Alexander S. Stasheuski

Capillary Electrophoresis for Quantitative Studies of Biomolecular Interactions

■ CONTENTS Kinetic Capillary Electrophoresis 157 Applications 159 Aptamers 159 KCE for Quantitative Characterization of Aptamer-Target Binding 159 KCE-Based Aptamer Selection 160 Small Molecules 161 Cyclodextrins 162 Proteins 162 Others 164 Instrumentation and Methodology 164 Sample Preparation 164 Capillary Coatings 165 KCE-MS 165 Computational and Mathematical Approaches 166 Validation 167 Concluding Remarks 169 Author Information 169 Corresponding Author 169 Notes 169 Biographies 169 Acknowledgments 170 References 170

Photosensitized Singlet Oxygen Luminescence from the Protein Matrix of Zn-Substituted Myoglobin

A nanosecond laser near-infrared spectrometer was used to study singlet oxygen ((1)O2) emission in a protein matrix. Myoglobin in which the intact heme is substituted by Zn-protoporphyrin IX (ZnPP) was employed. Every collision of ground state molecular oxygen with ZnPP in the excited triplet state results in (1)O2 generation within the protein matrix. The quantum yield of (1)O2 generation was found to be equal to 0.9 ± 0.1. On the average, six from every 10 (1)O2 molecules succeed in escaping from the protein matrix into the solvent. A kinetic model for (1)O2 generation within the protein matrix and for a subsequent (1)O2 deactivation was introduced and discussed. Rate constants for radiative and nonradiative (1)O2 deactivation within the protein were determined. The first-order radiative rate constant for (1)O2 deactivation within the protein was found to be 8.1 ± 1.3 times larger than the one in aqueous solutions, indicating the strong influence of the protein matrix on the radiative (1)O2 deactivation. Collisions of singlet oxygen with each protein amino acid and ZnPP were assumed to contribute independently to the observed radiative as well as nonradiative rate constants.

Photophysical characterization of oligopyrene modules for DNA-based nanosystems

The photophysics of free pyrenedicarboxamide (Py-DCA) in solution as well as of single-stranded and double-stranded oligonucleotides (ss and ds ONs) containing 1-7 pyrene building blocks per strand were studied by steady-state and time-resolved fluorescence spectroscopy. It was found that the fluorescence quantum yield Phi(F) of free Py-DCA chromophore in solution is rather high (Phi(F) = 0.44). However, after incorporation of the chromophore into a ss ON the monomeric chromophore fluorescence is quenched more than 40-fold due to electron-transfer reactions with ON bases. An increase of the number n of neighboring pyrenes in an ON results in Phi(F) growth up to 0.25 at n = 6. Starting from n = 2, all fluorescence belongs mainly to excimer formed by pyrene chromophores. Sections composed of multiple pyrenes may be considered as robust functional entities that may serve as independent modules in DNA-based, functional nano-architectures.

Photophysical properties and singlet oxygen generation efficiencies of water-soluble fullerene nanoparticles.

As various fullerene derivatives have been developed, it is necessary to explore their photophysical properties for potential use in photoelectronics and medicine. Here, we address the photophysical properties of newly synthesized water‐soluble fullerene‐based nanoparticles and polyhydroxylated fullerene as a representative water‐soluble fullerene derivative. They show broad emission band arising from a wide‐range of excitation energies. It is attributed to the optical transitions from disorder‐induced states, which decay in the nanosecond time range. We determine the kinetic properties of the singlet oxygen (1O2) luminescence generated by the fullerene nanoparticles and polyhydroxylated fullerene to consider the potential as photodynamic agents. Triplet state decay of the nanoparticles was longer than 1O2 lifetime in water. Singlet oxygen quantum yield of a series of the fullerene nanoparticles is comparably higher ranging from 0.15 to 0.2 than that of polyhydroxylated fullerene, which is about 0.06.

Does photodissociation of molecular oxygen from myoglobin and hemoglobin yield singlet oxygen

Time-resolved luminescence measurements in the near-infrared region indicate that photodissociation of molecular oxygen from myoglobin and hemoglobin does not produce detectable quantities of singlet oxygen. A simple and highly sensitive method of luminescence quantification is developed and used to determine the upper limit for the quantum yield of singlet oxygen production. The proposed method was preliminarily evaluated using model data sets and confirmed with experimental data for aqueous solutions of 5,10,15,20-tetrakis(4-N-methylpyridyl) porphyrin. A general procedure for error estimation is suggested. The method is shown to provide a determination of the integral luminescence intensity in a wide range of values even for kinetics with extremely low signal-to-noise ratio. The present experimental data do not deny the possibility of singlet oxygen generation during the photodissociation of molecular oxygen from myoglobin and hemoglobin. However, the photodissociation is not efficient to yield singlet oxygen escaped from the proteins into the surrounding medium. The upper limits for the quantum yields of singlet oxygen production in the surrounding medium after the photodissociation for oxyhemoglobin and oxymyoglobin do not exceed 3.4×10(-3) and 2.3×10(-3), respectively. On the average, no more than one molecule of singlet oxygen from every hundred photodissociated oxygen molecules can succeed in escaping from the protein matrix.

Achieving Single-Nucleotide Specificity in Direct Quantitative Analysis of Multiple MicroRNAs (DQAMmiR)

Direct quantitative analysis of multiple miRNAs (DQAMmiR) utilizes CE with fluorescence detection for fast, accurate, and sensitive quantitation of multiple miRNAs. Here we report on achieving single-nucleotide specificity and, thus, overcoming a principle obstacle on the way of DQAMmiR becoming a practical miRNA analysis tool. In general, sequence specificity is reached by raising the temperature to the level at which the probe-miRNA hybrids with mismatches melt while the matches remain intact. This elevated temperature is used as the hybridization temperature. Practical implementation of this apparently trivial approach in DQAMmiR has two major challenges. First, melting temperatures of all mismatched hybrids should be similar to each other and should not reach the melting temperature of any of the matched hybrids. Second, the elevated hybridization temperature should not deteriorate CE separation of the hybrids from the excess probes and the hybrids from each other. The second problem is further complicated by the reliance of separation in DQAMmiR on single-strand DNA binding protein (SSB) whose native structure and binding properties may be drastically affected by the elevated temperature. These problems were solved by two approaches. First, locked nucleic acid (LNA) bases were incorporated into the probes to normalize the melting temperatures of all target miRNA hybrids allowing for a single hybridization temperature; binding of SSB was not affected by LNA bases. Second, a dual-temperature CE was developed in which separation started with a high capillary temperature required for proper hybridization and continued at a low capillary temperature required for quality electrophoretic separation of the hybrids from excess probes and the hybrids from each other. The developed approach was sufficiently robust to allow its integration with sample preconcentration by isotachophoresis to achieve a limit of detection below 10 pM.

Getting the best sensitivity from on-capillary fluorescence detection in capillary electrophoresis - A tutorial.

Capillary electrophoresis with Laser-Induced Fluorescence (CE-LIF) detection is being applied to new analytical problems which challenge both the power of CE separation and the sensitivity of LIF detection. On-capillary LIF detection is much more practical than post-capillary detection in a sheath-flow cell. Therefore, commercial CE instruments utilize solely on-capillary CE-LIF detection with a Limit of Detection (LOD) in the nM range, while there are multiple applications of CE-LIF that require pM or lower LODs. This tutorial analyzes all aspects of on-capillary LIF detection in CE in an attempt to identify means for improving LOD of CE-LIF with on-capillary detection. We consider principles of signal enhancement and noise reduction, as well as relevant areas of fluorophore photochemistry and fluorescent microscopy.

Dependence of the spontaneous emission of singlet oxygen on the refractive index and molecular polarizability of the surrounding dielectric media

The rate constants (kr) for singlet oxygen O2 (a1Δg) luminescence in several selected solvents and in binary solvent mixture (acetone-toluene) were measured. All data have been normalized such that krrel = 1.0 in toluene. It has been demonstrated that the changes in these rate constants were caused both by optical properties of a medium (the local field factor and density of photon states) and by an inherent property of the emitter of 1O2 (the square of transition moment). In its turn, the value of the transition moment is directly proportional to molecular polarizability of the medium molecules.

Accurate MicroRNA Analysis in Crude Cell Lysate by Capillary Electrophoresis-Based Hybridization Assay in Comparison with Quantitative Reverse Transcription-Polymerase Chain Reaction

Accurate quantitation of microRNA (miRNA) in tissue samples is required for validation and clinical use of miRNA-based disease biomarkers. Since sample processing, such as RNA extraction, introduces undesirable biases, it is advantageous to measure miRNA in a crude cell lysate. Here, we report on accurate miRNA quantitation in crude cell lysate by a CE-based hybridization assay termed direct quantitative analysis of multiple miRNAs (DQAMmiR). Accuracy and precision of miRNA quantitation were determined for miRNA samples in a crude cell lysate, RNA extract from the lysate, and a pure buffer. The results showed that the measurements were matrix-independent with inaccuracies of below 13% from true values and relative standard deviations of below 11% from the mean values in a miRNA concentration range of 2 orders of magnitude. We compared DQAMmiR-derived results with those obtained by a benchmark miRNA-quantitation method-quantitative reverse transcription-polymerase chain reaction (qRT-PCR). qRT-PCR-based measurements revealed multifold inaccuracies and relative standard deviations of up to 70% in crude cell lysate. Robustness of DQAMmiR to changes in sample matrix makes it a perfect candidate for validation and clinical use of miRNA-based disease biomarkers.

Quantum yield and rate constant of the singlet 1 Δ g oxygen luminescence in an aqueous medium in the presence of nanoscale inhomogeneities

The quantum yields and lifetimes of photosensitized luminescence of the 1Δg state of singlet oxygen in an aquatic media with a controlled concentration of dielectric anisotropy centers (polyethylene glycol) have been measured using the methods of laser fluorometry. It is established that the quantum yield and the rate constant (kr) of the a1Δg → X3Σg- luminescence of 1O2 increase as the polymer concentration increases. The effect is analyzed within a general approach involving a relationship between kr and dielectric properties of the medium and is explained by the increased density of photon states and the local field factor in the space around O2(а1Δg).