Abstract: The present invention relates to oligonucleotides which hybridize specifically to the cytosine DNA methyltransferase gene of Neisseria gonorrhoeae and distinguish the cytosine DNA methyltransferase gene of N. gonorrhoeae from highly homologous sequences which have been discovered in some strains of other species of the genus Neisseria. The oligonucleotides are useful as primers for the polymerase chain reaction (PCR) amplification of a nucleic acid sequence from the cytosine DNA methyltransferase gene of N. gonorrhoeae and in N. gonorrhoeae amplification/detection assays.

Abstract: The present invention is related to the fields of genetic mapping and genetic identity detection, including forensic identification and paternity testing. This invention is more specifically directed to the use of mass spectrometry to detect length variation in DNA nucleotide sequence repeats (including variants of common alleles), such as microsatellites and short tandem repeats, and to DNA sequences provided as primers for the analysis of DNA tandem nucleotide repeat polymorphisms at specific loci on specific chromosomes.

Abstract: This invention provides methods of (a) diagnosing; (b) determining the stage of; and (c) monitoring the effect of a therapeutic intervention for a renal cell carcinoma in a human subject which comprises detecting the expression of the MN gene. In one embodiment, the method is directed to detection of the renal cell carcinoma known as clear cell carcinoma. In another embodiment, the method is used as a peripheral blood assay. In another embodiment, the method is a polymerase chain reaction assay for amplifying and detecting the presence of the cDNA molecule encoding the MN protein.

Abstract: A method of detection is provided that permits differentiation of each of Bacillus cereus, Bacillus thuringiensis, and Bacillus anthracis from other microorganisms, using oligonucleotide primers for amplification of the target nucleotide sequences characteristic to Bacillus cereus, Bacillus thuringiensis, and Bacillus anthracis, consisting of the oligonucleotide (A) having a nucleotide sequence obtained from SEQ ID NO:1 and containing at least one site that can amplify a nucleotide sequence characteristic to Bacillus cereus, the oligonucleotide (B) having a nucleotide sequence obtained from SEQ ID NO:3 and containing at least one site that can amplify a nucleotide sequence characteristic to Bacillus thuringiensis, and the oligonucleotide (C) having a nucleotide sequence obtained from SEQ ID NO:5 and containing at least one site that can amplify a nucleotide sequence characteristic to Bacillus anthracis.

Abstract: Methods are provided for analyzing DNA of a rare cell in a cell population. In one embodiment, the method involves covering a cell monolayer with a photosensitive material. By illuminating the area over a cell of interest, the material is solidified, permitting manipulation of the underlying cell and/or protection of the cell from DNA-inactivating agents that destroy DNA in other cells in the monolayer. In another embodiment, the monolayer is overlaid with a solid material that becomes soluble when illuminated. By illuminating the area over a cell of interest, that cell can be specifically exposed and DNA from the cell amplified. The methods are particularly useful for analyzing fetal cells found in maternal blood.

Abstract: A method and kit are provided for quantitatively determining the length distributions of the third complementarity determining region (CDR3) of the T cell receptor (TCR) .alpha. and .beta. chains from human lymphocytes in a tissue sample or in the peripheral blood.

Abstract: A method is presented which uses a unique opposite strand joining strategy during PCR of an original DNA to generate a product which, when sequenced with a single sequencing primer yields the sequence of both strands of the original DNA. The PCR primers include 1) a modified oligomer corresponding to the 5' end of a first strand of the DNA to be amplified wherein said modified oligomer includes the reverse complementary sequence to a sequence within said first strand of DNA and a specific PCR priming sequence which will specifically hybridize to a portion of the DNA to be amplified and 2) a second oligomer corresponding to the 5' end of the second strand of the DNA to be amplified and which contains the priming sequence for the second strand of the DNA and will specifically hybridize to a portion of the DNA to be amplified. During PCR an intermediate product is formed where one end of one strand loops around to hybridize to its complement on the same strand.

Abstract: Methods for amplifying target nucleic acid sequences using a nucleic acid polymerase lacking 5' exonuclease activity and a set of oligonucleotide primers. Preferably, a primer array is used. The primer array contains two sets of primers. One set contains at least two complementary primers. The other set contains at least two sense primers. Using the described methods amplification can be carried out under essentially constant environmental conditions without the requirement for exonuclease activity or restriction endonuclease activity.

Abstract: A method for detecting in a biological sample the presence of Lyme-disease causing spirochetes using the polymerase chain reaction (PCR). This method includes the steps of: isolating DNA from the biological sample; amplifying the isolated DNA under hybridizing conditions with a primer pair that targets portions of extrachromosomal linear plasmid gene encoding outer surface protein A (OspA) or outer surface protein B (OspB) of the Lyme-disease causing spirochetes, probing the amplified DNA under hybridizing conditions with a labeled gene probe; and detecting the labeled gene probe that hybridized to the amplified DNA of the Lyme-disease causing spirochetes.

Abstract: The present invention relates to a method for the rapid and reliable detection of drug-induced mutations in the reverse transcriptase gene allowing the simultaneous characterization of a range of codons involved in drug resistance using specific sets of probes optimized to function together in a reverse-hybridization assay.

Abstract: New mutations have been found in the BRCA1 gene. The mutations are located at nucleotide numbers 421-2, 815, 903, 926, 1506, 2034, 2428, 3888, 3904, 4164, 4643, 5053, 5150, 5210, or 5396+40 of the gene sequence of BRCA1. A process for identifying a sequence variation in a BRCA1 polynucleotide sequence is disclosed. The identification process includes allele specific sequence-based assays of known sequence variations. The methods can be used for efficient, and accurate detection of a mutation in a test BRCA1 gene sample.

Abstract: A novel method of primer walking using octamer oligonucleotides to prime DNA sequencing reactions is described. Octamer sequencing is compatible with isotopic and fluorescent sequencing chemistry, reaction conditions are optimized such that the samples can be processed in parallel and the procedures are automated. This strategy is faster than the traditional primer walking sequencing strategy as the existence of a primer library allows immediate access to a primer for the next sequencing reaction, eliminating delays associated with designing and synthesizing gene specific primers. The octamer library is comprised of optimized sequencing primers, such that octamer sequencing yields results equivalent to or better than traditional primer walking.

Abstract: Disclosed and claimed are Lyme disease vaccines and methods for making and using them. The vaccines include a vector containing DNA encoding OspA or an immunogenic fragment thereof or such DNA encoding OspA or an immunogenic fragment thereof which has been modified by substitution, addition, insertion or deletion of one or more nucleotides, whereby the DNA when expressed results in OspA, or an immunogenic fragment thereof, or a polypeptide having the immunological activity of OspA or the fragment thereof.

Abstract: A method determining the number of repeats in a tandem repeat sequence of a nucleic acid target comprises providing an array of nucleic acid probes immobilized at spaced locations on a surface of a support. Each probe of the array has a tandem repeat sequence complementary to that in the target and containing a different number of repeats. When the target is hybridized with the array and forms a perfect match with the probe having the same number of repeats in the tandem repeat sequence, it is not removed by exonuclease treatment and can be detected on the array.

Abstract: A method is described for generating blended nucleic acid ligands containing non-nucleic acid functional units. Specifically, a SELEX identified RNA ligand to the integrin gpIIbIIIa is conjugated to the peptide Gly-Arg-Gly-Asp-Thr-Pro (SEQ ID NO:1). This blended RNA ligand inhibits the biological activity of gpIIbIIIa with high specificity. Also described is a single-stranded DNA ligand to elastase coupled to N-methoxysuccinyl-Ala-Ala-Pro-Val-chloromethyl (SEQ ID NO:3) ketone. This elastase blended nucleic acid ligand inhibits the biological activity of elastase.

Abstract: A method of detecting polymorphisms in the S182 gene by detecting mutations in the S182 gene using selected mismatched PCR primers comprising sequences derived from intronic sequences of the S182 gene is provided. A method of identifying an individual susceptible to late onset Alzheimer's Disease is also provided.

Abstract: This invention relates to methods for making polynucleotides of any desired nucleotide sequence by repeating a series of reactions involving assembly of overlapping oligomers, ligation by DNA ligase, and cleavage with a restriction enzyme that cuts so as to add one or more additional nucleotides to a growing polynucleotide. This invention also relates to combining such a method for polynucleotide synthesis with a step employing localized melting of hybridized DNA oligomers, to synthesize an array of polynucleotides of different, defined nucleotide sequence on a substrate, and to the articles for polynucleotide hybridization so made.

Abstract: Method for detecting Campylobacter by PCR detection of DNA sequence highly conserved between species lari, coli, jejuni and upsaliensis. Speciation between these four is possible as the PCR product is differentially cleaved by restriction endonucleases.

Abstract: Unique DNA sequences are provided which are useful in identifying different pathogenic fungi, such as those which infect grape plants. These unique DNA sequences can be used to provide oligonucleotide primers in PCR based analysis for the identification of fungal pathogens. The DNA sequences of the present invention include the internal transcribed spacer (ITS) of the ribosomal RNA gene regions of particular fungal pathogens, as well as oligonucleotide primers which are derived from these regions which are capable of identifying the particular pathogen.

Abstract: The present invention relates to a method for isolating and cloning receptor DNA sequences. The invention also provides novel DNA sequences encoding a novel somatostatin receptor subtype.

Abstract: The present invention relates to kits and methods for conducting fluorescence based detection assays. The kits are configured in a manner to perform the method so as to reduce or eliminate interfering fluorescence signal.

Abstract: The invention relates generally to the quantitation of virus and viral nucleic acid. The invention relates to methods for quantitating an amount of virus present in a sample, comprising introducing into the sample a composition comprising a genetically tagged viral nucleic acid, isolating said wild type and said tagged nucleic acid, and quantitating said wild type and said tagged nucleic acid. The invention also relates to genetically tagged retroviral nucleic acid comprising a tag sequence, including insertions and deletions.

Abstract: The present invention relates to compositions of thermostable DNA polymerases derived from the hyperthermophilic eubacteria. In particular, the present invention comprises thermostable DNA polymerases from the hyperthermophilic eubacterium known as Thermotoga neapolitana. The present invention provides methods for utilizing naturally-occurring and non-naturally-occurring forms of T. neopolitana DNA polymerase. The T. neopolitana DNA polymerases of the present invention are used in combination with other compounds, including but not limited to pyrophosphatase and DNA polymerases from other thermophilic or hyperthermophilic organisms.

Abstract: Helicobacter pylori known to cause or be a cofactor in type B gastritis, peptic ulcers, and gastric tumors. In both developed and developing countries, a high percentage of people are infected with this bacterium. The present invention relates generally to certain H. pylori proteins, to the genes which express these proteins, and to the use of these proteins for diagnostic and vaccine applications. Specifically, molecular cloning, nucleotide, and amino add sequences for the H. pylori cytotoxin (CT), the "Cytotoxin Associated Immunodominant" (CAI) antigen, and the heat shock protein (hsp60) are described herein.

Abstract: A method of making full-length oligonucleotide arrays provides for the purification of pre-synthesized full-length oligonucleotides from shorter length oligonucleotides and other impurities at the same time the oligonucleotides are deposited on the array. A synthesized mixture that includes desired full-length oligonucleotides and some capped shorter length or "failed" oligonucleotide sequences, is reacted with a linking agent to add a linking group on to the free-end of the full-length oligonucleotides but not the shorter-length oligonucleotides. The resulting mixture is deposited on an array without first separately purifying the mixture to remove the unwanted shorter-length oligonucleotides. After deposition, unbound material, including the shorter length oligonucleotide sequences and other impurities, is removed.

Abstract: Improvements to nucleic acid fingerprinting are disclosed. The method generates profiles of increased fidelity characteristic of the nucleic acids analyzed. Novel primers and other means are taught. Useful products are disclosed.

Abstract: The present invention provides a melt-blown fibrous web with a high degree of weight uniformity. The present invention also provides methods of preparing, processing and using such fibrous webs, as well as products incorporating such fibrous webs.

Abstract: A method and primary pair and kit for the in vitro amplification of nucleic acid using amplification primers in amplification reactions. There is used a pair of primers comprising oligonucleotide sequences complementary to a part of a Direct Repeat sequence of a microorganism belonging to the M tuberculosis complex of microorganisms, whereby hybridization to a Direct Repeat occurs and subsequently elongation of the hybridized primer takes place. The primers are such that elongation in the amplification reaction occurs for one primer in a 5' direction and for the other primer in a 3' direction.

Abstract: The present invention relates to a cDNA probe for human methylenetetrahydrofolate reductase (MTHFR), and its uses. The probe of the present invention may be used for the identification of sequence abnormalities in patients with severe or mild MTHFR deficiency, including cardiovascular patients and patients with neurologic symptoms. A human MTHFR protein which hybridizes to the probe of the present invention may be used for therapy of MTHFR-deficiency patients by biochemical or pharmacological approaches.

Abstract: Disclosed is a method for determining a nucleotide sequence of DNA product amplified by polymerase chain reaction not requiring removal of primers and/or 2'-deoxyribonucleoside-5'-triphosphates and/or derivatives thereof, which comprises reacting ribonucleoside-5'-triphosphates comprising ATP, GTP, CTP, UTP and derivatives thereof and one or more of 3'-deoxyribonucleotide-5'-triphosphates comprising 3'-dATP, 3'-dGTP, 3'-dCTP, 3'-dUTP and derivatives thereof in the presence of an RNA polymerase and a DNA product which has been amplified by polymerase chain reaction and contains a promoter sequence for the RNA polymerase to afford a nucleic acid transcription product, separating the obtained nucleic acid transcription product and determining a nucleic acid sequence from the resluting separated fractions.

Abstract: The present invention discloses hybridization assay probes, amplification primers, nucleic acid compositions and methods useful for detecting Borrelia nucleic acids. Hybridization assay probes and amplification primers that selectively detect Lyme disease-associated Borrelia and distinguish those Borrelia from Borrelia hermsii are disclosed. Other hybridization probes selectively detect Borrelia hermsii and not Lyme disease-associated Borrelia are also described.

Abstract: Integrated microfluidic devices comprising at least an enrichment channel and a main electrophoretic flowpath are provided. In the subject integrated devices, the enrichment channel and the main electrophoretic flowpath are positioned so that waste fluid flows away from said main electrophoretic flowpath through a discharge outlet. The subject devices find use in a variety of electrophoretic applications, including clinical assays, high throughput screening for genomics and pharmaceutical applications, point-or-care in vitro diagnostics, molecular genetic analysis and nucleic acid diagnostics, cell separations, and bioresearch generally.

Abstract: A thermal cycling device comprising a ceramic sample plate, and method of use thereof, is provided.

Abstract: The complete sequence of the canine von Willebrand Factor cDNA and deduced amino acid sequence is provided. The mutation which causes von Willebrand's Disease in Scottish Terriers, Doberman pinschers, Shetland sheepdogs, Manchester terriers and Poodles are also provided. Methods for detecting carriers of the defective vWF gene are also provided.

Abstract: A method for the preparation of optimally fluorescent oligonucleotides wherein fluorescent dye-conjugated nucleotide triphosphates are incorporated into a nucleic acid sequence in a defined repetitive manner which allows for the optimal specific fluorescence of the oligonucleotide. The oligonucleotides of the present invention are useful in the assay of a wide variety of nucleic acid sequences, specifically wherever highly fluorescent nucleic acid probes are desired.

Abstract: A probe-bearing element according to the present invention includes a sheet-like body having a plurality of through holes which each bears a biopolymer probe. The sheet-like body may have a thickness of 100 .mu.m to 2 mm, and may be made of glass, acrylic resin, metal or plastic. Preferably, the size of the through hole is about 10-100 .mu.m in diameter considering the number of samples relative to the size of the element, amounts of probes required for hybridization and the detection sensitivity. The plurality of through holes are preferably arranged in concentric circles or in a spiral.

Abstract: Rapid and cost effective diagnosis of p53 mutations of a sample of patients is achieved by employing a selected plurality of diagnostic tools, in a hierarchy of increasing accuracy and cost per tool, in which each tool detects essentially no false positives. Diagnostic tests that may be included among the plurality of tests selected include, in order of increasing accuracy and cost:(a) immunoassays,(b) analysis of DNA from a patient sample by quantitative amplification of p53 exons using amplification primers complementary to intron regions flanking each exon and examination of the length or quantity of each amplified fragment for nucleotide insertions or deletions relative to the normal p53 gene.

Abstract: Internal Transcribed Spacer (ITS) DNA sequences from the ribosomal RNA gene region are described for different species and strains of Helminthosporium carbonum, Helminthosporium turcicum, Helminthosporium maydis, Cercospora zeae-maydis, Kabatiella zeae and Puccinia sorghi. Specific primers from within these sequences are identified as being useful for the identification of the fungal isolates using PCR-based techniques. Also described is a novel extraction buffer solution for use in isolating DNA from an organism.

Abstract: Methods, devices, apparatus and kits for amplifying and detecting nucleic acid are provided. The apparatus is a one or two-tier thermal cycling device that operates in conjunction with a reaction/detection unit. A sample is loaded into a reaction chamber of the device which is then mated with a detection chamber to form the reaction/detection unit. A first heating element of the thermal cycling apparatus applies a desired temperature to the reaction/detection device to amplify target nucleic acid in the sample. The reaction mixture is then transferred to the detection chamber by the second heating element and amplified target nucleic acid is immobilized on a support in the detection chamber. Microprocessor control controls the heat applied by the second element independently of the heat applied by the first element. A detection system associated with the apparatus detects and analyzes the immobilized amplified nucleic acid target.

Abstract: The present invention pertains to a method for sequencing genomes. The method comprises the steps of obtaining nucleic acid material from a genome. Then there is the step of constructing a clone library and one or more probe libraries from the nucleic acid material. Next there is the step of comparing the libraries to form comparisons. Then there is the step of combining the comparisons to construct a map of the clones relative to the genome. Next there is the step of determining the sequence of the genome by means of the map. The present invention also pertains to a system for sequencing a genome. The system comprises a mechanism for obtaining nucleic acid material from a genome. The system also comprises a mechanism for constructing a clone library and one or more probe libraries. The constructing mechanism is in communication with the nucleic acid material from a genome. Additionally, the system comprises a mechanism for comparing said libraries to form comparisons.

Abstract: This invention provides a method of detecting metastatic thyroid cancer in a subject which comprises detecting circulating thyroid cells in a bodily fluid sample of the subject by obtaining an appropriate nucleic acid sample from the bodily fluid sample of the subject; and determining whether the nucleic acid sample contains a marker sequence. Specifically, this invention provides wherein the marker sequence is mRNA corresponding to the reverse transcript of DNA encoding thyroglobulin. Also, this invention provides wherein the marker sequence is mRNA corresponding to the reverse transcript of DNA encodes thyroid peroxidase. This invention further provides a test kit for performing the above-described method.

Abstract: Methods for simultaneously selecting binding site sequences for multiple DNA-binding proteins are provided. A source of DNA-binding proteins is mixed with oligonucleotide duplexes containing a randomized internal sequence. Bound oligonucleotides are isolated, amplified and analyzed, such as by DNA sequence analysis. The oligonucleotide duplexes are also used to identify and isolate DNA-binding proteins.

Abstract: Methods for determining quantities of nucleic acid sequences in samples undergoing amplification utilize amplification ratio estimates (R*) in operations to accurately perform absolute quantitation even when amplification factors for the target and control sequences undergoing amplification are different, time dependent or vary as a function of starting concentrations of nucleic acid sequences. These operations also take into account conversion efficiencies associated with the conversion of probes upon generation of target or control amplicons, but do not require the explicit calculation of such efficiencies. The operations also recognize that a preferred R* should be determined based on a preferred statistical criterion to improve quantitation. In addition, the use of standard samples having known starting concentrations of target and control sequences therein may enable accurate absolute quantitation without the explicit calculation of amplification ratio estimates.

Abstract: The invention relates to novel modified oligonucleotides which contain at least one 8-azapurine base and form more stable hybridization complexes with nucleic acids; To a process for their preparation, and to their use as inhibitors of gene expression, as probes for detecting nucleic acids, as aids in molecular biology, and as a pharmaceutical or diagnostic agent.

Abstract: Nucleic acid starting material composed of a collection of single stranded nucleic acid molecules is anchored and processed by a direction random printing method to produce a mixture of shorter random size DNA molecules well-suited for achieving substantially uniform global PCR amplification. The processing and global amplification method disclosed is especially useful in conjunction with subtractive hybridization procedures applied, for example, to the study of differential gene expression.

Abstract: Amplification primers and methods for specific amplification and detection of a Campylobacter jejuni and C. coli target are disclosed. The primer-target binding sequences are useful for amplification and detection of C jejuni and C. coli target in a variety of amplification and detection reactions.

Abstract: A method of assay of a specific nucleic acid anticipated in a sample, which comprises:a DNA producing step which involves production of a double-stranded DNA having a promoter sequence for an RNA polymerase and the nucleic sequence of the specific nucleic acid (the specific nucleic acid sequence) downstream from the promoter sequence by using the specific nucleic acid in the sample as a template, andan RNA producing and measuring step which involves production of a single-stranded RNA having the specific nucleic acid sequence by the RNA polymerase and measurement of the single-stranded RNA,wherein the RNA producing and measuring step is initiated by adding at least the RNA polymerase, ribonucleoside triphosphates and a probe which is labeled with a fluorescent intercalative dye and is complementary to the single-stranded RNA to the reaction solution after the DNA producing step, involves measurement of the fluorescence intensity of the reaction solution, and is carried out at a constant temperature, and does

Abstract: Two mutations in the human cardiac actin gene are disclosed which have been associated with idiopathic dilated cardiomyopathy (IDC) in two families. These mutations cosegregate with IDC in the two families. Both mutations affect universally conserved amino acids in domains of actin that attach to Z bands and intercalated discs. Analysis of the cardiac actin gene can be used to determine the presence in a patient of IDC resulting from mutations in this gene. Such analysis is useful in the diagnosis and prognosis of the disease in patients with mutations in this gene.

Abstract: A method for the quantitative monitoring of gene expression without either co-amplification of an added template or use of an endogenous constitutive transcript is provided. The process involves a duplex amplification reaction in which a single set of primers is used to amplify both genomic DNA and expressed mRNA from the same gene sequence. These primers are targeted for sequences flanking the splice junction/intron sequences for the mRNA/DNA respectively. By their use, any suitable nucleic acid amplification technology yields mRNA and DNA amplimers which are distinguishable by length and sequence heterogeneity. These amplimers are present in the final amplification reaction in ratios which are dependent upon the ratios of the expressed mRNA to the DNA in the sample, allowing the quantitation of mRNA in a sample which is normalized to the number of copies of genomic DNA since the genomic DNA acts as the internal quantitation standard, and in effect yields the amount of mRNA per cell.

Abstract: The present invention relates to a novel advantageous process for amplifying nucleic acids using DNA/PNA primers and a temperature-stable polymerase enzyme.