Abstract: The invention is directed to a method and device for simultaneously testing a sample for the presence, absence, and/or amounts of one or more a plurality of selected analytes. The invention includes, in one aspect, a device for detecting or quantitating a plurality of different analytes in a liquid sample. The device includes a substrate which defines a sample-distribution network having (i) a sample inlet, (ii) one or more detection chambers, and (iii) channel means providing a dead-end fluid connection between each of the chambers and the inlet. Each chamber may include an analyte-specific reagent effective to react with a selected analyte that may be present in the sample, and detection means for detecting the signal. Also disclosed are methods utilizing the device.

Abstract: The invention is directed to a method and device for simultaneously testing a sample for the presence, absence, and/or amounts of one or more a plurality of selected analytes. The invention includes, in one aspect, a device for detecting or quantitating a plurality of different analytes in a liquid sample. The device includes a substrate which defines a sample-distribution network having (i) a sample inlet, (ii) one or more detection chambers, and (iii) channel means providing a dead-end fluid connection between each of the chambers and the inlet. Each chamber may include an analyte-specific reagent effective to react with a selected analyte that may be present in the sample, and detection means for detecting the signal. Also disclosed are methods utilizing the device.

Abstract: The invention relates to methods and compositions for simultaneously generating a plurality of polynucleotide sequencing ladders or PCR amplification products. Each sequencing ladder is generated from a recoverable primer, i.e., an oligonucleotide primer comprising a recovery tag. The recovery tag may be an oligonucleotide. Each sequencing ladder has a unique recovery tag. After the generation of the multiple sequencing ladders, the different sequencing ladders are separated from one another, i.e., purified, by binding to recovery tag binding compounds that have been immobilized on one or more solid supports. The recovery tag binding compounds are immobilized on the solid support in an addressable manner, i.e., the recovery tag binding compounds have distinct locations on the solid support. The binding of the sequencing ladders to the recovery tag binding compounds serves to separate the different polynucleotide sequencing ladders present in a given solution.

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 dibenzorhodarnine compounds, and nucleic acid analysis methods employing the dibenzorhodamine compounds.

Abstract: The present invention relates to assays for the detection of nucleotide bases at predetermined locations on polynucleotides of interest. The embodiments of the invention include techniques relating to methods in which a primer extension reaction is designed to only extend a single nucleotide base. The invention, in part, relates to the improvement of adding corresponding non-labeled chain terminators to a primer extension reaction so as to increase the accuracy and reliability of nucleotide base determinations made by the assay. The invention is particularly useful when applied to assay methods in which the primer extension reaction is detected by a fluorescent dyes conjugated to chain terminators incorporated in the extension reactions. A first embodiment of the invention relates to methods for identifying a nucleotide base at the predetermined location on a polynucleotide of interest.

Abstract: A method for typing HLA class 1 genes. The method entails first contacting a sample DNA with first and second amplification primers, wherein the first and second primers are each at least partially located in an exonic region. Next, using the first and second primers, a target sequence is amplified by the PCR to form an amplicon of the target sequence. Finally, the amplicon is detected with a sequence-specific detection means, e.g., DNA sequencing. The invention also includes specific amplification primers, specific sequencing primers, and kits especially adapted for use with the above HLA typing method.

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.

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: 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.

Abstract: A set of 4,7-dichlororhodamine compounds useful as fluorescent dyes are disclosed having the structures ##STR1## wherein R.sub.1 -R.sub.6 are hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, sulfonate, sulfone, amino, amido, nitrite, lower alkoxy, linking group, 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; R.sub.7 -R.sub.10, R.sub.12 -R.sub.16 and R.sub.18 may be hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, sulfonate, sulfone, amino, amido, nitrite, lower alkoxy, linking group; R.sub.11 and R.sub.17 may be hydrogen, lower alkyl, lower alkene, lower alkyne, phenyl, aryl, linking group; Y.sub.1 -Y.sub.4 are hydrogen, lower alkyl, or cycloalkyl, or, when taken together, Y.sub.1 and R.sub.2, Y.sub.2 and R.sub.1 Y.sub.3 and R.sub.3, and/or Y.sub.4 and R.sub.4 is propano, ethano, or substituted forms thereof, and X.sub.1 -X.sub.

Abstract: The invention provides an asymmetric cyanine dye compound having the structure ##STR1## including substituted forms thereof, wherein, at least one of R.sub.1 and R.sub.2 is linking group, X is O, S, or Se, and n ranges from 0 to 2. The invention further provides reporter-quencher dye pairs comprising the asymmetric cyanine dyes, dye-labeled polynucleotides incorporating the asymmetric cyanine dyes, and hybridization detection methods utilizing the dye-labeled polynucleotides.

Abstract: In a mass spectrometer, an ion source in combination with an accelerator comprising an electron source, a gate electrode constructed so as to block the flow of electrons from the source when a potential is applied, a sample introduction means for transporting carrier gas containing analytes, an ionization chamber positioned to receive the flow of electrons and the carrier gas, wherein the flow of electrons ionizes the carrier gas, a pulsed accelerator, and an ion transfer region situated so that the ionized carrier gas travels from the ionization chamber, through the ion transfer region and into an accelerator. The gate electrode and the pulsed accelerator are controlled in a timed relationship to control the amount off carrier gas being ionized and traveling into the accelerator between accelerator pulses so as to improve the dynamic range of the mass spectrometer and to selectively accelerate a particular mass range.

Abstract: The invention relates the discovery that the polymorphisms in 16S rRNA genes may be used to identify unknown bacterial isolates at the level of species, subspecies and strain identification. The invention also relates to the discovery that the sequences of individual are required. The invention involves the generation of composite polynucleotide sequence of the 16S rRNA genes of a microorganism of interest. The invention is to provide methods for identifying microorganisms. The methods comprise the steps of generating a composite 16S rRNA region sequence from a microorganism of interest. The composite 16S rRNA region sequence reveals polymorphisms within the 16S ribosomal RNA gene of the microorganism. The composite 16S rRNA region sequence may then be compared with a list of previously obtained composite 16S rRNA region sequences from reference microorganisms so as to determine the species, subspecies, or strain of the microorganism of interest.

Abstract: A novel class of compounds, exemplified by oligomers comprised of purine, pyrimidine, and other nucleobase monomers are disclosed. The nucleobase oligomers hydrogen bond through Watson/Crick base pairing to complementary nucleic acids, such as DNA and RNA, in an opposing strand. Each internal nucleobases in the oligomer has two attachment sites and is attached to two nucleobases by linkers. Terminating groups may contain reactive functionality, labels, reporters, or nucleic acids. The nucleobase oligomer compounds are useful as sequence specific recognition molecules for complementary nucleic acids. Where the molecule consists of sections of nucleobase oligomer and nucleic acid, the chimera may be an enzyme substrate in cleavage, ligation, and primer extension methods such as PCR and DNA sequencing.

Abstract: A capillary electrophoresis system and method of electrokinetically loading a capillary electrophoresis sample into a separation medium in a capillary tube in which an entangled polymer matrix is formed having the sample embedded therein. The matrix has a mesh size effective to retard movement of macromolecules such as DNA sequencing templates through the matrix when an electric field is applied across the matrix. The entangled polymer matrix is formed by a linear polymer having a molecular weight of at least 20K Daltons. Furthermore, the invention includes stable denaturants useful for the electrophoresis of nucleic acids.

Abstract: Dibenzorhodamine compounds having the structure ##STR1## are disclosed, including nitogen- and aryl-substituted forms thereof. In addition, intermediates useful for synthesizing such compounds are disclosed, such intermediates having the structure ##STR2## In Formula I, R.sub.1 is H or ##STR3## wherein Y is H, lower alkyl, lower alkene, lower alkyne, aromatic, phenyl, polycyclic aromatic, heterocycle, water-solubilizing group, or linking group, including substituted forms thereof. When R.sub.1 is H, the C-12-bonded nitrogen and the C-12 and C-13 carbons form a first ring structure having from 4 to 7 members, and/or the C-12-bonded nitrogen and the C-11 and C-12 carbons form a second ring structure having from 5 to 7 members. The compounds of Formula I further include aryl- and nitrogen-substituted forms thereof.

Abstract: The invention relates to novel chimeric phosphoramidate oligonucleotides and their use in primer-extension methods such as DNA sequencing and nucleic acid amplification. The subject chimeric phosphoramidate oligonucleotides have both N3'-phosphoramidate linkages and phosphodiester linkages. The invention includes methods of primer extension using the subject chimeric oligonucleotides as primers. Primer extension methods of interest include nucleic acid amplification reactions, e.g. PCR, and polynucleotide sequencing reactions. In the primer extension methods of the invention, a chimeric phosphoramidate oligonucleotide primer is annealed to a polynucleotide template. After annealing, the chimeric oligonucleotide primer is extended by joining a nucleotide to the 3' end of the primer by a DNA polymerase catalyzed reaction. Other embodiments of the invention include methods of primer extension using phosphoramidate linkage containing polynucleotide templates.

Abstract: A system for separating certain ions from an ion beam in a mass spectrometer. A magnetic or electrostatic field is applied at an angle to the ion beam, causing the ions to disperse according to their mass to charge ratio. The ions are dispersed enough to allow certain ions to be blocked and removed from the beam using a physical stop. A subsequent plurality of fields is then applied to reform the beam and adjust its direction and dispersion.

Abstract: A data collection method for scanning a scan window comprising one or more channels is described. In the method of the invention an integrated signal (S) is measured across a scan window including one or more channels using an integrating detector. Next, a velocity-normalized integrated signal (Sn) is determined based on the integrated signal (S) and a scan velocity.

Abstract: Apparatus and method for performing a nucleic acid amplification reaction and preferably a polymerase chain reaction (PCR) in a reaction mixture in at least one capillary tube. Several different embodiments are disclosed. One embodiment cycles a sample through a capillary tube loop passing through two thermostatted fluid baths. Another embodiment has the capillary tube routed alternatingly between two heat exchangers to that the sample makes only one pass through the tube. Other embodiments maintain the heat exchangers stationary and translate the samples between them. Still further embodiments maintain the samples stationary and either automatically translate or rotate the heat exchangers past the samples contained within the capillary tubes to perform the thermal cycles necessary for the amplification reaction.