Abstract: A process for purifying plasmid DNA from a nucleic acid containing sample comprising plasmid DNA and contaminants, which process comprises a step of contaminant removal, comprising: (a) treating the sample to form a nucleic acid solution having a concentration of monovalent cations; (b) contacting the nucleic acid solution with an ultrafiltration membrane having a molecular weight exclusion limit of at least 30 kDa under conditions in which substantially no gel-layer forms and in which the concentration of monovalent cations is sufficiently high for a time sufficient to remove substantially all RNA and form a retentate containing plasmid DNA; and (c) collecting the retentate.

Abstract: The invention relates to the Slug gene, the replication, transcription or expression products thereof and products related with the regulation of said Slug gene or with the regulation, elimination or degradation of the expression or translation products of same, which can be used in the identification, prevention or treatment of the spread or development of metastasis in cancer patients, such as a patient suffering from a cancer with cancer cells that express the Slug gene.

Abstract: Described are methods of assay design and assay image correction, useful for multiplexed genetic screening for mutations and polymorphisms, including CF-related mutants and polymorphs, using an array of probe pairs (in one aspect, where one member is complementary to a particular mutant or polymorphic allele and the other member is complementary to a corresponding wild type allele), with probes bound to encoded particles (e.g., beads) wherein the encoding allows identification of the attached probe. The methods relate to avoiding cross-hybridization by selection of probes and amplicons, as well as separation of reactions of certain probes and amplicons where a homology threshold is exceeded. Methods of correcting a fluorescent image using a background map, where the particles also contain an optical encoding system, are also disclosed.

Abstract: The disclosure provides methods of generating paired reads in sequencing-by-synthesis process, particularly, in systems with relatively short read lengths (e.g., 15-35bases), such as for example, in single molecule sequencing by synthesis. Several implementations of the methods are provided. Of particular advantage are the methods that permit re-sequencing of the template, which yields lower error rates. The invention further provides methods of using paired reads, for example, for positioning them over repeats or for assembly into large sequences, including whole genome assembly.

Abstract: Disclosed are newly discovered Ras mutations and combinations of mutations, proteins and peptides and fusion proteins containing these mutations, nucleic acid molecules encoding such proteins, peptides, and fusion proteins, and a variety of tools and diagnostic, therapeutic, and screening methods associated with the use of such mutations.

Abstract: The present invention describes reagents and methods for storing and/or processing of biological samples for direct use in PCR and other DNA applications. After storage, the preserved DNA in the samples may then be processed and analyzed by known methods, e.g., PCR. the present invention provides in one aspect, a method for simple and rapid storage and/or processing of nucleic acids, such as DNA, from various sources, including but not limited to body fluids, various solutions, cells, plants, tissues, bacterial cell lysates containing plasmids, etc. The present invention further comprises reagents and methods employing glycols at alkaline pH to process biological samples and make DNA usable in PCR without further sample purification.

Abstract: A method of specifically amplifying desired regions of nucleic acid from a sample is provided. The method uses a plurality of first and second PCR primers, each having a region of fixed nucleotide sequence identical or complementary to a consensus sequence of interest and a region of randomized nucleotide sequence located 5? to, 3? to, anywhere within, or flanking the region of fixed nucleotide sequence; and then amplifying the nucleic acid present in the sample via PCR using the plurality of first and second PCR primers; whereby a subset of the first primers binds to the consensus sequence of interest wherever it occurs in the sample, and a subset of the second primers binds to the sample at locations removed from the first primers such that DNA regions flanked by the first primer and the second primer are specifically amplified.

Abstract: Simultaneous sequencing and quantitation of a nucleic acid analyte in a sample using the same reagents for both assays is achieved by processing a sample containing, or suspected of containing the nucleic acid analyte of interest using a single set of reagents through a plurality of thermocycles to obtain a mixture of labeled polynucleotides which are used for the determination of both sequence information about the target nucleic acid and the amount of target nucleic acid present in the sample. The fragments are separated on the basis of size, for example by electrophoresis, and the label associated with the separated fragments is detected. The positions of the separated nucleic acid fragments are evaluated to obtain information about the sequence of the target nucleic acid analyte, and the intensity of a signal derived from the label associated with one or more of the separated fragments is evaluated to determine the quantity of the target nucleic acid analyte in the sample.

Abstract: Novel full-length cDNAs are provided. cDNA derived from human have been isolated. The full-length nucleotide sequences of the cDNA and amino acid sequences encoded by the nucleotide sequences have been determined. Because the cDNA of the present invention are full-length and contain the translation start site, they provide information useful for analyzing the functions of the polypeptide.

Abstract: Methods for predicting whether or not a patient is likely to experience restenosis after the placement of a bare metal stent are provided. The methods involve detecting and analyzing gene expression patterns of the cellular components of whole blood, where activation of selected genes has been found to be indicative of a high probability of restenosis. The method thus allows the identification, prior to placement of a stent, of patients who are i) likely to experience restenosis, and thus should receive a stent that includes anti-restenosis agents; or ii) unlikely to experience restenosis, and thus should receive a stent without anti-stenosis agents.

Abstract: When a probe medium is spotted on a substrate, a probe can be effectively and stably immobilized on the substrate. The probe medium includes a probe capable of specifically binding to a target substance, a medium containing an organic solvent, and a substance for solubilizing the probe in the organic solvent.

Abstract: A flat plate-shaped probe carrier for carrying probes such as single stranded DNAs, proteins, etc., which are reactive specifically with target substances comprises a plurality of ring bodies arranged substantially in parallel and the external space among the ring bodies is filled with a filler such that the openings of the ring bodies are oriented to the surface of the probe carrier. Each ring body has a region for fixing a probe adapted to be bonded specifically to a target substance on its inner wall. The probe carrier is produced by bundling a plurality of hollow tubular members in parallel, then filling the external space among the bundled hollow members with a filler, and cutting the bundle along a plane intersecting the axial direction of the tubular members. Probes are fixed to the fixing region before or after filling the external space.

Abstract: The method of differentiating beer yeast of the invention is a method which comprises a first step of synthesizing a primer capable of amplifying the linker portion between a base sequence (A) and a base sequence (B) in a novel gene (C) which has the base sequence (B) comprising a portion of yeast chromosome IX linked downstream from the base sequence (A) comprising a portion of the N-terminal end of yeast gene Lg-FLO1, and which includes the base sequences listed as SEQ. ID. Nos. 1-6 of the Sequence Listing; a second step of carrying out a PCR (Polymerase Chain Reaction) using the primer synthesized in the first step and DNA separated from a yeast specimen; and a third step of differentiating whether the yeast is bottom-fermenting yeast or wild yeast, based on the PCR amplification product obtained from the second step.

Abstract: Provided is a method of sensitively detecting nucleic acids in a nucleic acid sample, the method comprising: contacting the sample comprising the nucleic acid with a non-specific nucleic acid binding agent in an electrically conductive fluid medium; contacting the sample comprising the nucleic acid bound to the agent with a nanopore; and applying a voltage to the nanopore and monitoring a current change through the nanopore. The nucleic acid can be sensitively detected because a change in current amplitude through the nanopore is greater than when nucleic aid detection is performed without using an intercalator.

Abstract: Described are methods of assay design and assay image correction, useful for multiplexed genetic screening for mutations and polymorphisms, including CF-related mutants and polymorphs, using an array of probe pairs (in one aspect, where one member is complementary to a particular mutant or polymorphic allele and the other member is complementary to a corresponding wild type allele), with probes bound to encoded particles (e.g., beads) wherein the encoding allows identification of the attached probe. The methods relate to avoiding cross-hybridization by selection of probes and amplicons, as well as separation of reactions of certain probes and amplicons where a homology threshold is exceeded. Methods of correcting a fluorescent image using a background map, where the particles also contain an optical encoding system, are also disclosed.

Abstract: Apparatus and methods for separating different polynucleotide populations in a mixture are provided, wherein different polynucleotides or polynucleotide populations are captured on different solid support. After hybridization, polynucleotides are selectively released from a selected support by altering a physical property of that support. The released polynucleotides can be eluted from a common flow path and isolated.

Abstract: This invention relates to a method of an assay of genomic nucleic acid. Additionally, this invention relates to various methods to detect or screen for designated genetic sequences or portion thereof derived from a biological sample. More particularly, this invention relates to the use of magnetically responsive magnetic particles that function to reversibly bind genomic nucleic acid. A portion of the purified genomic nucleic acid is detected in solution by a variety of methods.

Abstract: The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site.

Abstract: The invention provides mutant SH3-binding protein (SH3BP2) nucleic acids, polypeptides, and agents which selectively bind to the mutant SH3BP2 molecules and which do not bind to the wild type SH3BP2 molecules. Methods for selecting agents which inhibit mutant SH3BP2 expression, as well as diagnostic and therapeutic methods which utilize the mutant SH3BP2 molecules for diagnosing and treating disorders of bone homeostasis, also are provided.

Abstract: The present invention relates to the isolation of gene sequences encoding mammalian cell cycle checkpoints, as well as the expression of the encoded proteins using recombinant DNA technology. The expressed proteins are used to generate specific antibodies and to inhibit the growth of cells. The human checkpoint gene sequences are used as a probe for a portion of the chromosome associated with tumors and other malignancies, as well as growth and/or development deficiencies.