Detection of human immunodeficiency virus type 1 DNA sequence using plasmonics nanoprobes

This paper describes the use of plasmonics-based nanoprobes that act as molecular sentinels for DNA diagnostics. The plasmonics nanoprobe comprises a metal nanoparticle and a stem-loop DNA molecule tagged with a Raman label. The nanoprobe utilizes the specificity and selectivity of the DNA hairpin probe sequence to detect a specific target DNA sequence of interest. In the absence of target DNA, the stem-loop configuration maintains the Raman label in proximity to the metal nanoparticle, inducing an intense surface-enhanced Raman scattering (SERS) effect that produces a strong Raman signal upon laser excitation. Upon hybridization of a complementary target DNA sequence to the nanoprobe, the stem-loop configuration is disrupted, causing the Raman label to physically separate from the metal nanoparticle, thus quenching the SERS signal. The usefulness and potential application of the plasmonics nanoprobe for diagnosis is demonstrated using the gag gene sequence of the human immunodeficiency virus type 1 (HIV-1). We successfully demonstrated the specificity and selectivity of the plasmonics nanoprobes to detect PCR amplicons of the HIV gene. The potential for combining the spectral selectivity and high sensitivity of the SERS process with inherent molecular specificity of DNA hairpins to diagnose molecular target sequences in homogeneous solutions is discussed.     

Detection of G proteins by affinity probe capillary electrophoresis using a fluorescently labeled GTP analogue

An affinity probe capillary electrophoresis (APCE) assay for guanine-nucleotide-binding proteins (G proteins) was developed using BODIPY FL GTPgammaS (BGTPgammaS), a fluorescently labeled GTP analogue, as the affinity probe. In the assay, BGTPgammaS was incubated with samples containing G proteins and the resulting mixtures of BGTPgammaS-G protein complexes and free BGTPgammaS were separated by capillary electrophoresis and detected with laser-induced fluorescence detection. Separations were completed in less than 30 s using 25 mM Tris, 192 mM glycine at pH 8.5 as the electrophoresis buffer and applying 555 V/cm over a 4-cm separation distance. BGTPgammaS-Galpha(o) peak heights increased linearly with Galpha(o) up to approximately 200 nM using a 50 nM BGTPgammaS probe. The detection limit for Galpha(o) was 2 nM, corresponding to a mass detection limit of 3 amol. The high speed of the APCE assays allowed reaction kinetics and the dissociation constant (Kd) to be determined. The on-rate and off-rate of BGTPgammaS to Galpha(o) were 0.0068 +/- 0.0004 and 0.000 23 +/- 0.000 01 s(-1), respectively. The half-life of the BGTPgammaS-Galpha(o) complex was 3060 +/- 240 s and Kd was 8.6 +/- 0.7 nM. The estimates of these parameters are in good agreement with those obtained using established techniques, indicating the suitability of this method for such measurements. Lowering the temperature of the separation improved the detection of the complex, allowing the assay to be performed on a commercial instrument with longer separation times. Additionally, the capability of the technique to detect several G proteins based on their binding to BGTPgammaS was demonstrated with assays for Galpha and Galpha(i1) and for Ras and Rab3A.     

Detection of nonderivatized peptides in capillary electrophoresis using quenched phosphorescence.

A capillary electrophoresis detection technique for (small) peptides is presented, i.e. quenched phosphorescence, a method that is generally applicable and does not require chemical derivatization. For this purpose, a novel phosphorophore, 1-bromo-4-naphthalenesulfonic acid (BrNS), was synthesized. BrNS has sufficient water solubility and provides strong phosphorescence at room temperature over a wide pH range. The detection is based on the dynamic quenching of the BrNS phosphorescence background signal by electron transfer from the amino group of the peptides at pH 9.5-10. For the di- and tripeptides Val-Tyr-Val, Val-Gly-Gly, Ala-Ser, Gly-Asn, Gly-Ala, and Gly-Tyr, detection limits in the range of 5-20 microg/L were obtained. The novel technique is even a good alternative for the (limited) group of peptides containing tyrosine and, thus, exhibiting native fluorescence as well as strong UV absorption: using Gly-Tyr, Val-Tyr-Val, methionine enkephalin, and human angiotensin II as test compounds, quenched phosphorescence detection was found to compare favorably with absorption detection at 190- and 266-nm laser-induced fluorescence detection, as performed with a recently developed, small-size, quadrupled Nd:YAG laser.     

Chiral separation of leucovorin with bovine serum albumin using affinity capillary electrophoresis.

A method for the determination of the (6R)- and (6S)-stereoisomers of leucovorin using electrokinetic chromatography (EKC) in the affinity mode has been developed. Bovine serum albumin (BSA) is used as a run buffer additive to incorporate enantiomeric selectivity into the system. Protein-wall interactions are minimized by using a poly(ethylene glycol) (PEG) coated capillary. Chiral resolution is obtained in 12.5 min with efficiencies greater than 200,000 theoretical plates using BSA as an additive, while no resolution is obtained in the absence of BSA. A general equation is derived to calculate the free energy of interaction between the leucovorin isomers and the BSA molecule. This method represents a new means of obtaining thermodynamic data for substrate binding interactions and for the general study of drug cross-reactions and interactions of drugs with serum and other proteins.     

Fluorescence polarization studies of affinity interactions in capillary electrophoresis.

Capillary electrophoresis (CE) combined with molecular recognition for ultrasensitive bioanalytical applications often requires the formation of stable complexes between an analyte and its binding partner. Previous studies of binding interactions using CE involve multiple-step titration experiments and are time-consuming. We describe a simple method based on laser-induced fluorescence polarization (LIFP) detection for CE separation, which allows for on-line monitoring of affinity complex formation. Because fluorescence polarization is sensitive to changes in the rotational diffusion arising from molecular association or dissociation, it is capable of providing information on the formation of affinity complexes prior to or during CE separation. Applications of the CE/LIFP method to three binding systems including vancomycin and its antibody, staphylococcal enterotoxin A and its antibody, and trp operator and trp repressor were demonstrated, representing peptide-protein, protein-protein, and DNA-protein interactions. The affinity complexes were readily distinguished from the unbound molecules on the basis of their fluorescence polarization. The relative increase in fluorescence polarization upon complex formation varied with the molecular size of the binding pairs.     

Study of lipid and apolipoprotein binding interactions using vesicle affinity capillary electrophoresis

Vesicle affinity capillary electrophoresis (VCE), a newly developed technique, was designed to assess the effect of physicochemical properties of apolipoprotein (apo) on the binding to lipoproteins, under physiological conditions (phosphate-saline buffer system at pH 7.4 and 37 degrees C), using vesicle as a model. The technique results in similar lipid binding properties of apo CIII (CIII) and its peptides compared to other techniques. It also offers a fast and more sensitive tool in determining the lipid affinity of apos in a unique system simulating the dynamic binding properties of apo in vivo. A noncompetitive binding model is used to determine the multiple binding properties of CIII and its peptides to vesicle. The VCE binding constants are dependent on temperature, physicochemical properties of the protein (hydrophobicity and charge), and nature of the vesicle. The vesicles used in the VCE experiments described here have been fully characterized and found to be stable under different temperatures (4 and 37 degrees C) and voltage conditions. Migration behavior of CIII and related peptides is reported in terms of relative mobility in order to correct for variability in viscosity at different vesicle concentrations. The VCE method provides very precise data on the migration time from 0.1 to 3.3% RSD at the highest concentration of vesicle. The model and current data have been used to determine VCE binding constants and protein-to-lipid binding ratios. The model predicts that higher lipid affinity (K(B)), protein-lipid binding ratio (n), and lower protein concentration result in a shift of the binding isotherm toward a lower concentration range of vesicle. A higher vesicle mobility, reflecting the size and charge of the vesicle, results in a larger separation window between the migration time of the free protein and the complex. The value of VCE for structure-function studies and drug design for peptides and proteins that are strongly bound to lipids has been illustrated.     

Aptamer-based detection and quantitative analysis of ricin using affinity probe capillary electrophoresis

The ability to detect sub-nanomolar concentrations of ricin using fluorescently tagged RNA aptamers is demonstrated. Aptamers rival the specificity of antibodies and have the power to simplify immunoassays using capillary electrophoresis. Under nonequilibrium conditions, a dissociation constant, Kd, of 134 nM has been monitored between the RNA aptamer and ricin A-chain. With use of this free-solution assay, the detection of 500 pM (approximately 14 ng/mL) or 7.1 amol of ricin is demonstrated. The presence of interfering proteins such as bovine serum albumin and casein do not inhibit this interaction at sub-nanomolar concentrations. When spiked with RNAse A, ricin can still be detected down to 1 nM concentrations despite severe aptamer degradation. This approach offers a promising method for the rapid, selective, and sensitive detection of biowarfare agents.     

Nanoliter-volume 1H NMR detection using periodic stopped-flow capillary electrophoresis.

Recent advances in the analysis of nanoliter volumes using 1H NMR microcoils have led to the application of microcoils as detectors for capillary electrophoresis (CE). Custom NMR probes consisting of 1-mm-long solenoidal microcoils are fabricated from 50-micron diameter wire wrapped around capillaries to create nanoliter-volume detection cells. For geometries in which the capillary and static magnetic field are not parallel, the electrophoretic current induces a magnetic field gradient which degrades the spectroscopic information obtainable from CE/NMR. To reduce this effect and allow longer analyte observation times, the electrophoretic voltage is periodically interrupted so that 1-min high-resolution NMR spectra are obtained for every 15 s of applied voltage. The limits of detection (LODs; based on S/N = 3) for CE/NMR for arginine are 57 ng (330 pmol; 31 mM) and for triethylamine (TEA) are 9 ng (88 pmol; 11 mM). Field-amplified stacking is used for sample preconcentration. As one example, a 290-nL injection of a mixture of arginine and TEA both at 50 mM (15 nmol of each injected) is stacked severalfold for improved concentration LODs while achieving a separation efficiency greater than 50,000. Dissolving a sample in a mixture of 10% H2O/90% D2O allows H2O to serve as the nearly ideal neutral tracer and allows direct observation of the parabolic and flat flow profiles associated with gravimetric and electrokinetic injection, respectively. The unique capabilities of CE and the rich spectral information provided by NMR spectroscopy combine to yield a valuable analytical tool, especially in the study of mass-limited samples.     

On-line drug metabolism in capillary electrophoresis. 1. Glucuronidation using rat liver microsomes

A rat liver microsome pseudostationary phase has been used for the on-line capillary electrophoresis monitoring of glucuronidation. Uridine diphosphate glucuronosyltransferase (EC 2.4.1.17) containing microsomes was isolated from rat liver and directly injected onto neutrally coated capillary containing polymeric replaceable gels followed by injection of the substrate mixture. On-line glucuronidation was observed within 15 min without any sample preparation. The factors affecting the separation of glucuronides and parent compounds were investigated by varying the applied electric fields and the size (length and internal diameter) of capillary. The Michaelis-Menten parameters (Km and Vmax) for the glucuronidation of 4-methyl-7-hydroxy coumarin and 4-nitrophenol were determined using the CE method and by off-line microsomal incubation. No significant differences were observed for Km and Vmax values for 4-methyl-7-hydroxycoumarin and 4-nitrophenol between on-line and off-line glucuronidation of these two compounds. This method was also used to determine the inhibition constant (IC50 value) for the competitive inhibition of morphine glucuronidation by codeine, IC50 (on-line) = 170 vs 580 microM (off-line). The results demonstrate that this method can be used to screen for the glucuronidation of test compounds and should reduce the time required for this screening process.     

Online concentration and affinity separation of biomolecules using multifunctional particles in capillary electrophoresis under magnetic field

To overcome several problems in affinity capillary electrophoresis (ACE), i.e., low detectability, need for sample derivatization, and difficulty in the fixation of affinity ligands (ALs), multifunctional magnetic particles (MFMPs) were prepared by immobilizing both fluorescent molecules and ALs for low-density lipoproteins onto the surface of magnetic polymer microspheres with a polyelectrolyte multilayer coating technique and applied to the ACE analysis. The prepared MFMPs showed a remarkable change in the electrophoretic mobility (mu ep) by the addition of low-density lipoproteins (LDL), whereas for high-density lipoproteins (HDL), mu ep of the MFMPs kept constant, so that it was confirmed that the MFMPs possess an affinity with LDL. On the other hand, the MFMPs can be trapped by the magnetic field even under a higher electric field for electrophoresis. By a successive on-off control of the magnetic field, online preconcentration of the LDL bound MFMPs and the selective separation of LDL from HDL were successfully achieved. In the ACE analysis of LDL employing UV detection, an 82-fold increase in the sensitivity was obtained by the on-capillary sample preconcentration using the MFMPs. When laser induced-fluorescence detection was employed, furthermore, the limit of detection for LDL was improved to the order of subpicomolar.     

Detection of human immunoglobulin in microchip and conventional capillary electrophoresis with contactless conductivity measurements

The detection of human immunoglobulin M (IgM) was performed using capacitively coupled contactless conductivity detection (CCD) in electrophoresis carried out in conventional capillaries as well as on glass and poly(meth-yl methacrylate) (PMMA) microdevices. Also achieved was the analyses of IgG (an anti-human IgM) and the complex formed in the reaction between the two immunoreagents. It is demonstrated that CCD is a powerful tool suitable not only for the detection of antibodies but also for monitoring an immunological interaction. Conductivity measurements allow the direct determination of immunoreagents, and it is advantageous, since no labels are required. The immunoglobulin IgM has been taken as model analyte. The reproducibility of the analytical signal (RSD = 1%), sensitivity and limits of detection obtained for IgM (0.15 ng/mL in conventional capillaries and 34 ng/mL in microchips) are comparable to those previously obtained with amperometric detection. The immunological reaction was performed either in conventional microtiter plates as used in ELISA or in situ on the glass chip.     

Specific base recognition of oligodeoxynucleotides by capillary affinity gel electrophoresis using polyacrylamide-poly(9-vinyladenine) conjugated gel.

Poly(9-vinyladenine) was synthesized and utilized as an affinity macroligand entrapped within the gel matrix. Base-specific separation of oligodeoxynucleotides was achieved with high resolution and high speed by electrophoresis, using capillaries filled with conjugated polyacrylamide-poly(9-vinyladenine) gel. Oligothymidylic acids were selectively separated from the mixture of oligothymidylic and oligodeoxyadenylic acids by utilizing a specific hydrogen bonding between poly(9-vinyladenine) and oligothymidylic acids. Migration time and resolution of oligodeoxynucleotides were influenced by several parameters, such as the size of poly(9-vinyladenine), capillary temperature, and concentrations of poly(9-vinyladenine) and urea. Some guidelines are presented, based on the theoretical formulation of the effect of these parameters, in order to find optimum electrophoretic conditions. Analytical capillary affinity gel electrophoresis was developed for the selective and sensitive base recognition of oligodeoxynucleotides with efficiencies as high as several 10(6) plates/m by using a urea-gel capillary with poly(9-vinyladenine) and temperature-programming.     

Detection of adenylyl cyclase activity using a fluorescent ATP substrate and capillary electrophoresis

A capillary electrophoresis laser-induced fluorescence (CE-LIF) assay was developed for detection of adenylyl cyclase (AC) activity using BODIPY FL ATP (BATP) as substrate. In the assay, BATP was incubated with AC and the resulting mixture of BATP and enzyme product (BODIPY cyclic AMP, BcAMP) separated in 5 min by CE-LIF. Substrate depletion and product accumulation were simultaneously monitored during the course of the reaction. The rate of product formation depended upon the presence of AC activators forskolin or Galpha(s)-GTPgammaS as evidenced by a more rapid BATP turnover to BcAMP compared to basal levels. The CE-LIF assay detected EC50 values for forskolin and Galpha(s)-GTPgammaS of 27 +/- 6 microM and 317 +/- 56 nM, respectively. These EC50 values compared well to those previously reported using [alpha-32P]ATP as substrate. When AC was concurrently activated with 2.5 microM forskolin and 25 nM Galpha(s)-GTPgammaS, the amount of BcAMP formed was 3.4 times higher than the additive amounts of each activator alone indicating a positively cooperative activation by these compounds in agreement with previous assays using radiolabeled substrate. Inhibition of AC activity was also demonstrated using the AC inhibitor 2'-(or-3')-O-(N-methylanthraniloyl) guanosine 5'-triphosphate with an IC50 of 9 +/- 6 nM. The use of a fluorescent substrate combined with CE separation has enabled development of a rapid and robust method for detection of AC activity that is an attractive alternative to the AC assay using radioactive nucleotide and column chromatography. In addition, the assay has potential for high-throughput screening of drugs that act at AC.     

Quantitative analysis of microRNA in blood serum with protein-facilitated affinity capillary electrophoresis

MicroRNAs (miRNAs) are small (～22 nt) regulatory RNAs that are frequently deregulated in cancer and have shown promise as tissue- and blood-based biomarkers for cancer classification and prognostication. Here we present a protein-facilitated affinity capillary electrophoresis (ProFACE) assay for rapid quantification of miRNA levels in blood serum using single-stranded DNA binding protein (SSB) and double-stranded RNA binding protein (p19) as separation enhancers. The method utilizes either the selective binding of SSB to a single-stranded DNA/RNA probe or the binding of p19 to miRNA-RNA probe duplex. For the detection of ultralow amounts of miRNA without polymerase chain reaction (PCR) amplification in blood samples we apply off-line preconcentration of synthetic miRNA-122 from serum by p19-coated magnetic beads followed by online sample stacking in the ProFACE assay. The detection limit is 0.5 fM or 30?000 miRNA molecules in 1 mL of serum as a potential source of nai?ve miRNAs.     

Analysis of free intracellular nucleotides using high-performance capillary electrophoresis.

High-performance capillary electrophoresis (HPCE) with UV absorbance detection (254 nm) has been applied for analyzing intracellular free ribonucleotides. The nucleotide profiles obtained from peripheral blood lymphocytes differ from those obtained from Molt4 human leukemic cells. With a 140 mM borate buffer, pH 9.4, a nearly complete profile can be obtained in 25 min. HPCE has comparable resolution to that of high-performance liquid chromatography (HPLC) but is faster in terms of time per sample run (25 min vs 45 min) and requires much less sample (nanoliter range for HPCE vs microliter range for HPLC).     

Enantiomeric separation using an l-RNA aptamer as chiral additive in partial-filling capillary electrophoresis

In this paper, we report the chiral resolution of arginine using an anti-arginine l-RNA aptamer chiral selector in partial-filling CE. The effects of the capillary temperature, sample load, and aptamer plug length on the enantiomeric separation were assessed. Very high chiral resolving capability was observed at low or moderate capillary temperatures (the target peak being not detected in the separation window), whereas the practical chiral resolution was achieved only at high enough temperatures (50-60 degrees C). Over this high-temperature range, the electrophoretic behavior of the target enantiomer appeared to result from a combination of binding site heterogeneity, slow desorption kinetics, and concentration overload of aptamer binding sites. From additional thermal UV melting experiments, three RNA conformations were identified for the 50-60 degrees C temperatures. It was suggested that the presence of these different RNA conformations was a plausible source of the binding site heterogeneity.     

In vitro selection of high-affinity DNA ligands for human IgE using capillary electrophoresis

Aptamers with high affinity for IgE were selected using capillary electrophoresis to demonstrate the compatibility of this technique with SELEX. The high selectivity and efficiency of CE gave rise to a very high rate of enrichment, allowing high-affinity, high-selectivity aptamers to be obtained in only four rounds of selection. Decreasing the number of rounds shortens the selection procedure from the 4-6 weeks typical of SELEX to several days. The use of "bulk" dissociation constant measurements was introduced as a method for assessing the DNA pool after each round of selection. The average dissociation constant of the sequences in the DNA pool for IgE after four rounds of selection was 29 nM. The distribution of the dissociation constants for the sequences in the pool was very narrow with a standard deviation of only 6 nM. All of the sequences assessed exhibited high specificity for human IgE when compared with human IgG or mouse IgE.     

High-performance capillary electrophoresis of SDS-protein complexes using UV-transparent polymer networks.

This paper demonstrates the use of UV-transparent replaceable polymer networks for the separation of SDS-protein complexes on the basis of molecular weight. First, the use of linear (i.e. non-cross-linked) polyacrylamide is shown to provide molecular separation of SDS-protein complexes. A study reveals such columns to yield significantly greater lifetime than cross-linked gels because of the flexibility of the noncovalently attached polymer chains. However, column lifetime was still found to be limited (approximately 20-40 injections), and detection at 214 nm was problematical because of the absorbance of polyacrylamide. UV-transparent polymer networks of dextran and PEG were substituted for polyacrylamide with successful molecular weight sieving of SDS-protein complexes at 214 nm. Due to their low to moderate viscosities, these networks could be routinely replaced leading to the possibility of hundreds of injections with a single column. Migration time reproducibilities of 0.5% RSD or less were found with replacement of the network. Using dextran, calibration plots of peak area vs concentration of standard protein were linear over the range of 0.5 microgram/mL up to at least 0.25 mg/mL. Furthermore, plasma samples could be directly utilized because of the strong solvating power of SDS. Rapid separation of protein mixtures are demonstrated with these UV-transparent polymer networks.