Quantum dot-conjugated hybridization probes for preliminary screening of siRNA sequences

In the present study, we describe the design and fabrication of quantum dot-conjugated hybridization probes and their application to the development of a comparatively simple and rapid procedure for the selection of highly effective small-interfering RNA (siRNA) sequences for RNA interference (RNAi) in mammalian cells, for example, siRNAs with high accessibility and affinity to the respective mRNA target. A single-stranded siRNA was conjugated with a quantum dot and used as a hybridization probe. The target mRNA was amplified in the presence of Cy5-labeled nucleotides, and Cy5-mRNA served as a hybridization sample. The formation of siRNA/mRNA duplexes during a comparatively short hybridization time (1 h) was used as a criterion for the selection of highly effective, target-specific siRNA sequences. The accessibility and affinity of the siRNA sequence for the target mRNA site were determined by fluorescence resonance energy transfer (FRET) between a quantum dot (donor) and a fluorescent dye molecule (Cy5, acceptor) localized at an appropriate distance from each other when hybridization occurred. The FRET signal was observed only when there was high accessibility between an antisense siRNA and a sense mRNA and did not appear in the case of mismatch siRNAs. Moreover, the amplitude of the FRET signal significantly correlated with the specific effect of siRNA on the expression of the target mRNA and protein, determined in native cells by RT-PCR and immunoblot analysis, respectively.     

Universal liposomes: preparation and usage for the detection of mRNA

Dye-encapsulating liposomes can serve as signaling reagents in biosensors and biochemical assays in place of enzymes or fluorophores. Detailed here is the use and preparation of streptavidin-coupled liposomes which offer a universal approach to biotinylated target detection. The universal approach provides two advantages, i.e. only one type of liposome is necessary despite varying target and probe sequences and the hybridization event can take place in the absence of potential steric hindrance occurring from liposomes directly conjugated to probes. One objective of this work was to optimize the one-step conjugation of SRB-encapsulating liposomes to streptavidin using EDC. Liposome, EDC, streptavidin concentrations, and reaction times were varied. The optimal coupling conditions were found to be an EDC:carboxylated lipid:streptavidin molar ratio of 600:120:1 and a reaction time of 15 min. The second goal was to utilize these liposomes in sandwich hybridization microtiter plate-based assays using biotinylated reported probes as biorecognition elements. The assay was optimized in terms of probe spacer length, probe concentration, liposome concentration, and streptavidin coverage. Subsequently, the optimized protocol was applied to the detection of DNA and RNA sequences. A detection limit of 1.7 pmol L⁻¹ and an assay range spanning four orders of magnitude (5 pmol L⁻¹−50 nmol L⁻¹) with a coefficient of variation ≤5.8% was found for synthetic DNA. For synthetic RNA the LOQ was half that of synthetic DNA. A comparison was made to alkaline phosphatase-conjugated streptavidin for detection which yielded a limit of quantitation approximately 80 times higher than that for liposomes in the same system. Thus, liposomes and the optimized sandwich hybridization method are well suited for detecting single-stranded nucleic acid sequences and compares favorably to other sandwich hybridization schemes recently described in the literature. The assay was then used successfully for the clear detection of mRNA amplified by nucleic acid sequence-based amplification (NASBA) isolated from as little as one Cryptosporidium parvum oocyst. The detection of mRNA from oocysts isolated from various water sample types using immunomagnetic separation was also assessed. Finally, to prove the wider applicability and sensitivity of this universal method, RNA amplified from the atxA gene of Bacillus anthracis was detected when the input to the preceding NASBA reaction was as low as 1.2 pg. This highly sensitive liposome-based microtiter plate assay is therefore a platform technology allowing for high throughput and wide availability for routine clinical and environmental laboratory applications.     

Validated method for determination of bromopride in human plasma by liquid chromatography--electrospray tandem mass spectrometry: application to the bioequivalence study

A simple, sensitive and specific liquid chromatography-tandem mass spectrometry method for the quantification of bromopride I in human plasma is presented. Sample preparation consisted of the addition of procainamide II as the internal standard, liquid-liquid extraction in alkaline conditions using hexane-ethyl acetate (1 : 1, v/v) as the extracting solvent, followed by centrifugation, evaporation of the solvent and sample reconstitution in acetonitrile. Both I and II (internal standard, IS) were analyzed using a C18 column and the mobile-phase acetonitrile-water (formic acid 0.1%). The eluted compounds were monitored using electrospray tandem mass spectrometry. The analyses were carried out by multiple reaction monitoring (MRM) using the parent-to-daughter combinations of m/z 344.20 > 271.00 and m/z 236.30 > 163.10. The areas of peaks from analyte and IS were used for quantification of I. The achieved limit of quantification was 1.0 ng/ml and the assay exhibited a linear dynamic range of 1-100.0 ng/ml and gave a correlation coefficient (r) of 0.995 or better. Validation results on linearity, specificity, accuracy, precision and stability, as well as application to the analysis of samples taken up to 24 h after oral administration of 10 mg of I in healthy volunteers demonstrated the applicability to bioequivalence studies.     

Inhibitory Effects of Phenylacetic Acid on Proliferation of Human Pancreatic Carcinoma BXPC-3 Cells by the Regulation of Adenosine Deaminases Acting on RNA

The effect and mechanism of phenylacetic acid on the proliferation of pancreatic carcinoma cells were investigated in cultured pancreatic carcinoma BXPC-3 cells by means of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay and flow cytometry assay.The results show that the treatment of pancreatic carcinoma cells with phenylacetic acid significantly inhibited the cell proliferation in time-dependent and dose-dependent manners.The proliferation of BXPC-3 cells was inhibited at the stage of S phase,the cells at the end stage of S phase were accumulated abundantly,and thus DNA synthesis could not be accomplished entirely.In addition,the expression of adenosine deaminases acting on RNA(ADARs) mRNA in BXPC-3 cells and pancreatic carcinoma specimen were detected by RT-PCR.Having been treated with phenylacetic acid,ADAR2 mRNA in BXPC-3 cells was significantly decreased,the differences were of statistical significance(P0.01).Taken together,these results suggest that phenylacetic acid may likely regulate the proliferation of pancreatic carcinoma cells through the regulation of ADAR2 mRNA expression.     

HPLC method for determination of DRF-4367 in rat plasma: validation and its application to pharmacokinetics in Wistar rats

A specific, accurate, precise and reproducible high-performance liquid chromatography (HPLC) method was developed for the estimation of DRF-4367, a novel cyclooxygenase-2 inhibitor in rat plasma. The assay procedure involved simple liquid/liquid extraction of DRF-4367 and internal standard (IS, celecoxib) from plasma into dichloromethane. The organic layer was separated and evaporated under a gentle stream of nitrogen at 40 degrees C. The residue was reconstituted in the mobile phase and injected onto a Kromasil KR 100-5C(18) column (4.6 x 250 mm, 5 microm). The mobile phase consisting of 0.01 M potassium dihydrogen ortho-phosphate (pH 3.2) and acetonitrile (40:60, v/v) was used at a flow rate of 1.0 mL/min. The eluate was monitored using an UV detector set at 247 nm. The ratio of peak area of analyte to IS was used for quantification of plasma samples. Nominal retention times of DRF-4367 and IS were 6.6 and 11.2 min, respectively. The standard curve for DRF-4367 was linear (r(2) > 0.999) in the concentration range 0.1-20 micro g/mL. Absolute recovery was >86% from rat plasma for both analyte and IS. The lower limit of quantification of DRF-4367 was 0.1 micro g/mL. The inter- and intra-day precisions in the measurement of quality control samples, 0.1, 0.3, 8.0 and 15.0 microg/mL, were in the range 6.93-9.34% relative standard deviation (RSD) and 0.48-6.59% RSD, respectively. Accuracy in the measurement of QC samples was in the range 91.24-109.36% of the nominal values. Analyte and IS were stable in the battery of stability studies, viz. benchtop, autosampler and freeze-thaw cycles. Stability of DRF-4367 was established for 1 month at -80 degrees C. The application of the assay to a pharmacokinetic study in rats is described.     

Determination of rosuvastatin in rat plasma by HPLC: Validation and its application to pharmacokinetic studies

A specific, accurate, precise and reproducible high-performance liquid chromatography (HPLC) method was developed for the estimation of rosuvastatin (RST), a novel, synthetic and potent HMG-CoA inhibitor in rat plasma. The assay procedure involved simple liquid-liquid extraction of RST and internal standard (IS, ketoprofen) from a small plasma volume directly into acetonitrile. The organic layer was separated and evaporated under a gentle stream of nitrogen at 40 degrees C. The residue was reconstituted in the mobile phase and injected onto a Kromasil KR 100-5C18 column (4.6 x 250 mm, 5 microm). Mobile phase consisting of 0.05 m formic acid and acetonitrile (55:45, v/v) was used at a flow rate of 1.0 mL/min for the effective separation of RST and IS. The detection of the analyte peak was achieved by monitoring the eluate using a UV detector set at 240 nm. The ratio of peak area of analyte to IS was used for quantification of plasma samples. Nominal retention times of RST and IS were 8.6 and 12.5 min, respectively. The standard curve for RST was linear (r2 > 0.999) in the concentration range 0.02-10 microg/mL. Absolute recoveries of RST and IS were 85-110 and >100%, respectively, from rat plasma. The lower limit of quantification (LLOQ) of RST was 0.02 microg/mL. The inter- and intra-day precisions in the measurement of quality control (QC) samples, 0.02, 0.06, 1.6 and 8.0 microg/mL, were in the range 7.24-12.43% relative standard deviation (RSD) and 2.28-10.23% RSD, respectively. Accuracy in the measurement of QC samples was in the range 93.05-112.17% of the spiked nominal values. Both analyte and IS were stable in the battery of stability studies, viz. benchtop, autosampler and freeze-thaw cycles. RST was found to be stable for a period of 30 days on storage at -80 degrees C. The application of the assay to determine the pharmacokinetic disposition after a single oral dose to rats is described.     

Development of a biomarker assay for 3‐indoxyl sulfate in mouse plasma and brain by liquid chromatography/tandem mass spectrometry

This paper describes the development and partial validation of a fast, sensitive and specific ultra‐performance liquid chromatography/tandem mass spectrometric method for the determination of 3‐indoxyl sulfate (3‐IS), an endogenous compound in mammals, in mouse plasma and brain samples. The analytical method involves direct dilution of samples with water and protein precipitation with acetonitrile containing an internal standard, followed by separation of 3‐IS on a MonoChrom C₁₈ column and detected by selected reaction monitoring (SRM) in negative ionization mode using turbo ion‐spray ionization. Due to high endogenous levels of 3‐IS in control mouse plasma and brain, blank guinea pig plasma and brain were used for the preparation of standard curves and quality controls (QCs). The compound of interest was well separated from interference peaks from the matrices with a total runtime of 2.7 min under a gradient condition. The method was partially validated. The linear concentration range was 0.1 to 100 µg/mL in mouse plasma and 10 to 10,000 ng/g in mouse brain. Inter‐assay mean bias and relative standard deviation (RSD) for plasma were in the range of ?4.8% to 3.1% and 2.5% to 3.2%, respectively. Intra‐assay mean bias and RSD for plasma were in the range of ?3.3% to 1.4% and 1.9% to 2.8%, respectively. Inter‐assay mean bias and RSD for brain were in the range of ?1.8% to 3.5% and 1.7% to 8.1%, respectively. Intra‐assay mean bias and RSD for brain were in the range of ?1.7% to 3.9% and 4.1% to 7.3%, respectively. The lower limit of quantitation (LLOQ) for this assay was 0.1 µg/mL for plasma and 10 ng/g for brain. The matrix effect was not observed in both guinea pig plasma and mouse plasma. Copyright © 2009 John Wiley & Sons, Ltd.     

Quantitative determination of ragaglitazar in rat plasma by HPLC: validation and application in pharmacokinetic study

A specific, accurate, precise and reproducible high-performance liquid chromatography (HPLC) method was developed for the estimation of ragaglitazar [(-) DRF 2725, NNC 61-0029], a novel anti-diabetic agent, in rat plasma. The assay procedure involved simple liquid/liquid extraction of ragaglitazar and internal standard (IS, troglitazone) from plasma into ethyl acetate. The organic layer was separated and evaporated under a gentle stream of nitrogen at 40 degrees C. The residue was reconstituted in the mobile phase and injected onto a Kromasil KR 100 - 5C(18) column (4.6 x 250 mm, 5 micro m). Mobile phase consisting of 0.01 M potassium dihydorgen ortho phosphate (pH 3.2) and acetonitrile (30:70, v/v) was used at a flow rate of 1.0 mL/min. The eluate was monitored using an UV detector set at 240 nm. Ratio of peak area of analyte to IS was used for quantification of plasma samples. Nominal retention times of IS and ragaglitazar were 6.9 and 12.2 min, respectively. The standard curve for ragaglitazar was linear (r(2) > 0.999) in the concentration range 0.2-100 micro g/mL. Absolute recovery was >87% from rat plasma for both analyte and IS. The lower limit of quantification (LLOQ) of ragaglitazar was 0.2 micro g/mL. The inter- and intra-day precision in the measurement of quality control (QC) samples, 0.2, 1.0, 5.0 and 50 micro g/mL, were in the range 1.32-3.70% relative standard deviation (RSD) and 1.19-9.39% RSD, respectively. Accuracy in the measurement of QC samples was in the range 94.28-107.45%. Analyte and IS were stable in the battery of stability studies, viz. benchtop, autosampler and freeze/thaw cycles. Stability of ragaglitazar was established for 1 month at -20 degrees C. The application of the assay to a pharmacokinetic study in rats is described.     

Quantitative analysis of active compounds in pharmaceutical preparations by use of attenuated total-reflection Fourier transform mid-infrared spectrophotometry and the internal standard method

A new method is presented for the quantitative analysis of compounds in pharmaceutical preparations Fourier transform (FT) mid-infrared (MIR) spectroscopy with an attenuated total reflection (ATR) module. Reduction of the quantity of overlapping absorption bands, by interaction of the compound of interest with an appropriate solvent, and the employment of an internal standard (IS), makes MIR suitable for quantitative analysis. Vigabatrin, as active compound in vigabatrin 100-mg capsules, was used as a model compound for the development of the method. Vigabatrin was extracted from the capsule content with water after addition of a sodium thiosulfate IS solution. The extract was concentrated by volume reduction and applied to the FTMIR-ATR module. Concentrations of unknown samples were calculated from the ratio of the vigabatrin band area (1321-1610 cm(-1)) and the IS band area (883-1215 cm(-1)) using a calibration standard. The ratio of the area of the vigabatrin peak to that of the IS was linear with the concentration in the range of interest (90-110 mg, in twofold; n=2). The accuracy of the method in this range was 99.7-100.5% (n=5) with a variability of 0.4-1.3% (n=5). The comparison of the presented method with an HPLC assay showed similar results; the analysis of five vigabatrin 100-mg capsules resulted in a mean concentration of 102 mg with a variation of 2% with both methods.     

Ionization enhancement in atmospheric pressure chemical ionization and suppression in electrospray ionization between target drugs and stable-isotope-labeled internal standards in quantitative liquid chromatography/tandem mass spectrometry

The phenomena of ionization suppression in electrospray ionization (ESI) and enhancement in atmospheric pressure chemical ionization (APCI) were investigated in selected-ion monitoring and selected-reaction monitoring modes for nine drugs and their corresponding stable-isotope-labeled internal standards (IS). The results showed that all investigated target drugs and their co-eluting isotope-labeled IS suppress each other's ionization responses in ESI. The factors affecting the extent of suppression in ESI were investigated, including structures and concentrations of drugs, matrix effects, and flow rate. In contrast to the ESI results, APCI caused seven of the nine investigated target drugs and their co-eluting isotope-labeled IS to enhance each other's ionization responses. The mutual ionization suppression or enhancement between drugs and their isotope-labeled IS could possibly influence assay sensitivity, reproducibility, accuracy and linearity in quantitative liquid chromatography/mass spectrometry (LC/MS) and liquid chromatography/tandem mass spectrometry (LC/MS/MS). However, calibration curves were linear if an appropriate IS concentration was selected for a desired calibration range to keep the response factors constant.     

A liquid chromatography–mass spectrometric method for the quantification of azithromycin in human plasma

A liquid chromatographic mass spectrometric assay for the quantification of azithromycin in human plasma was developed. Azithromycin and imipramine (as internal standard, IS) were extracted from 0.5 mL human plasma using extraction with diethyl ether under alkaline conditions. Chromatographic separation of drug and IS was performed using a C₁₈ column at room temperature. A mobile phase consisting of methanol, water, ammonium hydroxide and ammonium acetate was pumped at 0.2 mL/min. The mass spectrometer was operated in positive ion mode and selected ion recording acquisition mode. The ions utilized for quantification of azithromycin and IS were m/z 749.6 (M + H) ⁺ and m/z 591.4 (fragment) for azithromycin, and 281.1 m/z for internal standard; retention times were 6.9 and 3.4 min, respectively. The calibration curves were linear (r² > 0.999) in the concentration ranges of 10–1000 ng/mL. The mean absolute recoveries for 50 and 500 ng/mL azithromycin and 1 µg/ mL IS were >75%. The percentage coefficient of variation and mean error were <11%. Based on validation data, the lower limit of quantification was 10 ng/mL. The present method was successfully applied to determine azithromycin pharmacokinetic parameters in two obese volunteers. The assay had applicability for use in pharmacokinetic studies. Copyright © 2013 John Wiley & Sons, Ltd.     

Bioluminescent quantitation and detection of gene expression during infectious disease

By combining the advantages of RT-PCR with the sensitivity of bioluminescence using the photoprotein aequorin, a bioluminescence assay has been applied to the determination of message regulation during infectious disease. The bioluminescence produced by the aequorin conjugate covers more than seven logs concentration, of which approximately five logs produces a linear relationship between product and bioluminescence signal. Aequorin - based bioluminescent detection protocols for mRNA are sensitive into the attomolar range, which obligate fewer cycles of PCR and avoid the plateau effect traditionally associated with other noncompetitive RT-PCR techniques. Additional advantages of aequorin-based bioluminescence methods are ease of automation, compatibility with microtiter plate format, low cost, and flexibility.     

Development of a microcapillary column for detecting targeted messenger RNA molecules

A capillary column in a rapid-flow system has been developed for detecting targeted messenger RNA (mRNA) molecules. The column has a structure made of two beds-one bed of porous microbeads and one bed of microbeads with a polythymidine base sequence. The targeted eukaryotic mRNA molecules are detected by two-step hybridization (sandwich hybridization) composed of polyadenosine selection of mRNA molecules and formation of a probe-target (targeted mRNA) hybrid. The sandwich hybridization, which is accomplished within 1 h, was tested using synthetic polydeoxynucleotides. Ten picomoles of the targeted polydeoxynucleotide were detected.     

Ribonuclease protection assay on microchip electrophoresis

We describe the potential of microchip electrophoresis with a Hitachi SV1210, which can be used to evaluate the integrity of total RNA, for the analysis of mRNA expression. The ribonuclease (RNase) protection assay was performed by using microchip electrophoresis with cyanine 5 (Cy5) labeled 248-base antisense RNA probe (riboprobe) encoding adipose-type fatty acid binding protein (A-FABP) as the riboprobe. The fluorescence intensity corresponding to the protected RNA fragment increased in a dose-dependent manner with respect to the complementary strand RNA. Results were obtained in 120 s, and the same amount of Cy5-labeled antisense riboprobe as used in the conventional method can be used. Furthermore, 8 times more sensitive detection of mRNA by microchip electrophoresis could be obtained. An obvious increase in the mRNA expression of A-FABP, which is known as a differentiation marker of adipocytes, occurred during the adipocyte differentiation of 3T3-L1 cells. These results clearly indicate the potential of microchip electrophoresis for the analysis of mRNA expression in cells.