Fiber-optic evanescent wave biosensor for the detection of oligonucleotides.

An automated optical biosensor system based on fluorescence excitation and detection in the evanescent field of a quartz fiber was used to detect 16-mer oligonucleotides in DNA hybridization assays. A biotinylated capture probe was immobilized on the fiber surface via avidin or streptavidin. The hybridization with fluorescein-labeled complementary strands was monitored in real time by fluorescence detection. The double strands formed by hybridization could be dissociated by chemical or thermal regeneration, allowing one to perform hundreds of assay cycles with the same fiber. The signal loss during longtime measurements, i.e., consecutive hybridization assays, can be described by a single-exponential function. Over more than 200 cycles, the net signal decreased by 50% with a signal variation of 2.4% after correction for this signal loss. By binding the capture probe with the 5'-end to the optical fiber surface, and by using a 50% (w/w) aqueous urea solution for chemical regeneration, the duration of an assay cycle could be reduced to 3 min. By applying longer assay cycles, the detection limit for the hybridization with a complementary fluorescein-labeled oligonucleotide was 2.0 x 10(-13) M (24 fmol). To detect an unlabeled complementary 16-mer oligonucleotide, competitive hybridization assays were performed, resulting in a detection limit of 1.1 x 10(-9) M (132 pmol). Poly-(acrylic acid) 5100 sodium salt and Tween 20 were used in the hybridization buffer to prevent nonspecific binding caused by ionic or hydrophobic interaction. The amount of nonspecific binding of noncomplementary oligonucleotides was in the range of 1-2%, compared with the specific binding in the different hybridization assays.

The influence of buffer composition on separation efficiency and resolution in capillary electrophoresis of 8-aminonaphthalene-1,3,6-trisulfonic acid labeled monosaccharides and complex carbohydrates.

The effect of buffer conditions -- varying in salt type, pH, and concentration -- on the separation of 8-aminonaphthalene-1,3,6-trisulfonic acid (ANTS)-labeled monosaccharides and complex-type carbohydrates was investigated. Different buffer systems for high and low electroosmotic flow conditions were chosen: a phosphate and a citrate background electrolyte, each at pH 2.5, a phosphate buffer, pH 9.0, and a borate buffer at pH 9.5. All buffer systems displayed differences in resolution and selectivity. Phosphate and borate buffer demonstrated the greatest selectivity changes for ANTS-labeled carbohydrates. While separation in the phosphate system relies mainly on differences in the charge-to-mass-ratio, additional selectivity can be achieved with borate complexation of glycoconjugates. The use of borate buffers improved monosaccharide separations whereas complex carbohydrates showed a loss in resolution. The citrate background electrolyte at low pH caused no significant changes in the separation performance. The pH 9.0 phosphate buffer showed a reversed migration order of the ANTS conjugates with a decreased resolution, compared to the pH 2.5 phosphate buffer, due to the strong electroosmotic flow generated under high pH conditions. An ovalbumin-derived oligosaccharide library demonstrates the significance of buffer selectivity for complex carbohydrate separations. The separation in the acidic phosphate and the alkaline borate buffer generates a different pattern and only the combination of both buffer systems allows an appropriate assessment of sample complexity.

Continuous separation of high molecular weight compounds using a microliter volume free-flow electrophoresis microstructure.

A microliter volume free-flow electrophoresis microstructure (µ-FFE) was used to perform a continuous separation of high molecular weight compounds. The µ-FFE microstructure had a separation bed volume of 25 µL and was fabricated from silicon using standard micromachining technology. Laser-induced fluorescence was used to detect the sample components, which were labeled with fluorescein isothiocyanate (FITC) prior to analysis. The continuous separation of human serum albumin (HSA), bradykinin, and ribonuclease A demonstrated that only 25 V/cm was required to isolate HSA from bradykinin and ribonuclease A, while 100 V/cm was needed for the separation of bradykinin from ribonuclease A. Comparison of the observed band broadening with the theoretical variance indicated that dispersion due to the initial bandwidth, diffusion, and hydrodynamic broadening were the main contributors to the band broadening of HSA and bradykinin. However, the band broadening for ribonuclease A could not be sufficiently accounted for using the above contributors. Adsorption was found to be a possible contributor to the overall variance for ribonuclease A. Calculation of the theoretical variance due to Joule heating indicated that broadening due to Joule heating effects was insignificant. This was likely due to the narrow cross-sectional area of the device, which facilitated efficient cooling. Electrohydrodynamic distortion was observed for HSA as it migrated toward the side bed. Studies of the resolution of bradykinin and ribonuclease A as a function of field strength at various sample and carrier flow rates indicated that, for maximum throughput, high field strengths and high flow rates were required. However, no optimal conditions were found. The µ-FFE device has a peak capacity of ∼8 bands/cm, while for a typical separation of proteins using a commercial system, a peak capacity of 10 bands/cm is obtained. Thus, the resolving power of the µ-FFE device is similar to those of conventional systems. The continuous separation of tryptic digests of mellitin and cytochrome c demonstrated the ability to continuously separate more complex mixtures. Finally, modifications were made to the microstructure to facilitate fraction collection, and the fractionation of whole rat plasma was performed. Off-line analysis of the resulting fractions indicated that the complete isolation of serum albumin and globulins was possible using a field strength of 25 V/cm.

Separation of 8-aminonaphthalene-1,3,6-trisulfonic acid-labelled neutral and sialylated N-linked complex oligosaccharides by capillary electrophoresis.

Complex oligosaccharides, both neutral and sialylated, were derivatized with 8-aminonaphthalene-1,3,6-trisulfonic acid (ANTS) and separated by capillary electrophoresis. The derivatization reaction was carried out in a total reaction volume of 2 microliters. The separated peaks were detected by laser-induced fluorescence detection using the 325-nm line of a He-Cd laser. Concentration and mass detection limits of 5 x 10(-8) M and 500 amol, respectively, could be achieved. The limiting step for higher sensitivity is not the detector performance, however, but the chemistry with a derivatization limit of 2.5 x 10(-6) M. Two labelling protocols were established, one with overnight reaction at 40 degrees C and the other with a 2.5-h derivatization time at 80 degrees C. Neutral oligosaccharides could be labelled with either protocol. However, sialylated oligosaccharides hydrolysed when labeled at 80 degrees C. Low nanomole to picomole amounts of oligomannose-type and complex-type oligosaccharide mixtures were derivatized and separated in less than 8 min with excellent resolution using a phosphate background electrolyte at pH 2.5. The linear relationship between the electrophoretic mobility and the charge-to-mass ratios of the ANTS conjugates was used for peak assignment. Further, the influence of the three-dimensional structure of the complex oligosaccharides on their migration behaviour is discussed. The suitability of the ANTS derivatization and the subsequent separation for the analysis of complex oligosaccharide patterns is demonstrated with oligosaccharide libraries derived from ovalbumin and bovine fetuin. For peak assignment the patterns are compared with those of the oligomannose and the complex-type oligosaccharide mixtures.(ABSTRACT TRUNCATED AT 250 WORDS)

Stability measurements of antisense oligonucleotides by capillary gel electrophoresis.

The approach of using antisense oligonucleotides as potential drugs is based on hybridization of a short chemically-modified oligonucleotide with complementary cellular DNA or RNA sequences. A critical question is the stability of chemically modified antisense oligonucleotides in cellular environments. In a model system, resistance against various nucleases was evaluated by capillary gel electrophoresis (CGE). For some of the samples, matrix assisted laser desorption and ionization mass spectrometry (MALDI-MS) was used as an additional analytical tool to perform stability measurements. Using CGE, the enzymatic degradation of single nucleotides from the oligomer can be followed after different incubation times. 10% T polyacrylamide gels give baseline resolution for oligonucleotides ranging between 5 and 30 bases in length. The kinetic influence of a specific nuclease concentration and the antisense oligonucleotide structure on the cleavage reaction are discussed. Also, a simple desalting method to improve the injection efficiency and sensitivity of the method are described. Examples of measurements of chemically modified antisense 19-mers are presented.

Matrix-assisted laser desorption/ionization mass spectrometry: improved matrix for oligosaccharides.

The aim of this article was to study the influence of different matrix molecules on the quality of matrix-assisted laser desorption/ionization mass spectra of oligosaccharides. An important criterion was the sample preparation, i.e. the crystallization process leading to the matrix from which the analytes were desorbed and investigated. Quality criteria were, among others, the resulting molecular peak intensity, the mass resolution, and the suppression of unwanted matrix peak. It was found that a mixture of 2,5-dihydroxy benzoic acid (DHB) and 1-hydroxy isoquinoline (HIC) in a weight ratio of 3:1 was best suited for the analytical investigation of oligosaccharides. In addition, this matrix mixture was found to be quite tolerant against all kinds of buffers, salts, and even additives such as sodium dodecyl sulfate (SDS). Furthermore, we determined the different affinities of the alkaline metals to the carbohydrates and found that cesium and potassium ions ionize oligosaccharides about three times better than sodium ions and therefore have an important influence on the quantum yield.

Determination of acid phosphatase in cultivation medium using asymmetrical flow field-flow fractionation.

Highly glycosylated proteins and proteins larger than 100,000 Da are difficult to analyze in complex media with standard liquid chromatography techniques. Asymmetrical flow field-flow fractionation is a simple bio-compatible method for such analysis which can also be used for on-line monitoring. A method for determination of acid phosphatase (EC 3.1.3.2), molecular weight 1,000,000, produced by a recombinant DNA yeast strain is presented.

An integrated silicon thermophile as biosensor for the thermal monitoring of glucose, urea and penicillin.

A new kind of calorimetric biosensor for the measurement of the heat (molar enthalpy change) of enzymatic reactions is presented. The device operates according to the Seebeck effect, the same principle on which thermocouples are based. The thermopile used in this work consists of an array of p-type silicon/aluminium strips integrated on a thin silicon membrane (5 microns). Its sensitivity is about 1 V output voltage per watt of heating power, corresponding to a temperature resolution in the order of 10(-5) K and a heating power resolution of some tenths of a mu W in the flow system used. Furthermore, this performance is obtained without any control of external temperature because of the high common-mode thermal noise rejection ratio of the thermopile. The universal technique of calorimetry combined with the specificity of biochemical reactions makes this biosensor very versatile, with a broad range of possible applications. Glucose oxidase together with catalase for the determination of glucose, urease and penicillinase for the monitoring of urea and penicillin G, respectively, were immobilized directly onto the back side of the thermopile. The sensor was operated in conjunction with flow injection analysis which, in addition to its traditional advantages, allows preconditioning of the samples. Thus, artefacts due to mixing effects were suppressed and interference caused by differences in ionic strength between sample and carrier was strongly decreased. Detection limits between 1 and 2 mM were reported in the flow injection conditions described.

Laser-based refractive-index detection for capillary electrophoresis: ray-tracing interference theory.

The fringe pattern observed in a far field after a laser beam illuminates a fused silica capillary immersed in a refractive-index matching material and filled with an analyte fluid is exploited to develop a sensitive optical detector for capillary chemical analysis. The inner capillary interface splits the laser beam into a reflected beam fan and a refracted beam fan, which, on overlapping in the far field, lead to interferences. The intensity and the position of the fringes for capillaries with 250 microm >/= i.d. (inner diameter) >/= 25 microm are well reproduced by the presented model. The calculation predicts the fringe pattern for various beam/i.d. geometric configurations and is used to optimize the performance of the nanoliter-picoliter refractive-index on-column detection studied. It is found that the best contrast corresponds to a capillary that is illuminated with a beam waist of omega(0) ~ i.d./12, which is off-center focused with an offset of s ~ i.d./2. For a given interference pattern, the fringes that are found to be more sensitive to Deltan are those that appear near the optical axis but still retain high intensity and contrast. The sensitivity increases approximately linearly with the fringe number, and the maximal fringe number increases proportionally with the i.d.

Characterization of yeast cultivations by steric sedimentation field-flow fractionation.

The characterization and quantification of biomass is often time consuming and dependent on the cultivation media and gives no detailed information between cell size and shape and their productivity. By monitoring the bioprocess with steric sedimentation field-flow fractionation (Sd/StFFF) in combination with laser light scattering, not only cell growth, but also the variation of cell size and shape during the cultivation, can be observed. In this work, the feasibility of separating and characterizing cell populations by steric sedimentation field-flow fractionation is demonstrated by its application to three different yeast cultivation broths. For this purpose samples which were collected at different cultivation times were injected into an FFF system. Fractograms were obtained in less than 4 min. Due to the relatively high resolution of the method, a cell sample could be fractionated in several subpopulations differing in their size as well as in their number of buds.

Flow injection analysis and in-line biosensors for bioprocess control: a comparison.

Miniaturization will unify the different approaches chosen for the application of biosensors in bioprocess control. The most versatile system, which in our opinion is flow injection analysis will be the method of choice for the introduction of biosensors in bioprocess control. A lot of experience will be gained for the future development of miniaturized total chemical analysis systems.

Flow injection analysis and biosensors: applications for biotechnology and environmental control.

Our experience in industrial bioprocess monitoring and environmental control let us develop a concept for biosensor research which distinguishes itself from other, more popular, approaches. Biosensors must improve and/or simplify existing state-of-the-art analysis systems. Only the parallel development of biosensors and their complementary metrology leads to industrially sound solutions. The combination of flow injection analysis with immobilized enzymes in the form of enzyme columns is already used today for the solution of on-line analytical problems in bioprocesses and environmental control.