Protein labeling with red squarylium dyes for analysis by capillary electrophoresis with laser-induced fluorescence detection

Two new red luminescent asymmetric squarylium dyes (designated "Red-1c and Red-3") have been shown to exhibit absorbance shifts to longer wavelengths upon the addition of protein, along with a concomitant increase in fluorescence emission. Specifically, the absorbance maxima for Red-1c and Red-3 dyes are 607 and 622 nm, respectively, in the absence of HSA, and 642 and 640 nm in the presence of HSA, making the excitation of their protein complexes feasible with inexpensive and robust diode lasers. Fluorescence emission maxima, in the presence of HSA, are 656 and 644 nm for Red-1c and Red-3, respectively. Because of the inherently low fluorescence of the dyes in their free state, Red-1c and Red-3 were used as on-column labels (that is, with the dye incorporated into the separation buffer), thus eliminating the need for sample derivatization prior to injection and separation. A comparison of precolumn and on-column labeling of proteins with these squarylium dyes revealed higher efficiencies and greater sensitivities for on-column labeling, which, when conducted with a basic, high-salt content buffer, permitted baseline resolution of a mixture of five model proteins. LOD for model proteins, such as transferrin, alpha-lactalbumin, BSA, and beta-lactoglobulin A and B, labeled with these dyes and analyzed by CE with LIF detection (CE-LIF) were found to be dependent upon dye concentration and solution pH, and are as low as 5 nM for BSA. Satisfactory linear relationships between peak height (or peak area) and protein concentration were obtained by CE-LIF for this on-column labeling method with Red-3 and Red-1c.     

Dimethylditetradecylammonium bromide (2C14DAB) as a self-assembled surfactant coating for detection of protein–dye complexes by CE-LIF

A self-assembled column coating for capillary electrophoresis in conjunction with laser-induced fluorescence detection (CE-LIF) has been evaluated for the separation and quantitation of protein–dye complexes. This semi-permanent coating, composed of dimethylditetradecyl-ammonium bromide (2C₁₄DAB), is inexpensive and easily assembled onto the column and it allows for better peak resolution and greater control over electroosmotic flow. The versatility of long-chained surfactant coatings was determined particularly with respect to their use with fluorescent probes, different pH buffers, and different proteins. Studies were performed to determine the stability of the coating under various pH and buffer conditions. Red-1c, a red luminescent squarylium dye, was used for on-column protein labeling concurrently with the surfactant coating and LIF detection. Protein–Red-1c complexes were excited with a 650-nm diode laser and their emission detected by a photomultiplier tube with a 664-nm filter. A comparison of pre-column labeling and on-column labeling of a two-model protein system (human serum albumin and β-lactoglobulin A) revealed higher efficiencies and greater sensitivities for both proteins using on-column labeling and coated columns. A linear relationship between peak height and protein concentration was obtained by CE-LIF for this on-column labeling method with 2C₁₄DAB-coated columns and the Red-1c probe.     

Determination of protein-dye association by near infrared fluorescence-detected circular dichroism

Near-infrared (NIR) squarylium dye spectral properties were evaluated by absorption, fluorescence, circular dichroism (CD), and fluorescence-detected circular dichroism (FDCD). Substituents of the two NN dyes differed at R₁ and R₂, located symmetrically on the chromophore. The side chains of NN525 are R₁=hexanoic acid, R₂=butyl sulfonate and R₁=R₂=ethyl for NN127. FDCD signals were first confirmed by denaturing BSA with 2–8 M urea showing a diminution of dye FDCD peaks, but no change occurred in spectral properties of the dyes in urea. This indicated that the observed cotton effects occurred by noncovalent interactions with the secondary structure of the protein. The average BSA–dye association constants found by fluorescence, absorbance, and FDCD were 1.27×10⁶ (n=1) and 3.3×10⁶ M⁻¹ (n=1) for NN127 and NN525 respectively. These values were in good agreement when calculated by the three spectroscopic methods validating the use of NIRFDCD for optical parameter calculations. These results are useful to describe NIR squarylium dye labeling of BSA.     

Analysis of Bacillus globigii spores by CE

It is imperative in today's world that harmful airborne or solution-based microbes can be detected quickly and efficiently. Bacillus globigii (Bg) spores are used as a simulant for Bacillus anthracis (Ba) due to their similar shape, size, and cellular makeup. The utility of CE to separate and detect low levels of Bg spore concentrations will be evaluated. To differentiate spores from background particulates, several dyes, including fluorescamine, C-10, NN-127, Red-1c, and indocyanine green (ICG), were utilized as noncovalent labels for proteins on the Bg spore surface, as well as for HSA and homoserine standards. On-column labeling, with dye present in the running buffer, was utilized to obtain greater sensitivity and better separation. CE with LIF detection enables interactions between the dye and spore surface proteins to be observed, with enhanced fluorescence occurring upon binding of the dye to surface protein. Resulting electropherograms showed unique fingerprints for each dye with Bg spores. Migration times were under 10 min for all dye-spore complexes, with net mobilities ranging from 3.5x10(-4) to 6.9x10(-4) cm(2) V(-1) s(-1), and calibration curves yielded correlation coefficients of 0.98 or better for four of the dyes studied.     

Nonequilibrium capillary electrophoresis of equilibrium mixtures--a single experiment reveals equilibrium and kinetic parameters of protein-DNA interactions

We introduce a novel electrophoretic method, nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM), and demonstrate its use for studying protein-DNA interactions. The equilibrium mixture of protein and DNA contains three components: free protein, free DNA, and the protein-DNA complex. A short plug of such a mixture is injected into the capillary, and the three components are separated under nonequilibrium conditions. The resulting electropherograms are composed of characteristic peaks and exponential curves. An easy nonnumerical analysis of a single electropherogram reveals two parameters: the equilibrium binding constant and the monomolecular rate constant of complex decay. The bimolecular rate constant of complex formation can then be calculated as the product of the two experimentally determined constants. NECEEM was applied to study the interaction between single-stranded DNA binding protein and a fluorescently labeled 15-mer oligonucleotide. It allowed us to measure for the first time the rate constant of complex decay for this important protein-DNA pair, k-1 = 0.03 s-1. The value of the equilibrium binding constant, Kb = 3.6 x 10-6 M-1, was in good agreement with those measured by other methods. As low as 10-18 mol of the protein was sufficient for the measurements. Thus, the new method is simple, informative, and highly sensitive. Moreover, it can be equally applied to other noncovalent protein-ligand complexes. These features of NECEEM make this method an indispensable tool in studies of macromolecular interactions. They also emphasize the potential role of NECEEM in the development of extremely sensitive protein assays using nucleotide aptamers.     

Non-equilibrium capillary electrophoresis of equilibrium mixtures--appreciation of kinetics in capillary electrophoresis

We describe a new electrophoretic method (patent pending), Non-Equilibrium Capillary Electrophoresis of Equilibrium Mixtures (NECEEM), and demonstrate its application to the study of protein-DNA interactions. A single NECEEM experiment allows for the determination of equilibrium and kinetic parameters of protein-DNA complex formation. The equilibrium mixture is prepared by mixing protein and DNA; it contains three components: free protein, free DNA, and the protein-DNA complex. A small plug of such a mixture is injected onto a capillary and the three components are separated under non-equilibrium conditions using a run buffer that does not contain the components of the equilibrium mixture. The protein-DNA complex decays during the NECEEM separation; the resulting electropherograms contain characteristic peaks and exponential curves. A simple analysis of a single electropherogram reveals two parameters: the equilibrium dissociation constant of the protein-DNA complex and the monomolecular rate constant of complex decay. The bimolecular rate constant of complex formation can then be calculated as the ratio of the two experimentally-determined constants. NECEEM was applied to find the equilibrium and kinetic parameters of interaction between an E. coli single-stranded DNA binding protein and a fluorescently-labeled oligonucleotide. The constants determined by NECEEM are in good agreement with those obtained by other methods. The new method is simple, fast, and accurate. It can be equally applied to other non-covalent molecular complexes.     

Study of the noncovalent interaction of squarylium dyes with serum albumins

The noncovalent interaction of zwitterionic indolium squarylium dyes (hydrophilic and hydrophobic) and a structurally analogous ionic indodicarbocyanine (hydrophilic) dye with serum albumins was studied by spectral and fluorescent methods. It has been found that the hydrophilic squarylium dye with sulfonate groups most efficiently interacts with albumins, which is probably due to the double negative charge of the dye molecule at the expense of the sulfonate groups and the possibility to form hydrogen bonds with albumin. The hydrophobic squarylium dye, as well as the hydrophilic indodicarbocyanine dye without the squarylium fragment in its structure, bind with albumins much weaker than the structurally relevant hydro- philic squarylium dye. The properties of the latter dye permit us to recommend it for using as a spectral and fluorescent probe for serum albumins in extracellular media of living organisms.     

Characterization and determination of poly(vinylpyrrolidone) by complexation with an anionic azo-dye and nonequilibrium capillary electrophoresis

Using capillary zone electrophoresis in nonequilibrium conditions, the complexes of poly(vinylpyrrolidone) (PVP) with anionic azo-dyes dissociate following a first-order kinetics. Two peaks due to the remaining PVP–dye complexes and the equilibrium concentration of the free dye, plus an exponential region due to the dye liberated by the complexes during the electrophoretic run, are obtained. This behaviour was closely similar to that described in the literature for protein–probe and DNA–protein mixtures, upon application of the technique known as nonequilibrium capillary electrophoresis of equilibrium mixtures or NECEEM. Using Congo Red and Acid Blue 113, information about the maximal stoichiometry and average stability of the PVP–dye complexes was obtained. The procedure was also useful to predict the average molecular mass of PVP and to determine PVP in cleaning products and pharmaceutical preparations. By using an appropriate probe, the procedure should be also useful to characterize and determine many other synthetic or natural nonionic polymers, and to study polymer–probe interactions.     

Novel monofunctional and bifunctional boronic acid‐functionalized squarylium dyes as precolumn and on‐column labels for protein analysis by capillary electrophoresis with laser‐induced fluorescence

This article presents a continuous capillary electrophoresis with laser‐induced fluorescence (CE‐LIF) following spectral studies of the noncovalent interactions between novel Squarylium Boronic Acid 4 (SQ‐BA4) & Squarylium Diboronic Acid 2 (SQ‐DBA2) squarylium dyes and human serum albumin (HSA). Two protocols were used wherein the on‐column‐labeling protocol was found to be more sensitive than the precolumn one by showing a better enhancement in the peak area of the HSA–dye complex besides lower limits of detection (LODs) for HSA. Also, stability studies were conducted with or without HSA using precolumn‐labeling mode over one week exhibiting the superiority of SQ‐BA4 to SQ‐DBA2. Then, a mixture containing three model proteins, HSA, β‐lactoglobulin B, and transferrin, was labeled on‐column with both dyes and completely resolved by CE‐LIF after optimization of several parameters. Both dyes provided lower LODs for HSA than those of β‐lactoglobulin B and transferrin with higher sensitivities. In addition, the SQ‐BA4 dye showed again greater sensitivities with all the three proteins than SQ‐DBA2.     

Characterization of acid-induced protein conformational changes and noncovalent complexes in solution by using coldspray ionization mass spectrometry

Coldspray ionization (CSI) mass spectrometry, a variant of electrospray ionization (ESI) operating at low temperature (20 to −80°C), has been used to characterize protein conformation and noncovalent complexes. A comparison of CSI and ESI was presented for the investigation of the equilibrium acid-induced unfolding of cytochrome c, ubiquitin, myoglobin, and cyclophilin A (CypA) over a wide range of pH values in aqueous solutions. CSI and nanoelectrospray ionization (nanoESI) were also compared in their performance to characterize the conformational changes of cytochrome c and myoglobin. Significant differences were observed, with narrower charged-state distribution and a shift to lower charge state in the CSI mass spectra compared with those in ESI and nanoESI mass spectra. The results suggest that CSI is more prone to preserving folded protein conformations in solution than the ESI and nanoESI methods. Moreover, the CSI-MS data are comparable with those obtained by other established biophysical methods, which are generally acknowledged to be the suitable techniques for monitoring protein conformation in solution. Noncovalent complexes of holomyoglobin and the protein-ligand complex between CypA and cyclosporin A (CsA) were also investigated at a neutral pH using the CSI-MS method. The results of this study suggest the ability of CSI-MS in retaining of protein conformation and noncovalent interactions in solution and probing subtle protein conformational changes. Additionally, the CSI-MS method is capable of analyzing quantitatively equilibrium unfolding transitions of proteins. CSI-MS may become one of the promising techniques for investigating protein conformation and noncovalent protein-ligand interactions in solution.     

Fluorimetric studies and noncovalent labeling of protein with the near-infrared dye HITCI for analysis by CE-LIF

1,1',3,3,3',3'-Hexamethylindotricarbocyanine iodide (HITCI) is a commercially available, positively charged, indocarbocyanine dye used typically as a laser dye in the near infrared (NIR). The absorbance and fluorescence properties of HITCI in a variety of solvent systems were determined. Results indicate that the fluorescence of HITCI is not significantly affected by the pH. Titration of HITCI with human serum albumin (HSA) and trypsinogen was carried out to investigate the interactions between this dye and proteins. These studies revealed that the absorbance and fluorescence properties of the dye change upon binding to protein in a wide range of solution pH's. The potential use of HITCI as a noncovalent protein labeling probe, therefore, was explored. Determination and separation of HITCI and HITCI-protein complexes was performed by capillary electrophoresis with diode-laser induced fluorescence detection (CE-LIF). Both pre-column and on-column noncovalent labeling methods are demonstrated.     

Noncovalent labeling of biomolecules with red and near- infrared dyes

Biopolymers such as proteins and nucleic acids can be labeled with a fluorescent marker to allow for their detection. Covalent labeling is achieved by the reaction of an appropriately functionalized dye marker with a reactive group on a biomolecule. The recent trend, however, is the use of noncovalent labeling that results from strong hydrophobic and/or ionic interactions between the marker and biomolecule of interest. The main advantage of noncovalent labeling is that it affects the functional activity of the biomolecule to a lesser extent. The applications of luminescent cyanine and squarylium dyes are reviewed.     

Laser-induced fluorescence detection schemes for the analysis of proteins and peptides using capillary electrophoresis

Over the past few years, a large number of studies have been prepared that describe the analysis of peptides and proteins using capillary electrophoresis (CE) and laser-induced fluorescence (LIF). These studies have focused on two general goals: (i) development of automatic, selective and quick separation and detection of mixtures of peptides or proteins; (ii) generation of new methods of quantitation for very low concentrations (nm and subnanomolar) of peptides. These two goals are attained with the use of covalent labelling reactions using a variety of dyes that can be readily excited by the radiation from a commonly available laser or via the use of noncovalent labelling (immunoassay using a labelled antibody or antigen or noncovalent dye interactions). In this review article, we summarize the works which were performed for protein and peptide analysis via CE-LIF.     

Structural study of BSA/poly(ethylene glycol) lipid conjugate complexes

In this work we report the structural characteristics of bovine serum albumin/poly(ethylene glycol) lipid conjugate (BSA/PEG(2000)-PE) complexes under physiological conditions (37 degrees C and pH 7.4) for particular fractions of BSA to PEG-lipid concentration, c(BSA)/c(PEG)(2000)-PE. Ultraviolet fluorescence spectroscopy (UV) results shown that PEG(2000)-PE is associated to BSA, leading to protein unfolding for fixed c(BSA) = 0.01 wt % and variable c(PEG)(2000)-PE = 0.0015-0.6 wt %. Tryptophan groups on the BSA surface are in contact with the PEG-lipid at c(PEG)(2000)-PE = 0.0015 wt %, while they are exposed to water at c(PEG)(2000)-PE > 0.0015 wt %. Dynamic and static light scattering (DLS and SLS) and small-angle neutron scattering (SANS) point out the existence of individual BSA/PEG-lipid complexes in the system for fixed c(BSA) = 1 wt % and variable c(PEG)(2000)-PE = 0.15-2 wt %. DLS shows that there is only one BSA molecule per protein/PEG-lipid complex, while SLS shows that the PEG-lipid associates to the BSA without promoting aggregation between adjacent protein/polymer-lipid conjugate complexes. SANS was used to show that BSA/PEG(2000)-PE complexes adopt an oblate ellipsoidal shape. Partially unfolded BSA is contained in the core of the oblate ellipsoid, which is surrounded by an external shell containing the PEG(2000)-PE.     

Frontal analysis in microchip CE: a simple and accurate method for determination of protein-DNA dissociation constant

Equilibrium constants, such as the dissociation constant (K(d)), are a key measurement of noncovalent interactions that are of importance for the proper functioning of molecules in living systems. Frontal analysis (FA) is a simple and accurate CE method for the determination of K(d). Microchip CE coupled with LIF detection was used to determine K(d) of protein-DNA interactions using the FA method. A model system of IgE and the IgE-binding aptamer was selected to demonstrate the capability of FA in microchip CE. Because the fluorescence emission was dependent on the dye migration velocity, the velocity of the free aptamer was adjusted to be the same as that of the aptamer-IgE complex by setting up individual separation voltage configurations for the free and bound aptamers. The ratio of the free and bound aptamers in the equilibrium mixture was directly measured from the heights of their plateaus detected at 1.0 cm from the intersection of the microchip, and no internal standard was needed. The K(d) of the IgE-aptamer pair was determined as 6 +/- 2 nM which is consistent with the reported results (8 nM).     

Characterization of the interaction between a new merocyanine dye and bovine serum albumin

A new merocyanine dye was synthesized, and its acidity constant was determined by spectrophotometric and chemometrics methods. The interactions of the new cyanine dye with bovine serum albumin (BSA) have been studied by fluorescence and UV absorption spectroscopy at pH 7.40. A visual color change from red to blue was observed by addition of BSA to aqueous solution of the dye. The quenching constants and binding parameters (binding constants and number of binding sites) were determined at different temperatures. The calculated thermodynamic parameters confirmed that the binding reaction is mainly entropy-driven, whereas electrostatic interaction plays major role in the reaction. The displacement experiment confirmed binding of the dye to the subdomain IIA (site 1) of albumin. Moreover, synchronous fluorescence spectroscopy studies revealed the dye induces some local conformational change in BSA. The binding distance, r, between donor (serum albumin) and acceptor (dye) was obtained according to Förster’s theory.     

1H NMR study of complexation of ethidium bromide with single-stranded noncomplementary desoxytetranucleotide 5′-d(GpApApG) in aqueous solution

Complication of the ethidium bromide dye (3,8-diamino-6-phenyl-5-ethylphenanthridine) with single-stranded noncomplementary desaxytetranucleotide 5′-d(GpApApG) in aqueous salt solution was studied by one- and two-dimensional¹H NMR (500 and 600 MHz). The concentration dependences of the proton chemical shifts of the reactant molecules were measured at different temperatures (T₁ = 298 K, T₂ = 308 K). Investigations of self-association of the tetranucleotide showed that duplices can hardly form in solution. Therefore, dye complexes with single-stranded tetranucleotide play a major role in the equilibrium in solution; this makes it possible to analyze the specifics of interactions of aromatic ligands with single-stranded DNA. Various schemes of complexation are discussed; the equilibrium constants and the limiting values of the proton chemical shifts of ethidium bromide in the complexes are determined. The constants of dye binding to the single-stranded tetranucleotide 5′-d(GAAG) involving only purine bases is approximately an order of magnitude lower than the constants of ethidium bromide complexation with desaxytetranucleotide monomers whose sequences contain alternating types of base in the chain. The relative contents of complexes of different types are analyzed, and peculiarities of dynamic equilibrium, depending on the ratio of concentrations between the dye and the tetranucleotide, are revealed. Based on the data obtained it is concluded that the binding between ethidium bromide and the single-stranded nucleotide is sequence-specific. The estimated values of the induced chemical shifts of the dye protons are used to establish the most probable structures of the 1:1 and 2:1 complexes of ethidium bromide with single-stranded desaxytetranucleotide. Translated fromZhumal Struktumoi Khimii, Vol. 39, No. 5, pp. 808–820, September–October, 1998. This work was supported by INTAS grant NUD 7200.     

Electrospray Mass Spectrometry of Biomacromolecular Complexes with Noncovalent Interactions—New Analytical Perspectives for Supramolecular Chemistry and Molecular Recognition Processes

The development of “soft” ionization methods in recent years has enabled substantial progress in the mass spectrometric characterization of macromolecules, in particular important biopolymers such as proteins and nucleic acids. In contrast to the still existing limitations for the determination of molecular weights by other ionization methods such as fast atom bombardment and plasma desorption, electrospray ionization (ESI) and matrix-assisted laser desorption have provided a breakthrough to macromolecules larger than 100 kDa. Whereas these methods have been successfully applied to determine the molecular weight and primary structure of biopolymers, the recently discovered direct characterization by ESI-MS of complexes containing noncovalent interactions (“noncovalent complexes”) opens new perspectives for supramolecular chemistry and analytical biochemistry. Unlike other ionization methods ESI-MS can be performed in homogeneous solution and under nearly physiological conditions of pH, concentration, and temperature. ESI mass spectra of biopolymers, particularly proteins, exhibit series of multiply charged macromolecular ions with charge states and distributions (“charge structures”) characteristic of structural states in solution, which enable a differentiation between native and denatured tertiary structures. In the first part of this article, fundamental principles, the present knowledge about ion formation mechanism(s) of ESI-MS, the relations between tertiary structures in solution and charge structures of macro-ions in the gas phase, and experimental preconditions for the identification of noncovalent complexes are described. The hitherto successful applications to the identification of enzyme–substrate and –inhibitor complexes, supramolecular protein–and protein–nucleotide complexes, double-stranded polynucleotides, as well as synthetic self-assembled complexes demonstrate broad potential for the direct analysis of specific noncovalent interactions. The present results suggest new applications for the characterization of supramolecular structures and molecular recognition processes that previously have not been amenable to mass spectrometry; for example, the sequence-specific oligomerization of polypeptides, antigen–antibody complexes, enzyme–and receptor–ligand interactions, and the evaluation of molecular specificity in combinatorial syntheses and self-assembled systems.     

Methods for the determination of binding constants by capillary electrophoresis

Apparent equilibrium constants for molecular association (e.g., association constants, binding constants, dissociation constants, partition coefficients) can be determined with a variety of different capillary electrophoresis (CE) approaches. In many cases, the investigated association behavior is between a smaller molecule or ion (i.e., the solute, drug, or analyte of interest) and a larger entity (e.g., proteins, micelles, polymers, chiral selectors such as cyclodextrins, etc.). Each experimental approach has advantages and disadvantages. Frequently, it is the nature of the system being evaluated that determines the optimal experimental approach. Six different CE-based techniques for evaluating binding constants are reviewed. Examples of each method, and recent references on its use are given.     

Application of micellar and microemulsion electrokinetic chromatography for characterization of gallium(III) complexes of pharmaceutical significance

CE with conventional UV detection has recently been shown as a highly effective means to assaying cytotoxic gallium(III)-based compounds with regard to desirable drug-like properties such as the stability and binding to serum proteins. In this extension of that work, different CE techniques are used to further characterize a given set of gallium coordination compounds with established antiproliferating efficacy. Using free-zone CE mode, the electrophoretic profiles of complexes are recorded in order to assess their actual charge state under physiological buffer conditions. Micellar and microemulsion electrokinetic chromatographic techniques are tested as tools for the rapid estimation of the n-octanol-water partition coefficient (log P) that provides a rationale estimate of a drug's ability to cross biological membranes. A range of electrolyte buffer systems with varying (both in the nature and concentration) organic modifiers are examined to evaluate their effect on the relationship between experimental or calculated log P and the retention factors of compounds (log k'). Both methods were found to be better applicable for neutral than for cationic Ga complexes, the microemulsion mode demonstrating superior lipophilicity estimations as well as statistically meaningful log P versus log k' correlations when all the complexes were included in one regression set.