Abstract: Method and composition for detecting one or more selected polynucleotide regions in a target polynucleotide. In the method, a mixture of sequence-specific probes are reacted with the target polynucleotide under hybridization conditions, and the hybridized probes are treated to selectively modify those probes which are bound to the target polynucleotide in a base-specific manner. The resulting labeled probes include a polymer chain which imparts to each different-sequence probe, a distinctive ratio of charge/translational frictional drag, and a detectable label. The labeled probes are fractionated by electrophoresis in a non-sieving matrix, and the presence of one or more selected sequences in the target polynucleotide are detected according to the observed electrophoretic migration rates of the labeled probes in a non-sieving medium.

Abstract: A viscous electrophoresis separation medium is disclosed. The medium is formed by a matrix formed by a copolymer composed of hydrophilic polymer segments having selected, substantially uniform segment lengths, and a plurality of hydrophobic polymer segments carried on, and spaced from one another by the hydrophilic polymer segments. Also disclosed is an electrophoresis method which employs the separation medium, and novel copolymers used in forming the medium.

Abstract: A cartridge containing a dry polymer composition carrying trapped biopolymer subunits for use in synthesis of biopolymer chains provides a discrete unit for stepwise supply of subunits, such as protected amino acids, in an automated apparatus for biopolymer synthesis. The composition is swellable in organic solvent to release and supply the subunits to a growing biopolymer chain immobilized on a polymer support. An automated synthesizer uses the cartridges for sequential subunit supply and monitors conductivity of deprotection reagents to control cycling and timing of steps.

Abstract: A fluorescence flow cell having a capillary through which a sample fluid is moved, an optical source that directs an exposing beam of light through the sample fluid, a collector that collects fluorescent light from the exposed region of the sample and directs such collected light to a detector. A beam blocker prevents light that is scattered by the capillary walls from reaching the detector, thereby improving the signal-to-noise ratio of the system. The beam blocker also has a pair of legs that prevent the sample fluid from being exposed by either the exposing light or the collected light outside of the exposing region. The structure of the components enables the various components to be quickly and accurately assembled and enables easy replacement of the capillary.

Abstract: An instrument for capillary electrophoresis has a vertically translatable carrier holding one end of the capillary and an electrode connected to a power supply, and a rotary carousel for presenting containers of sample and buffer solutions to a load position where the end of the capillary and the electrode may be inserted by operating the carrier. The other end of the capillary and a second electrode connected to the power supply are immersed in an outlet buffer reservoir. The instrument has a vacuum supply for providing a relative vacuum over the solution in the outlet buffer reservoir, so simple material may be injected into the capillary either by electromigration or by differential pressure. After injection, the first end of the capillary and the electrode may be immersed in buffer to accomplish electrophoresis. By manipulating the carousel and carrier, multiple samples may be electrophoresed in series.

Abstract: The present invention is directed to improved side spacers for use in slab gel electrophoresis that prevent the formation of channels between the electrophoresis gel and the side spacer and methods employing the side spacer. The improvement consists of forming the side spacer with one or more notches cut into the edge of the side spacer in contact with the gel, such that, when the gel hardens, the side spacer is anchored into the gel, thereby preventing the formation of channels between the side spacer and the gel.

Abstract: A DNA sequencing method for use in sequencing a DNA target sequence up to 300 bases, preferably up to 500 bases or greater in length, by electrophoretically separating a mixture of single-stranded DNA sequencing fragments in a capillary tube. The method employs an aqueous denaturing solution comprising between about 4 and about 7 weight percent linear polyacrylamide molecules having an average molecular weight of between about 20 and about 100 kDa. The low-viscosity of the solution allows rapid loading and reloading of such solution into the capillary tube.

Abstract: A capillary electrophoresis system incorporates an application specific cassette having run buffers and capillary column selected for the specific separation procedure, with buffer reservoirs sealed for storage and shipment. A serving apparatus is provided to accept the cassette and perform the specific electrophoresis procedure until buffer is depleted or the performance of the separation column deteriorates. The serving apparatus comprises liquid transfer apparatus, removable covers for the reservoirs of the cassette, electrodes for establishing voltage potential, and a control system.

Abstract: Sample DNA is analyzed by joining dsDNA sample fragments to labeling moieties having a primer binding sequence, to provide labeled dsDNA. After denaturation of the labeled dsDNA, strands binding to a probe are separated, conveniently using particles and a specific binding pair, followed by amplification of the sample strands and analysis and/or isolation of the amplified strands.

Abstract: A spectrally resolvable set of rhodamine dyes are provided for use in the chain termination method of nucleic acid sequencing. A different rhodamine dye from the group consisting of tetramethylrhodamine, rhodamine X, rhodamine 6G, and rhodamine 110 is attached to the base of each of the dideoxynucleotides used in the sequencing method by way of an alkynylamino linker. Preferably, the labeled dideoxynucleotides are incorporated into the growing DNA chains by Taq DNA polymerase.

Abstract: An automated apparatus is provided which implements a new method of extracting and purifying nucleic acids from cells without the use of centrifugation. In the method, a lysate is created by treating the cells with proteinase K in the presence of a lysis buffer having a high concentration of a salt. The lysate is mixed with a phenol-based solvent system, thereby creating an emulsion. The emulsion is heated to promote phase separation. Similarly, the rate of phase separation is also enhanced by increasing the surface area of the emulsion. Once the phase separation is complete, the lower organic phase is removed and the upper aqueous phase is repeatedly extracted with the phenol-based solvent a preselected number of times, and is finally extracted using chloroform. The remaining aqueous phase is then dialyzed to further purify and concentrate the nucleic acid solution. Two preferred embodiments of apparatus are presented to accomplish this extraction.

Abstract: An electrophoresis apparatus has a gel film cast between two plates and buffer reservoirs at each end of the film with electrodes connectable to an external power supply for providing electromotive force for driving electrophoresis. The reservoirs are configured to wet the ends of the gel film and submerge the electrodes with the apparatus positioned either horizontally or vertically, so gel films can be cast horizontally with sample wells formed in the end of the gel between the plates. Samples may be added to the wells and run into the gel with the apparatus positioned vertically, and the analytical separation may be performed with the apparatus again positioned horizontally, such as in an automatic scanning apparatus.

Abstract: A method of forming a thiohydantoin from an N-protected amino acid. The method employs a uronium or phosphonium compound to activate the terminal carboxyl group of the amino acid and a thiocyanate reagent to cyclize the activated amino acid to the thio-hydantoin. The thiohydantoin can be cleaved from its N-protecting group, for use in C-terminal peptide sequencing. Particularly preferred uronium compounds include salts of 2-chlorouronium. Preferred thiocyanate reagents include trimethylsilyl isothiocyanate and crown ether adducts of metallothiocyanates, such as the 18-crown-6 adduct of KSCN.

Abstract: A time-of-flight mass spectrometer in which sample ions are generated from a target and are focussed into an ion beam that is incident onto a detector. A barrier that defines an aperture in the path of the ion beam is positioned to block ions having an extra large deviation from an average time-of-flight of the ions, thereby improving resolution. The aperture can be adjusted to adjust a tradeoff between sensitivity and resolution. Alternatively, the position of the aperture or the bias on an einzel lens can be adjusted to control this resolution.

Abstract: A polymer composition having a biopolymer subunit entrapped in a swellable polymer matrix is described. The composition may be supplied in a disposable cartridge, for use in delivering a solution of the subunit in an automated biopolymer synthesis operation.

Abstract: A viscous electrophoresis separation medium is disclosed. The medium is formed by a matrix formed by a copolymer composed of hydrophilic polymer segments having selected, substantially uniform segment lengths, and a plurality of hydrophobic polymer segments carried on, and spaced from one another at regular repeating intervals, by the hydrophilic polymer segments. Also disclosed is an electrophoresis method which employs the separation medium, and novel copolymers used in forming the medium.

Abstract: A method and compositions are provided for synthesizing polynucleotides wherein the exocyclic amino groups of 5'-O-protected-2'O-alkylsilyl-adenosine phosphoramidite and 5'-O-protected-2'-O-alkylsilylguanosine phosphoramidite monomers are protected with dialkylformamidine. In a preferred embodiment, the ribonucleoside phosphoramidite monomers are activated with ethylthiotetrazole.

Abstract: A detector cell, having a capillary entrance elbow through which a beam of exposing light can be directed into the bore of a central leg of the detector cell capillary. Ray traces, to determine the effect of the entrance elbow on the beam of exposing light are used to optimize performance of this detector cell. Back ray tracing is implemented to illustrate an optimized embodiment. Forward ray tracing is also illustrated and can be used to determine system performance for a range or choices of a single parameter or for concurrent ranges of choices of a subset of the parameters of the beam of exposing light.

Abstract: An automated system for providing a preselected sequence of chemicals to a reaction. This apparatus includes a track on which a set of cartridges are placed in a preselected order corresponding to an order in which they are to be used in a reaction process. These cartridges are moved past a point at which these chemicals are extracted for use in the process. The chemicals are preferably in liquid form and are contained in containing having a top seal through which a needle can penetrate to extract chemicals for use in the process. These containers preferably contain the aliquot portion needed for the process, thereby providing a mechanism for providing accurate amounts of each chemical to the process.

Abstract: A capillary tube with a charged inner surface for use in capillary electrophoresis and methods. The tube is filled with an electrolyte solution containing 0.05-30% weight/weight of a hydrophilic polymer which is characterized by (A) a molecular weight of 20-5,000 kilodaltons, and (B) a charge between 0.01 and 1.0% as measured by the molar percent of charged monomer subunits to the total polymer subunits, where said charged monomer subunits have the charge opposite to the wall charge at a selected electrophoresis pH.