Abstract: Apparatus are disclosed that thermally cycles samples between at least two temperatures. These apparatus operate by impinging fluid jets onto the outer walls of a sample containing region. Because the impinging fluid jets provide a high heat transfer coefficient between the jet and the sample containing region, the sample containing regions are uniformly cycled between the two temperatures. The heat exchange rate between the jets and the sample regions are substantially uniform.

Abstract: Dibenzorhodamine compounds having the structure ##STR1## are disclosed, including nitogen- and aryl-substituted forms thereof. In addition, two intermediates useful for synthesizing such compounds are disclosed, a first intermediate having the structure ##STR2## including nitrogen- and aryl-substituted forms thereof, and a second intermediate having the structure ##STR3## including nitrogen- and aryl-substituted forms thereof, wherein substituents at positions C-14 to C18 taken separately are selected from the group consisting of hydrogen, chlorine, fluorine, lower alkyl, carboxylic acid, sulfonic acid, --CH.sub.2 OH, alkoxy, phenoxy, linking group, and substituted forms thereof. The invention further includes energy transfer dyes comprising the dibenzorhodamine compounds, nucleosides labeled with the dibenzorhodamine compounds, and nucleic acid analysis methods employing the dibenzorhodamine compounds.

Abstract: A method and system for polynucleotide synthesis are provided which employ solid phase synthesis on a nonswellable porous polystyrene support by phosphoramidite or hydrogen phosphonate chemistries. The polystyrene support gives rise to fewer tritylated failure sequences caused by chain growth from extraneous support sites, and allows lower amounts of monomer reactants to be used to achieve equal or better coupling efficiencies as those achieveable with CPG. The method and system also employ nucleoside intermediates whose exocyclic amines are protected by base-labile groups which permit simultaneous cleavage and deprotection of the completed polynucleotide chain in the presence of the solid phase support. This latter feature allows practical automation of both the synthesis and purification of polynucleotides.

Abstract: A method where the relationship between the observed retention time and the applied carrier gas pressure can be fitted to an expected theoretical relationship and thus enable the retention time on just the precolumn to be precisely derived. This method, used in conjunction with a dual column gas chromatography system having a precolumn, a separation column and programmable pneumatic controls to enable the inlet and midpoint pressures of the system to be independently adjusted, facilitates the use of dual-column backflush techniques without the need for a second detector or for any replumbing in order to connect the first column directly to the detector.

Abstract: A system is provided for carrying out real time fluorescence-based measurements of nucleic acid amplification products. In a preferred embodiment of the invention, an excitation beam is focused into a reaction mixture through a surface, the reaction mixture containing (i) a first fluorescent indicator capable of generating a first fluorescent signal whose intensity is proportional to the amount of an amplification product in the volume of the reaction mixture illuminated by the excitation beam and (ii) a second fluorescent indicator homogeneously distributed throughout the reaction mixture capable of generating a second fluorescent signal proportional to the volume of reaction mixture illuminated by the excitation beam. Preferably, the excitation beam is focused into the reaction mixture by a lens through a portion of a wall of a closed reaction chamber containing the reaction mixture.

Abstract: In a mounting apparatus for an induction coupled plasma generator, a housing assembly has a receptacle with a central opening aligned over a housing wall opening, electrical contact rings in the receptacle, and a gas block with a central aperture aligned with the openings. An outer passage in the gas block receives a plasma forming gas and extends to the central aperture. A mounting assembly has a mounting member with an annular contact ring, a second gas block, and a gas tube and a sample tube extending from the second gas block. The second gas block has an inner passage extending into the gas tube. The mounting assembly removably engages to the housing assembly, with the mounting member on the receptacle, the second gas block in the first gas block, and the rings in contact. The tubes extend to a load coil for the plasma, and the passages align to convey the plasma forming gas into the gas tube.

Abstract: The invention provides uncharged water-soluble silica-adsorbing polymers for suppressing electroendoosmotic flow and to reduce analyte-wall interactions in capillary electrophoresis. In one aspect of the invention, one or more of such polymers are employed as components of a separation medium for the separation of biomolecules, such as polynucleotides, polysaccharides, proteins, and the like, by capillary electrophoresis. Generally, such polymers are characterized by (i) water solubility over the temperature range between about 20.degree. C. to about 50.degree. C., (ii) concentration in a separation medium in the range between about 0.001% to about 10% (weight/volume), (iii) molecular weight in the range of about 5.times.10.sup.3 to about 1.times.10.sup.6 daltons, and (iv) absence of charged groups in an aqueous medium having pH in the range of about 6 to about 9.

Abstract: In a gas chromatograph system having a column with a stationary phase and a carrier gas moving through the column to contact the stationary phase, the system being useful for detecting analytes in a sample, a method and apparatus for predicting the retention times for the analytes under various conditions, the method utilizing the steps of:a) detecting the analytes under a number of sets of given conditions;b) calculating values for various parameters characteristic of the system based on a mathematical model that includes a correction to compensate for the permeability of said column to said carrier gas;c) entering into the model the values for the characteristic parameters and at least one further set of conditions; andd) using the model to predict retention times for conditions other than those of step a;the apparatus composed of a data handling system including a model for predicting retention times at a variety of conditions of operation of the system, the model having a first set of inputs including ret

Abstract: A method based on polymerase chain reaction (PCR) amplification and oligonucleotide ligase assay (OLA) reaction is provided for analyzing complex genetic systems in a single reaction vessel. The method involves simultaneously incubating a sample containing one or more target polynucleotides with PCR primers and OLA probes in a single reaction mixture. The presence of variant polynucleotide sequences in the sample is determined by detecting and identifying the products of the OLA reaction.

Abstract: The presence or absence of an organism in a sample is detected by isolating the organism from the sample by a suitable affinity matrix, releasing the organism from the affinity matrix, rupturing the cells of the organism to release total nucleic acid and hydrolyzing or digesting the total nucleic acid to form mononucleotides or individual free nucleic acid basic and inorganic phosphate to form an analyte solution, and assaying the analyte solution for the at least one presence of free nucleic acid base or inorganic phosphate to thereby determine whether the organism was present in the sample.

Abstract: Apparatus and method for detection of low levels of about 1 ppb of hydrophobic analyte in environmental samples using an enclosed permeable membrane enrichment device and agglutination reaction slide test apparatus.

Abstract: Long wavelength, narrow emission bandwidth fluorecein dyes are provided for detecting spacially overlapping target substances. The dyes comprise 4,7-dichlorofluoresceins, and particularly 2',4',5',7'-tetrachloro-4,7-dichloro-5- (and 6-) carboxyfluoresceins. Methods and kits for using the dyes in DNA analysis are provided.

Abstract: A calorimeter apparatus includes a facility for rapid cooling of a heating vessel therein. A jacket surrounds the vessel wall. A partition member between the jacket and the vessel wall defines an inlet plenum adjacent the jacket and a spatial gap adjacent the vessel wall. Pressurized cooling gas is conveyed into the inlet plenum after termination of heating the vessel. The partition member has a distributed plurality of orifices such that the gas is jetted through the orifices to impingement cool the vessel wall. The gas is discharged from the spatial gap through an outlet plenum at an end wall of the vessel. The plurality of orifices are distributed in a pattern of varying density across the partition member such that uniform cooling of the vessel wall by the jetted gas is effected.

Abstract: A hybridization assay is provided which uses an oligonucleotide probe which includes a fluorescent reporter molecule and a quencher molecule capable of quenching the fluorescence of the reporter molecule. The oligonucleotide probe is constructed such that the probe exists in at least one single-stranded conformation when unhybridized where the quencher molecule is near enough to the reporter molecule to quench the fluorescence of the reporter molecule. The oligonucleotide probe also exists in at least one conformation when hybridized to a target polynucleotide where the quencher molecule is not positioned close enough to the reporter molecule to quench the fluorescence of the reporter molecule. By adopting these hybridized and unhybridized conformations, the reporter molecule and quencher molecule on the probe exhibits different fluorescence signal intensities when the probe is hybridized and unhybridized.

Abstract: Methods of genotyping canines by analysis of polymorphisms in the number of microsatellite DNA repeats are provided. The internal repeat sequence is amplified by the use of specific primers. The number of repeats, and therefore the distance between the primers, is highly variable in a population, thereby providing an allelic marker for the locus. The combined information from multiple loci provides a means of distinguishing individuals, even among inbred dog breeds, for parentage testing, forensic testing and analysis of individuals relatedness.

Abstract: Methods for assigning a quantitative score to the relatedness of aligned polymorphic biopolymer sequences such that small differences between otherwise identical sequences are highlighted are disclosed, including computer systems and program storage devices for carrying out the methods on a computer. Specifically, the methods of the invention comprise the steps of providing a test sequence and a basis set of sequences such that the test sequence and the basis set of sequences are aligned; determining the identity of a monomer unit at a position m in the test sequence; assigning a value of 1 to a local matching probability x.sub.m if the monomer unit at position m in the test sequence matches any members of the basis set at position m, or, assigning a value of between 0 and 1 to a local matching probability x.sub.m if the monomer unit at position m in the test sequence does not match any members of the basis set at position m.

Abstract: Energy transfer fluorescent dyes, reagents incorporating the dyes, kits and methods for using the dyes and reagents are provided. The energy transfer fluorescent dyes include a donor dye which absorbs light at a first wavelength and emits excitation energy in response, the donor dye including a xanthene ring structure having a 4' ring position, an acceptor dye capable of absorbing the excitation energy emitted by the donor dye and fluorescing at a second wavelength in response, and a linker attaching the donor dye to the acceptor dye, the linker having a 4' end which includes a R.sub.1 XC(O)R.sub.2 group where R.sub.1 is a C.sub.1-5 alkyl attached to the 4' ring position of the donor dye, X selected from the group consisting of NH, sulfur and oxygen, C(O) is a carbonyl group, and R.sub.2 includes an alkene, diene, alkyne, a five and six membered ring having at least one unsaturated bond or a fused ring structure which is attached to the carbonyl carbon.

Abstract: Solvents for salt-gradient anion-exchange separation of nucleic acids, especially double-stranded DNA and especially by liquid chromatography, are improved by replacing NaCl as the eluting salt with any of a wide range of alkyl ammonium salts and can be used to elute nucleic acids in strict order of increasing length, with reduced sensitivity to elution temperature and salt concentration. Anion-exchange chromatography with these solvents is well suited for identification of DNA fragments on the basis of size, with greater accuracy, precision, and resolvable size range than often is possible with gel electrophoresis.

Abstract: A class of 4,7-dichlororhodamine compounds useful as fluorescent dyes are disclosed having the structure ##STR1## wherein R.sub.1 -R.sub.6 are hydrogen, fluorine, chlorine, lower alkyl lower alkene, lower alkyne, sulfonate, sulfone, amino, amido, nitrile, lower alkoxy, lining group, or combinations thereof or, when taken together, R.sub.1 and R.sub.6 is benzo, or, when taken together, R.sub.4 and R.sub.5 is benzo; Y.sub.1 -Y.sub.4 are hydrogen or lower alkyl or, when taken together, Y.sub.1 and R.sub.2 is propano and Y.sub.2 and R.sub.1 is propano, or, when taken together, Y.sub.3 and R.sub.3 is propano and Y.sub.4 and R.sub.4 is propano; and X.sub.1 -X.sub.3 taken separately are selected from the group consisting of hydrogen, chlorine, fluorine, lower alkyl carboxylate, sulfonic acid, --CH.sub.2 OH, and linking group. In another aspect, the invention includes reagents labeled with the 4,7-dichlororhodamine dye compounds, including deoxynucleotides, dideoxynucleotides, and polynucleotides.

Abstract: Cloning systems useful for the isolation of recombinant nucleic acid are disclosed in which the recombination of cloning-system nucleic acid and foreign nucleic acid is linked to the expression of a moiety on the surface of a host organism, the moiety being a first member of a binding pair. When recombination occurs between the nucleic acid and the foreign nucleic acid, the moiety is expressed on the surface of the host organism. The isolation of recombinant nucleic acid is then performed by attaching a second member of the binding pair to a solid support and contacting the host organism with the support. When the first member of the binding pair is expressed on the surface of the host organism, the host organism binds to the second member of the binding pair attached to the solid support, thereby selectively isolating those organisms.