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D M Kelso

Publications and source records attributed to D M Kelso.

10 recordsLinked to original sources
PubMed2003

Improved sensitivity for solid-support invasive cleavage reactions with flow cytometry analysis.

A new configuration of the solid-support invasive cleavage reaction provides a small reaction-volume format for high-sensitivity discrimination of nucleic acid targets with single nucleotide differences. With target concentrations as low as 2 amol/assay, the solid-support invasive cleavage reaction clearly distinguishes single base mutations. Two oligonucleotides tethered to the solid support hybridize to the target nucleic acid, forming a tripartite substrate that can be recognized and cleaved by Cleavase, a structure-specific 5'-nuclease. Each cleavage event yields fluorescence signal on the surface. When microspheres serve as the solid-support surface, analysis by fluorometer imparts real-time information about change in the reaction signal over time. Flow cytometry provides an alternative detection technology that collects endpoint information about the reaction signal on individual microspheres. A reaction volume of 10 microL with as few as 3000 microspheres is sufficient to distinguish single nucleotide differences at target concentrations less than 200 fM. This sensitivity level is within the range required for analysis of SNPs in genomic DNA. In addition, the flow cytometry format has multiplexing potential, making the microsphere-based invasive cleavage assay attractive for high-throughput genomic applications.

Apolipoproteins E↗
PubMed2001

Analysis of single nucleotide polymorphisms with solid phase invasive cleavage reactions.

Using microparticles as the capture surface and fluorescence resonance energy transfer as the detection technology, we have demonstrated the feasibility of performing the invasive cleavage reaction on a solid phase. An effective tool for many genomic applications, the solution phase invasive cleavage assay is a signal amplification method capable of distinguishing nucleic acids that differ by only a single base mutation. The method positions two overlapping oligonucleotides, the probe and upstream oligonucleotides, on the target nucleic acid to create a complex recognized and cleaved by a structure-specific 5'-nuclease. For microarray and other multiplex applications, however, the method must be adapted to a solid phase platform. Effective cleavage of the probe oligonucleotide occurred when either of the two required overlapping oligonucleotides was configured as the particle-bound reagent and also when both oligonucleotides were attached to the solid phase. Positioning probe oligonucleotides away from the particle surface via long tethers improved both the signal and the reaction rates. The particle-based invasive cleavage reaction was capable of distinguishing the ApoE Cys158 and Arg158 alleles at target concentrations as low as 100 amol/assay (0.5 pM).

Alleles↗
PubMed1999

Real-time measurements of DNA hybridization on microparticles with fluorescence resonance energy transfer.

When capture oligonucleotides are tethered on planar surfaces, mass transport limitations influence the kinetics of solid-phase nucleic acid hybridizations. By diffusion theory, however, hybridization of oligonucleotides on microparticles should be reaction-rate limited. In an initial effort to understand the kinetics of microparticle hybridization reactions, we developed a fluorescence resonance energy transfer method for monitoring oligonucleotide hybridization on microparticles. Microparticles were coated with a fluoresceinated oligomer at surface densities of 20, 40, and 80% saturation, hybridized to a complementary oligonucleotide labeled with tetramethylrhodamine, and monitored over time for quenching of the fluorescein signal as hybridization occurred on the particle surface. Association rate constants were compared for microparticle-based hybridization and solution-phase hybridization. Rate constants for hybridizations on the particle surface were about an order of magnitude less than those for hybridization in solution, but decreasing the surface density of the capture oligonucleotide to 20% saturation improved particle hybridization rates. Although a bimolecular reaction model adequately described solution-phase hybridization kinetics, oligonucleotide hybridization on microparticles did not fit this model but exhibited biphasic reaction kinetics. Based on two different lines of reasoning, we argue that microparticle-based oligonucleotide hybridization was indeed reaction-rate limited in our system and not diffusion-rate limited.

Base Sequence↗
PubMed1999

DNA hybridization on microparticles: determining capture-probe density and equilibrium dissociation constants.

Many DNA-probe assays utilize oligonucleotide-coated microparticles for capture of complementary nucleic acids from solution. During development of these assays, as well as in other particle-based nucleic acid applications, it is useful to know both the amount of duplex formation expected under various experimental conditions and the coating density of the capture oligonucleotide on the particle surface. We examined the simplest form of a DNA-probe microparticle assay: hybridization of a particle-bound capture oligonucleotide to its solution-phase complement. Fluorescein-labeled solution-phase oligonucleotide was hybridized to varying amounts of particles, and the amount of labeled oligonucleotide remaining in solution at equilibrium was measured. We present a simple two-state, all-or-none model for bimolecular hybridization of non-self-complementary sequences that can be used to calculate the equilibrium dissociation constant ( Kd ) from hybridization data. With experimental conditions where both the Kd value and the concentration of capture probe in the reaction are small relative to the concentration of labeled complementary oligonucleotide in the reaction, density of the capture probe on the particle's surface can also be determined. Kd values for particle-based hybridization were different from those obtained from solution-phase thermodynamic parameters. At higher temperatures, hybridization on particles was more efficient than hybridization in solution.

DNA↗
PubMed1995

Assessment of adsorption and adhesion of proteins to polystyrene microwells by sequential enzyme-linked immunosorbent assay analysis.

Originally developed as a method for estimating the solid-phase concentration of an adsorbed protein, sequential enzyme-linked immunosorbent assay (ELISA) analysis (P. A. Underwood and J. G. Steele (1991) J. Immunol. Methods 142, 83-94) is also useful for assessing other aspects of protein-surface interactions without radioactively labeled reagents. The method provides a way to compare protein adsorption on various microwell surfaces and to track adhesion of the protein throughout an assay's wash and incubation steps. In cases where adsorption complies with Langmuir-type binding and protein desorption is minimal, sequential ELISA data can be analyzed with a mathematical model to quantitatively estimate the microwell's protein-binding capacity. Even for protein-surface interactions where the mathematical model is not appropriate, characteristics of sequential ELISA binding data qualitatively differentiate between initial adsorption with subsequent desorption and poor initial adsorption of the protein. Using this method, we analyzed the binding of three proteins (rabbit immunoglobulin G, bovine serum albumin, and horse spleen ferritin) to four types of polystyrene microwell surfaces (Immulons 1, 2, 3, and 4). In addition, we examined differences in protein adhesion to the four surfaces when Tween 20 was omitted from the assay's wash buffer or when fewer washes were used.

Absorption↗
PubMed1995

Estimation of the protein-binding capacity of microplate wells using sequential ELISAs.

A non-linear mathematical method for estimating the protein binding capacity of a microwell is developed by applying Langmuir-type binding principles to data obtained from sequential ELISAs (Underwood and Steele (1991) J. Immunol. Methods 142, 83). Experimental data from sequential ELISAs measuring the binding of rabbit and mouse immunoglobulin G and of BSA to Immulon 2 microwells agree well with the binding curves predicted by our simple mathematical model. Estimates of Immulon 2 microwell capacity for these proteins when coated in a 100 microliters/well volume are between 250 and 325 ng/well. The method provides a convenient, quantitative method for estimating microwell capacity without the use of radioisotopes. A spreadsheet form of the method is also presented, so that the mathematical calculations for any set of experimental data may be performed readily using the spreadsheet's SOLVER function. The method is not applicable to data from experiments where significant desorption occurs or where binding to the solid phase deviates significantly from the simple Langmuir model.

Adsorption↗
PubMed1984

Particle concentration fluorescence immunoassay (PCFIA): a new, rapid immunoassay technique with high sensitivity.

A new solid-phase fluorescence immunoassay technique is described and is exemplified by the detection of murine monoclonal antibodies to human IgG in hybridoma culture supernatants and the detection of murine IgG. The assay is performed in a specially designed 96-well plate. For antibody detection, antigen bound to submicron polystyrene particles is bound to its specific antibody, which is in turn reacted with fluorescein-labeled affinity-purified goat anti-mouse IgG. The reaction is complete in 10 min at ambient temperature. The solid phase is separated from the reaction mixture by filtration, washed and the total particle-bound fluorescence is determined by front-surface fluorimetry. The sensitivity of the technique for antibody detection is equivalent to enzyme-linked immunoabsorbent assay and 2-4 ng/ml for murine IgG detection. It is readily amenable to automation.

Animals↗
PubMed1981

Fluorescence polarization immunoassay. II. Analyzer for rapid, precise measurement of fluorescence polarization with use of disposable cuvettes.

This instrument, developed for quantitating fluorescence polarization immunoassays, automatically measures both polarization components and computes a polarization value corrected for background and optical bias. An electronically switched liquid crystal provides a nonmechanical means of rotating the plane of polarization in the excitation optics. The electronic design features digital integration and microprocessor controlled functions. Readings are made in disposable 12 X 75 mm round culture tubes. in less than 10 s. Results are precise to 0.001 polarization unit, linear from 10(-7) to 10(-10) mol of fluorescein per liter, and correlate well with those obtained with other "high-performance" instrumentation.

Autoanalysis↗
PubMed1981

Fluorescence polarization immunoassay. iii. an automated system for therapeutic drug determination.

A fully automated system for performing fluorescence polarization immunoassay has been developed. Reagents for each assay are contained in coded reagent packs, and no reagent reconstitution is required. A common buffer is used for all assays, minimizing changeover and set-up times for each assay. A single sample may be assayed in 5 min, or 20 samples in 10 min. A single-tube blank subtraction for each sample results in highly precise polarization values and obviates sample interferences. We have used this method for assays of gentamicin, theophylline, phenytoin, and phenobarbital. CVs are 1-4%, and the results correlate well with those by other methods. Because of the instrument design and the stability of the reagents, daily calibration is not required; samples may therefore be run immediately upon receipt or batched as desired.

Autoanalysis↗