Abstract: Ion trap apparatus and methods for efficiently addressing the effects of charge space caused by ion trap overfilling, useful in linear ion traps of mass spectrometers.

Abstract: A method of operating a mass spectrometer having a rod set is provided. The rod set has a first end, a second end opposite to the first end, and a longitudinal axis extending between the first end and the second end.

Abstract: An instrument for performing highly accurate PCR employing an assembly, a heated cover, and an internal computer, is provided. The assembly is made up of a sample block, a number of Peltier thermal electric devices, and a heat sink, clamped together. A control algorithm manipulates the current supplied to thermoelectric coolers such that the dynamic thermal performance of a block can be controlled so that pre-defined thermal profiles of sample temperature can be executed. The sample temperature is calculated instead of measured using a design specific model and equations. The control software includes calibration diagnostics which permit variation in the performance of thermoelectric coolers from instrument to instrument to be compensated for such that all instruments perform identically. The block/heat sink assembly can be changed to another of the same or different design.

Abstract: In various aspects, the present teachings provide labeling reagents and sets of labeling reagents for the relative quantitation, absolute quantitation, or both, of hydroxylated compounds including, but not limited to, hydroxylated ring containing compounds, steroids and sterols. In various aspects, the present teachings also provide methods for the analysis hydroxylated compounds including, but not limited to, hydroxylated ring containing compounds, steroids and sterols my MS/MS methods.

Abstract: Nucleic acid sequences are detected by a multi-step process, involving labeling sample nucleic acid sequences, duplexing the labeled sample with a probe having a coupling element, immobilizing all of the duplexed probe and target sequence and unduplexed probe, separating specifically immobilized nucleic acid from free and non-specifically immobilized nucleic acid, releasing specifically immobilized nucleic acid, and detecting the presence of the sequence of interest by means of the label. The labeled sequence may be characterized by sizing, e.g. electrophoresis. The method provides for a sensitive and rapid means for accurate detection of sequences of interest in a wide variety of situations.

Abstract: A manifold block and valving system using the manifold block are provided, which are used for conducting chemical reagents, solvents, and other fluids. The manifold block includes a "straight-through" common passage in fluid connection with several entry ports, including also a number of projections in the common passage in the vicinity of the entry ports. These projections partially obstruct the fluid flow, causing a turbulence that provides a washing action in those port regions. The manifold may be constructed of a photosensitive glass ceramic such as Fotoceram.TM. which consists of a number of layers which have been processed to form the manifold block, or of other suitable materials such as silicon.

Abstract: A method of testing for the presence or absence of a target sequence in a mixture of single-stranded nucleic acid fragments is disclosed. The method involves reacting a mixture of single-stranded nucleic acid fragments with a first probe which is complementary to a first region of the target sequence, and with a second probe which is complementary to a second region of the target sequence, where the first and second target regions are contiguous with one another, under hybridization conditions in which the two probes become stably hybridized to their associated target regions. Following hybridization, any of the first and second probes hybridized to contiguous first and second target regions are ligated, and the sample is tested for the presence of expected probe ligation product. The presence of ligated product indicates that the target sequence is present in the sample.

Abstract: Method and composition for detecting one or more selected polynucleotide regions in a target polynucleotide. In one embodiment of the invention, a plurality of different-sequence probe pairs are added to a target polynucleotide, where each probe pair includes two polynucleotide probe elements which are complementary in sequence to adjacent portions of a selected one of the target sequences in the target polynucleotide. In each probe pair, one of the probe elements contains a non-polynucleotide polymer chain which imparts a distinctive mobility to the associated probe pair, when the elements in the pair are ligated. The other element in the pair contains a detectable reporter label. After the probe pairs have been allowed to hybridize with the target polynucleotide, the hybridized polynucleotides are treated under conditions effective to ligate the end subunits of target-bound probe elements when their end subunits are base-paired with adjacent target bases.

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: 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: 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: 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: 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.