Abstract: The present invention describes methods of detecting a nucleic acid in a sample, based on the use of terminal-phosphate-labeled nucleotides as substrates for nucleic acid polymerases. The methods provided by this invention utilize a nucleoside polyphosphate, dideoxynucleoside polyphosphate, or deoxynucleoside polyphosphate analogue which has a colorimetric dye, chemiluminescent, or fluorescent moiety, a mass tag or an electrochemical tag attached to the terminal-phosphate. When a nucleic acid polymerase uses this analogue as a substrate, an enzyme-activatable label would be present on the inorganic polyphosphate by-product of phosphoryl transfer. Cleavage of the polyphosphate product of phosphoryl transfer via phosphatase leads to a detectable change in the label attached thereon. When the polymerase assay is performed in the presence of a phosphatase, there is provided a convenient method for real-time monitoring of DNA or RNA synthesis and detection of a target nucleic acid.

Abstract: The present invention describes new compositions of matter in the form of labeled nucleoside polyphosphates with four or more phosphates. In addition compositions of nucleoside polyphosphates with four or more phosphates that are substrates for nucleic acid polymerases with enhanced substrate properties and methods of using these nucleoside polyphosphates for nucleic acid detection, characterization and quantification are described. The compositions provided by this invention include nucleoside polyphosphate, dideoxynucleoside polyphosphate, or deoxynucleoside polyphosphate analogues which have colorimetric, chemiluminescent, or fluorescent moieties, mass tags or an electrochemical tags attached to the terminal-phosphate. When a nucleic acid polymerase uses this analogue as a substrate, an enzyme-activatable label would be present on the inorganic polyphosphate by-product of phosphoryl transfer.

Abstract: A method of characterizing a nucleic acid sample is provided that includes the steps of: (a) conducting a DNA polymerase reaction that includes the reaction of a template, a non-hydrolyzable primer, at least one terminal phosphate-labeled nucleotide, DNA polymerase, and an enzyme having 3??5? exonuclease activity which reaction results in the production of labeled polyphosphate; (b) permitting the labeled polyphosphate to react with a phosphatase to produce a detectable species characteristic of the sample; (c) detecting the detectable species; and (d) characterizing the nucleic acid sample based on the detection.

Abstract: Energy transfer dyes, their preparation, and their use as labels in biological systems is disclosed. The dyes are preferably in the form of cassettes which enable their attachment to a variety of biological materials. The dyes and the reagents that can be made from them offer a wide variety of fluorescent labels with large Stokes' shifts enabling their use in a variety of fluorescence applications over a wide range of the visible spectrum.

Abstract: A kit for DNA sequencing comprising a first, second, third and fourth dye terminator molecules, each of the dye terminator molecules comprising a dye molecule, a linker of at least 10 atoms in length and either ddATP, ddCTP, ddGTP or ddTTP as a mono or tri-phosphate and a thermostable DNA polymerase.

Abstract: Method of producing controls for use in gene expression analysis systems such as macroarrays, real-time PCR, northern blots, SAGE and microarrays. The controls are generated either from near-random sequence of DNA, or from inter- or intragenic regions of a genome. Ten specific control sequences are also disclosed. Also presented are methods of using these controls, including as negative controls, positive controls, and as calibrators of a gene expression analysis system.

Abstract: Derivatives of 7-deaza-2?-deoxyguanosine are described. Also described is the use of such compounds in synthesis of nucleic acid polymers and in methods for determining a nucleotide base sequence.

Abstract: A low molecular weight non-entangled polyvinylpyrrolidone for use as a separation media for microchannel electrophoretic separation. The separation media may be used in a system in which multiple samples of small compounds are injected into a single microchannel at time spaced intervals followed by a continuous detection interval.

Abstract: A method for purifying an oligonucleotide that comprises providing an oligonucleotide attached to a substrate, wherein the oligonucleotide contains phosphate protecting groups; contacting the oligonucleotide with a reagent, e.g., an organic amine, that cleaves the phosphate protecting groups from the oligonucleotide without detaching the oligonucleotide from the substrate; isolating the oligonucleotide attached to the substrate from the cleaved phosphate protecting groups; and cleaving the oligonucleotide from the substrate. This method provides crude oligonucleotide mixtures that are easier to purify and from which the desired full-length oligonucleotide product can be isolated in higher yields.

Abstract: Thermostable DNA polymerases both in native form and having single amino acid substitutions and optionally N-terminal deletions are disclosed. These polymerases exhibit a substantial improvement of DNA sequencing performance compared to Taq DNA polymerase. The instant DNA polymerases also possess improved salt tolerance.

Abstract: Exploitation of suitably functionalized heterocyclic molecules, in the design and synthesis of Fluorescence Resonance Energy Transfer (FRET) cassettes and their corresponding dideoxynucleotide terminators culminated into efficient reagents for DNA sequencing. Additionally, these FRET cassettes/terminators, of the present invention, derived from different classes of heterocyclic systems have high potential to be used for general labelling of biological molecules to generate highly sensitized signals. Their preparation, energy transfer efficiency, and use as labels, specifically, in DNA sequencing reactions is disclosed.

Abstract: Systems and methods for acquiring images of biological samples and analyzing contrast features are provided. The present invention may determine whether a contrast feature in a image of a biological example qualifies as a grain (textural feature of interest). The size, intensity of contrast features, or other parameters may be tuned to find contrast features that correspond to features having significance in a given application. In addition, the total number of grains per image, the number of grains per sample, the number of grains per unit area, the area fraction occupied by grains, the ratio of intensity of grains to the intensity of the image, or other suitable characteristics may be determined.

Abstract: Image acquisition and analysis systems and methods are provided. A ray-based approach may be used to process images for cell-based assays. Such cell-based assays may be used to evaluate drugs or other compounds or to perform other biological studies. A scanning laser microscope or other equipment may be used to gather image data from fluorescently-marked cells or other suitable specimens. The rays are radially-oriented with respect to the cell nuclei. Seed points within the nuclei may be identified. The rays may extend outward from the seed points or other suitable ray origins until the rays are terminated according to ray termination criteria. The intensity of the image data that is associated with each of the rays may be analyzed to generate various parameters. For example, a peak intensity of the image data along each ray may be identified. Statistical calculations may be performed.

Abstract: A capillary valve, connector and router where one or more cylindrical fibers, which may be capillaries, plugged capillaries, optical fibers, or the like, including at least one capillary tube are contained in a first bundle of fibers that terminates at a first face. A second cylindrical bundle of fibers also containing one or more fibers including at least one capillary tube terminates in a second face abutting the first face. A fastener or adapter holds the members together with faces in mutually biased alignment. Connection of a plurality of macroscale pumps enables push-pull fluid motion, with routing, in a capillary system formed by a plurality of fibers coupled by switches, connectors and routers. Chemical reactions, separations and analysis may be carried out with microliter volumes or smaller.

Abstract: A method for anchoring oligonucleotides containing multiple reaction sites to a substrate. The substrate can be glass, inorganic or organic polymer, and metal. The reactive group of the substrate can contain electophilic C═C double bonds for a nucleophilic addition, or disulfide for disulfide exchange. The multiple reactive groups contained on the oligonucleotide primer can be, for example, aminoalkyl, sulfhydryl, and thiophosphate groups. The oligonucleotide primer may take the configuration of a gairpin having a loop containing multiple reactive sites. In particular, a method for attaching an oligonucleotide primer to a glass substrate is disclosed that comprises preparing a bromoacetamide derivatized silane glass surface on a glass substrate, and reacting the bromoacetamide derivatized silane glass surface with an oligonucleotide primer containing multiple thiophosphate groups to bind the oligonucleotide primer to the glass substrate.