on turnover is due to the changing protonation state of His381. We have now exploited the changes in ionic inhibition in combination with the pH-dependent increase in turnover as a novel approach for triggering the PmHMGR reaction in crystals and capturing information about its intermediate states along the reaction pathway.

Ferrocenoyl-substituted quinolinone and coumarin as organometallic inhibitors of SARS-CoV-2 3CLpro main protease.

The 3-chymotrypsin-like protease 3CLpro from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a potential target for antiviral drug development. In this work, three organometallic ferrocene-modified quinolinones and coumarins were compared to their benzoic acid ester analogues with regard to inhibition of 3CLpro using an HPLC-based assay with a 15mer model peptide as the substrate. In contrast to FRET-based assays, this allows direct identification of interference of buffer constituents with the inhibitors, as demonstrated by the complete abolishment of ebselen inhibitory activity in the presence of dithiothreitol as a redox protectant. The presence of the organometallic ferrocene moiety significantly increased the stability of the title compounds towards hydrolysis. Among the studied compounds, 4-ferrocenyloxy-1-methyl-quinol-2-one was identified as the most stable and potent inhibitor candidate. IC50 values determined for ebselen and this sandwich complex compound are (0.40±0.07) and (2.32±0.21) μM, respectively.

Liquid crystals purity assay using nonaqueous capillary electrokinetic chromatography.

A method for purity control of newly synthesized lactic acid-based liquid crystals has been developed. The electrokinetic chromatography proved to be suitable for the separation of these electroneutral substances from their impurities. The separations were performed in an acidic acetonitrile-based background electrolyte (BGE) with a pseudostationary phase formed by a cationic surfactant. During the optimization step, appropriate concentrations of cetyltrimethylammonium bromide, acetic acid, and water were seeked. In the optimized method, separations were carried out in acetonitrile with 1-mol/L acetic acid, 80-mmol/L cetyltrimethylammonium bromide, and 6% (v/v) water. Interesting positive effects of a small water content in the BGE on electroosmotic flow and resolution of liquid crystal substances from their impurities were observed and discussed. Samples of five liquid crystal substances, both pure and containing impurities from synthesis, were analyzed. The identification of analytes was based on a comparison of relative migration times related to the migration time of mesityl oxide. For all five samples, impurities were separated from the liquid crystals and the method thus showed its viability. To the best of our knowledge, this method is used for the first time for the purity control of newly synthesized liquid crystals. This method can be used to confirm or complement the results obtained by commonly used high-performance liquid chromatography and supercritical fluid chromatography methods. Furthermore, the electrokinetic chromatography method requires very small amounts of sample, solvents, and buffer constituents. Overall, its operational costs are significantly lower.

Autonomous, Real-Time Monitoring Electrochemical Aptasensor for Circadian Tracking of Cortisol Hormone in Sub-microliter Volumes of Passively Eluted Human Sweat.

The proposed work involves the development of an autonomous, label-free electrochemical sensor for real-time monitoring of cortisol levels expressed naturally in sub-microliter sweat volumes, for prolonged sensing periods of ∼8 h. Highly specific single-stranded DNA (ssDNA) aptamer is used for affinity capture of cortisol hormone eluted in sweat dynamically. The cortisol present in sweat binds to the aptamer capture probe that changes conformation and modulates electrochemical properties at the electrode-buffer interface, which was studied using dynamic light scattering studies for the entire physiological sweat pH. Attenuated total reflectance-Fourier transform infrared spectroscopy and UV-vis spectroscopy were used to optimize the binding chemistry of the elements of the sensor stack. Nonfaradaic electrochemical impedance spectroscopy was used to calibrate the sensor for a dynamic range of 1-256 ng/mL. An R2 of 0.97 with an output signal range of 20-50% was obtained. Dynamic cortisol level variation tracking was studied using continuous dosing experiments to calibrate the sensor for temporal variation. The sensor did not show significant susceptibility to noise due to cross-reactive interferents and nonspecific buffer constituents. The performance of the developed aptasensor was compared with the previously established cortisol immunosensor in terms of surface charge behavior and nonfaradaic biosensing. The aptamer sensor shows a higher signal-to-noise ratio, better resolution, and has a larger output range for the same input range as the cortisol immunosensor. The feasibility of deploying the developed aptasensing scheme as continuous lifestyle and performance monitors was validated through human subject studies.

New Insights into the Chromatography Mechanisms of Ion-Exchange Charge Variant Analysis: Dispelling Myths and Providing Guidance for Robust Method Optimization.

Charge variant analysis is a widely used analytical tool in characterization of monoclonal antibodies (mAbs). It depicts the heterogeneity of charge variant forms, some of which may differ by only minor modifications of a single amino acid. The analysis ensures product consistency with no unwanted changes to the protein. With increasing numbers of new mAb drug products emerging in the market, the need for a robust charge variant analysis has intensified. The charge variant profiles often display partially resolved peaks on shoulders of larger peaks. This puts considerably more pressure on the robustness of the method to maintain the suboptimum selectivity. New products and techniques have emerged to address these requirements, in addition to the pre-existing older methods that may not have been optimized correctly in the past. This has led to some confusion as to the best approach and strategies in optimization of charge variant analysis. We show studies from several different approaches using on-line pH monitoring to check the performance characteristics of the methods. This has led to new insights on the interactions between the protein, column, and buffer constituents. We dispel some inaccurate assumptions about the different ion-exchange elution mechanisms and suggest ways to develop high-throughput methods that remain robust and of high resolution. Streamlined automatable method development tools are presented that will result in more efficient method optimization. The mechanisms behind poor chromatography design have provided an alternative explanation behind some methods failing when in the QC laboratories.

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) method development for screening of potential tamoxifen-drug/herb interaction via in vitro cytochrome P450 inhibition assay

Screening for potential drug-drug interaction (DDI) or herb-drug interaction (HDI) using in vitro cytochrome P450 inhibition (IVCI) assays requires robust analytical methods with high sensitivity and reproducibility. Utilization of liquid chromatography-mass spectrometry (LC-MS) for analyte quantification is often hampered by the presence of non-volatile IVCI sample buffer constituents that often results in ion suppression. In this study, to enable screening of drug interactions involving tamoxifen (TAM) metabolism using IVCI-LC-MS/MS, a liquid–liquid extraction (LLE) method was developed and optimized for sample clean-up. Utilization of chloroform as extraction solvent and adjustment of sample pH to 11 was found to result in satisfactory recovery (>70%) and low ion suppression (<19%). A LC-MS/MS method was subsequently developed and validated for simultaneous quantification of major TAM metabolites, such as N-desmethyltamoxifen (NDT), endoxifen (EDF) and 4-hydroxytamoxifen (HTF) to enable IVCI sample analysis. Satisfactory separation of E-/Z-isomers of endoxifen with peak resolution (Rs) of 1.9 was achieved. Accuracy and precision of the method was verified within the linear range of 0–50 ng/mL for NDT, 0–25 ng/mL for HTF and 0–25 ng/mL for EDF (E/Z isomers). Inhibitory potency (IC50, Ki and mode of inhibition) of known CYP inhibitors and Strobilanthes crispus extract was then evaluated using the validated method. In summary, the results demonstrated applicability of the developed LLE and validated LC-MS/MS method for in vitro screening of DDI and HDI involving TAM metabolism.

A simple purification procedure of buffalo lung cathepsin H, its properties and influence of buffer constituents on the enzyme activity

BackgroundCathepsin H (E.C.3.4.22.16) belongs to a family of lysosomal cysteine protease which regulates diverse normal biological processes mainly in intracellular proteolysis. MethodsPurification of cathepsin H from an unstudied system i.e. buffalo lung has been achieved by a simple process developed after incorporating appropriate alteration in the available methods for isolation of the enzyme from other sources. The use of DEAE-Cellulose and SP-Sephadex C-50 helped in better and simultaneous separation of cathepsin B and H up to homogeneity. ResultsThe SDS-PAGE result showed buffalo cathepsin H to be a single-chain molecule having MW, NH2- and COOH- terminal residues of 25.4 kDa, Lys and Val respectively. The enzyme was a glycoprotein with pI of 6.2; it hydrolyzed Leu-NA (Vmax/Km = 301.6) as the most efficient substrate followed by Arg-NA, Arg-Arg-NA and BANA. Buffalo enzyme showed maximum activity at 36 °C, pH 6.75 and at a buffer concentration of 2 × 10−3 M. ConclusionCatheptic activity was found to be quite stable at least for 20–30 min between pH 4.5–7.0, buffer concentration of 1 × 10−2 to 4 × 10−2 M and the temperature resistance up to 36 °C. The effects of various substances present in the buffers routinely used for the assay of catheptic activity revealed that the activity of buffalo lung cathepsin H depends not only qualitatively but also quantitatively on the constituents of assay buffer. General significanceThis study seems to provide valuable information regarding the biochemistry of cathepsin H in general as well as influence of buffer constituents on enzyme activity and physiological role in particular.

Development of Container Free Sample Exposure for Synchrotron X-ray Footprinting.

The method of X-ray footprinting and mass spectrometry (XFMS) on large protein assemblies and membrane protein samples requires high flux density to overcome the hydroxyl radical scavenging reactions produced by the buffer constituents and the total protein content. Previously, we successfully developed microsecond XFMS using microfluidic capillary flow and a microfocused broadband X-ray source at the Advanced Light Source synchrotron beamlines, but the excessive radiation damage incurred when using capillaries prevented the full usage of a high-flux density beam. Here we present another significant advance for the XFMS method: the instrumentation of a liquid injection jet to deliver container free samples to the X-ray beam. Our preliminary experiments with a liquid jet at a bending magnet X-ray beamline demonstrate the feasibility of the approach and show a significant improvement in the effective dose for both the Alexa fluorescence assay and protein samples compared to conventional capillary flow methods. The combination of precisely controlled high dose delivery, shorter exposure times, and elimination of radiation damage due to capillary effects significantly increases the signal quality of the hydroxyl radical modification products and the dose-response data. This new approach is the first application of container free sample handling for XFMS and opens up the method for even further advances, such as high-quality microsecond time-resolved XFMS studies.

Generalized model of the linear theory of electromigration and its application to electrokinetic chromatography: Capillary zone electrophoretic systems with complex-forming equilibria

We discuss several possible phenomena in electrophoretic systems with complexing agents present in the background electrolyte. In our previous work, we extended the linear theory of electromigration with the first-order nonlinear term, which originally applied to acid-base equilibria only, by generalizing it to any fast chemical equilibria. This extension provides us with a fresh insight into the well-established technique of elecktrokinetic chromatography (EKC). We combine mathematical analysis of the generalized model with its solution by means of the new version of our software PeakMaster 6, and experimental data. We re-examine the fundamental equations by Wren and Rowe and Tiselius in the frame of the generalized linear theory of electromigration. Besides, we show that selector concentration can increase inside the interacting-analyte zone due to its complexation with the analyte, which contradicts the generally accepted idea of a consumption of a portion of the selector inside the zone. Next, we focus our discussion on interacting buffers (i.e., buffer constituents that form a complex with the selector). We demonstrate how such side-interaction of the selector with another buffer constituent can influence measuring analyte-selector interactions. Finally, we describe occurrence and mobilities of system peaks in these EKC systems.We investigate systems with fully charged analytes and neutral cyclodextrins as selectors. Although the theory is not limited in terms of the charge and/or the degree of (de)protonation of any constituent, this setup allows us to find analytical solutions to generalized model under approximate, yet realistic, conditions and to demonstrate all important phenomena that may occur in EKC systems. An occurrence of system peaks in a system with fully charged selector is also investigated.

Retention-pH profiles of acids and bases in hydrophilic interaction liquid chromatography

The high proportion of acetonitrile used in many HILIC mobile phases significantly changes the acid-base properties of pH buffers and analytes foreseen from available data in water. In this paper, the recommended stability pH range for chromatographic columns is examined with various acetonitrile/water mixtures, resulting in a significant broadening in the operational pH window with the content of organic solvent. Additionally, the challenge of buffer selection in HILIC is also addressed. Commonly used ammonium acetate shrinks its pH buffering range in acetonitrile-rich mobile phases due to variations in the dissociation constants of the buffer constituents (acetic acid and ammonium). Thus, other organic acids such as formic acid, TFA, and succinimide have been studied as buffers in order to fully cover the pH range of use of the column. Also the retention-pH profiles of several acids and bases have been studied in 80% and 90% acetonitrile using the proposed buffers and their behavior compared to that obtained with buffers prepared from oxalic acid, pyrrolidine, and triethylamine. The latter two show additional interactions in 80% acetonitrile that distort the expected retention-pH profiles of acid analytes, but not the ones of bases. In 90% acetonitrile the profiles are affected by significant additional solute-buffer interactions that might be caused by ion pairing, homo- and heteroassociation in this low ion solvating medium.

“Pseudostationary Ion-Exchanger” Sweeping as an Online Enrichment Technique in the Determination of Nucleosides in Urine via Micellar Electrokinetic Chromatography

The presented study aims to develop a new online enrichment strategy [“pseudostationary ion-exchanger” (PSIE) sweeping] for the analysis of highly hydrophilic nucleosides in urine samples with a special focus on the fundamental aspects regarding the enrichment process itself. In the first method, we employ the ionic liquid (IL)-type surfactant 1-tetradecyl-3-methylimidazolium bromide (C14MImBr) as micelle forming agent under alkaline pH conditions. It is shown that maximum enrichment efficiency can be obtained by keeping the retention factors very high within the sample zone and very low within the background electrolyte (BGE) while maintaining a sufficient resolution for the studied analytes. With this method, detection limits as low as 0.1 µg mL−1 are obtained for all analytes studied. For the nucleosides, adenosine and cytidine, a second method is developed using sodium dodecyl sulfate (SDS) as micelle forming agent under acidic pH conditions. In addition, we investigate the effect of replacing ionic buffering constituents with a zwitterionic/isoelectric buffering compound (aspartic acid) with regard to separation and enrichment efficiency. With the second method, the achieved limits of detection are as low as 0.1 µg mL−1 for Ado and 0.2 µg mL–1 for Cyd. The applicability of the two complementary methods to the analysis of the nucleosides under investigation is shown for blank and spiked human urine samples after their extraction using the commercially available phenylboronate affinity gel.

Optimization of intestinal microsomal preparation in the rat: A systematic approach to assess the influence of various methodologies on metabolic activity and scaling factors.

The metabolic capacity of the intestine and its importance as the initial barrier to systemic exposure can lead to underestimation of first‐pass, and thus overestimation of oral bioavailability. However, the in vitro tools informing estimates of in vivo intestinal metabolism are limited by the complexity of the in vitro matrix preparation and uncertainty with the scaling factors for in vitro to in vivo extrapolation. A number of methods currently exist in the literature for the preparation of intestinal microsomes; however, the impact of key steps in the preparation procedure has not been critically assessed. In the current study, changes in enterocyte isolation, the impact of buffer constituents heparin and glycerol, as well as sonication as a direct method of homogenization were assessed systematically. Furthermore, fresh vs. frozen tissue samples and the impact of microsome freeze thawing was assessed. The rat intestinal microsomes were characterized for CYP content as well as metabolic activity using testosterone and 4‐nitropheonol as probes for CYP and UGT activity, respectively. Comparisons in metabolic activity and scaled unbound intestinal intrinsic clearance (CL intu,gut) were made to commercially available microsomes using 25 drugs with a diverse range of metabolic pathways and intestinal metabolic stabilities. An optimal, robust and reproducible microsomal preparation method for investigation of intestinal metabolism is proposed. The importance of characterization of the in vitro matrix and the potential impact of intestinal scaling factors on the in vitro–in vivo extrapolation of F G needs to be investigated further. © 2017 The Authors Biopharmaceutics & Drug Disposition Published by John Wiley & Sons Ltd.

Resuscitation fluid composition affects hepatic inflammation in a murine model of early sepsis

BackgroundFluid resuscitation is a crucial therapy for sepsis, and the use of balanced fluids and/or isotonic albumin may improve patient survival. We have previously demonstrated that resuscitation with normal saline results in increased hepatic leukocyte recruitment in a murine model of sepsis. Given that clinical formulations of albumin are in saline, our objectives were to develop a novel balanced electrolyte solution specifically for sepsis and to determine if supplementing this solution with albumin would improve the inflammatory response in sepsis.MethodsWe developed two novel buffered electrolyte solutions that contain different concentrations of acetate and gluconate, named Seplyte L and Seplyte H, and administered these solutions with or without 5% albumin. Normal saline with or without albumin and Ringer’s lactate served as controls. Sepsis was induced by cecal ligation and puncture (CLP), and the liver microvasculature was imaged in vivo at 6 h after CLP to quantify leukocyte recruitment. Hepatic cytokine expression and plasma cell-free DNA (cfDNA) concentrations were also measured.ResultsSeptic mice receiving either Seplyte fluid showed significant reductions in hepatic post-sinusoidal leukocyte rolling and adhesion compared to normal saline. Hepatic cytokine concentrations varied in response to different concentrations of acetate and gluconate in the novel resuscitation fluids but were unaffected by albumin. All Seplyte fluids significantly increased hepatic TNF-α levels at 6 h compared to control fluids. However, Seplyte H exhibited a similar cytokine profile to the control fluids for all other cytokines, whereas mice given Seplyte L had significantly elevated IL-6, IL-10, KC (CXCL1), and MCP-1 (CCL2). Plasma cfDNA was generally increased during sepsis, but resuscitation fluid composition did not significantly affect cfDNA concentrations.ConclusionsElectrolyte concentrations and buffer constituents of resuscitation fluids can modulate hepatic cytokine production and leukocyte recruitment in septic mice, while the effects of albumin are modest during early sepsis. Therefore, crystalloid fluid choice should be an important consideration for resuscitation in sepsis, and the effects of fluid composition on inflammation in other organ systems should be studied to better understand the physiological impact of this vital sepsis therapy.

Differential influence of 7 cations on 16 non-competitive NMDA receptor blockers.

The specific binding of the NMDA receptor (NR) channel ligand [(3)H]MK-801 to rat brain membranes is sensitive to positively charged buffer ingredients as to tris(hydroxymethyl)aminomethane (Tris), to Na(+), or to protons. Here we demonstrate that 16 non-competitive NR antagonists, including 5 long-chain diamines, classical NR channel blockers and several less known compounds, differ widely in their sensitivities to cationic buffer constituents. Although chemically distinguished either as extended di-cationic or as compact mono-cationic, their sensitivities to cationic buffer ingredients did not suggest this grouping. While the di-cationic compounds are known for their sensitivity to spermine (polyamine inverse agonists), also some of the mono-cationic blockers exhibited this feature. They might share as common target a recently described negatively charged extracellular GluN1/GluN2B interface.

Development, validation and quantitative assessment of an enzymatic assay suitable for small molecule screening and profiling: A case-study

The successful discovery and subsequent development of small molecule inhibitors of drug targets relies on the establishment of robust, cost-effective, quantitative, and physiologically relevant in vitro assays that can support prolonged screening and optimization campaigns. The current study illustrates the process of developing and validating an enzymatic assay for the discovery of small molecule inhibitors using alkaline phosphatase from bovine intestine as model target. The assay development workflow includes an initial phase of optimization of assay materials, reagents, and conditions, continues with a process of miniaturization and automation, and concludes with validation by quantitative measurement of assay performance and signal variability. The assay is further evaluated for dose–response and mechanism-of-action studies required to support structure–activity-relationship studies. Emphasis is placed on the most critical aspects of assay optimization and other relevant considerations, including the technology, assay materials, buffer constituents, reaction conditions, liquid handling equipment, analytical instrumentation, and quantitative assessments. Examples of bottlenecks encountered during assay development and strategies to address them are provided.

Effect of Buffer Constituents on Retention and Separation in Achiral and Chiral HPLC Systems with β-Cyclodextrin-Based Stationary Phase

In HPLC, cyclodextrin-based stationary phases allow separation of both achiral and chiral analytes. Complexation of analytes into the cyclodextrin cavity is a very important part of the interaction mechanism. However, possible complexation of buffer constituents must be also considered. This fact should not be overlooked in method development procedures. In this study, β-cyclodextrin-based stationary phase (CYCLOBOND I 2000) was used, and two different buffers, namely aqueous solutions composed of lithium hydroxide/benzoic acid 10.0/24.5 mM, pH 4.00 and lithium hydroxide/acetic acid 9.9/60.0 mM, pH 4.01 of the same ionic strength were compared. Methanol was added as organic modifier in a methanol/buffer volume ratio 40/60. The linear free energy relationship method was used for evaluation of interactions contributing to chromatographic performance of the separation system. Strong complexation of benzoic acid with cyclodextrin was obvious from the results. This effect was clearly reflected in reduced retention and restricted (enantio) separation ability of the separation system containing benzoic acid in the buffer. On the other hand, complexing buffer constituents of mobile phases can offer a worthy alternative, to less “green”organic solvents, for reduction of the analysis time.

Metabolism of diosbulbin B in vitro and in vivo in rats: formation of reactive metabolites and human enzymes involved.

Diosbulbin B (DB), a major constituent of the furano-norditerpenes in Dioscorea bulbifera Linn, exhibits potential antineoplasmic activity and hepatotoxicity. The metabolism and reactive metabolites of DB in vitro (with human and animal liver microsomes) and in vivo in rats were investigated. The human enzymes involved in DB metabolism were identified. DB was first catalyzed into reactive metabolites of 2-butene-1,4-dial derivatives dependent on NADPH and then trapped by Tris base or oxidized to hemiacetal lactones (M12 and M13) in microsomal incubations. Tris base was used as buffer constituent and as a trapping agent for aldehyde. Methoxylamine and glutathione (GSH) were also used as trapping agents. DB metabolism in vivo in rats after oral administration was consistent with that in vitro. The structures of M12 and M13, as well as mono-GSH conjugates of DB (M31), were confirmed by nuclear magnetic resonance spectroscopy of the chemically synthesized products. The bioactivation enzymes of DB were identified as CYP3A4/5, 2C9, and 2C19. CYP3A4 was found to be the primary enzyme using human recombinant cytochrome P450 enzymes, specific inhibitory studies, and a relative activity factor approach for pooled human liver microsomes. Michaelis-Menten constants K(m) and V(max) were determined by the formation of M31. The reactive metabolites may be related to the hepatotoxicity of DB. The gender difference in CYP3A expression in mice and rats contributed to the gender-related liver injury and pharmacokinetics in mice and rats, respectively.

Investigation of the retention behavior of structurally diverse drugs on alpha1 acid glycoprotein column: Insight on the molecular factors involved and correlation with protein binding data

Retention of 49 structurally diverse drugs on alpha1 acid glycoprotein column was investigated under different chromatographic conditions. Acetonitrile and 2-propanol were used as organic modifiers at different percentages and the pH was adjusted at 7.0 using PBS. Analysis of extrapolated and isocratic retention in terms of lipophilicity and electrostatic interactions revealed significant effect of the nature and percentage of organic modifier, which was attributed to the different shielding degree of the charged sites on the stationary phase by the buffer constituents. AGP retention factors were compared to HSA retention factors analyzed previously. Application of LSER analysis, extended to incorporate fractions ionized, demonstrated hydrogen bond acidity, dipolarity/polarizability and excess molar refraction as the most significant parameters for all AGP chromatographic indices, elucidating the differentiation of AGP retention from octanol–water partitioning and HSA retention. An attempt to correlate AGP chromatographic indices to AGP association constants, available in literature, supported the importance of stationary shielding in retention mechanism. Thus, isocratic retention factors logk10(ACN)AGP show a moderate but still better performance than lipophilicity in the case of A variant and may be a useful tool for the estimation of relevant association constants. For F1/S binding simulation lower stationary phase shielding is needed to obtain a significant two term regression equation, where logk20(ACN)AGP exerts a secondary contribution next to the most important bulk effect expressed by molecular weight.

An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures.

Aptamers can be highly specific for their targets, which implies precise molecular recognition between aptamer and target. However, as small polymers, their structures are more subject to environmental conditions than the more constrained longer RNAs such as those that constitute the ribosome. To understand the balance between structural and environmental factors in establishing ligand specificity of aptamers, we examined the RNA aptamer (NEO1A) previously reported as specific for neomycin-B. We show that NEO1A can recognize other aminoglycosides with similar affinities as for neomycin-B and its aminoglycoside specificity is strongly influenced by ionic strength and buffer composition. NMR and 2-aminopurine (2AP) fluorescence studies of the aptamer identified a flexible pentaloop and a stable binding pocket. Consistent with a well-structured binding pocket, docking analysis results correlated with experimental measures of the binding energy for most ligands. Steady state fluorescence studies of 2AP-substituted aptamers confirmed that A16 moves to a more solvent accessible position upon ligand binding while A14 moves to a less solvent accessible position, which is most likely a base stack. Analysis of binding affinities of NEO1A sequence variants showed that the base in position 16 interacts differently with each ligand and the interaction is a function of the buffer constituents. Our results show that the pentaloop provides NEO1A with the ability to adapt to external influences on its structure, with the critical base at position 16 adjusting to incorporate each ligand into a stable pocket by hydrophobic interactions and/or hydrogen bonds depending on the ligand and the ionic environment.

Modification of gel architecture and TBE/TAE buffer composition to minimize heating during agarose gel electrophoresis

Agarose gel electrophoresis of DNA and RNA is routinely performed using buffers containing either Tris, acetate, and EDTA (TAE) or Tris, borate, and EDTA (TBE). Gels are run at a low, constant voltage (∼10V/cm) to minimize current and asymmetric heating effects, which can induce band artifacts and poor resolution. In this study, alterations of gel structure and conductive media composition were analyzed to identify factors causing higher electrical currents during horizontal slab gel electrophoresis. Current was reduced when thinner gels and smaller chamber buffer volumes were used, but was not influenced by agarose concentration or the presence of ethidium bromide. Current was strongly dependent on the amount and type of EDTA used and on the concentrations of the major acid–base components of each buffer. Interestingly, resolution and the mobilities of circular versus linear plasmid DNAs were also affected by the chemical form and amount of EDTA. With appropriate modifications to gel structure and buffer constituents, electrophoresis could be performed at high voltages (20–25V/cm), reducing run times by up to 3-fold. The most striking improvements were observed with small DNAs and RNAs (10–100bp): high voltages and short run times produced sharper bands and higher resolution.