Abstract: Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.

Abstract: Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.

Abstract: Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.

Abstract: Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.

Abstract: Arrays for genome-wide analysis of methylation are disclosed. IN a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within cpG islands in samples from human, mouse and rat genomes.

Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set.

Abstract: Arrays for genome-wide analysis of methylation are disclosed. IN a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within cpG islands in samples from human, mouse and rat genomes.

Abstract: Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.

Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set.

Abstract: Oligonucleotide analogue arrays attached to solid substrates and methods related to the use thereof are provided. The oligonucleotide analogues hybridize to nucleic acids with either higher or lower specificity than corresponding unmodified oligonucleotides. Target nucleic acids which comprise nucleotide analogues are bound to oligonucleotide and oligonucleotide analogue arrays.

Abstract: The presently claimed invention provides methods, compositions, and apparatus for studying nucleic acids. Specifically, the present invention provides a novel enrichment and labeling strategy for ribonucleic acids. In one embodiment, the invention provides enriching for a population of interest in a complex population by diminishing the presence of a target sequence. In a further embodiment, the invention can be used to reproducibly label and detect extremely small amounts of nucleic acids.

Abstract: A process is provided for labeling with signal amplification a ribonucleic acid (RNA), comprising fragmenting the RNA to form RNA fragments, fixing a first ligand to a terminal phosphate located at least one of the 3′ end and the 5′ end of each of a plurality of the RNA fragments, the terminal phosphate having been released during the fragmentation, and binding a plurality of labeling agents to the first ligand on each of a plurality of the fragments.

Abstract: The invention provides methods for detecting variations in polymorphic sites and/or variations in gene copy number. The methods are particularly useful for analysis of biotransformation genes, such as cytochromes P450.

Abstract: A process is provided for labeling with signal amplification a ribonucleic acid (RNA), comprising fragmenting the RNA to form RNA fragments, fixing a first ligand to a terminal phosphate located at least one of the 3′ end and the 5′ end of each of a plurality of the RNA fragments, the terminal phosphate having been released during the fragmentation, and binding a plurality of labeling agents to the first ligand on each of a plurality of the fragments.

Abstract: The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set.

Abstract: A nucleotide sequence characteristic of Neisseria gonorrhoeae is disclosed. The sequence can be the basis for hybridization type, nucleic acid-based, rapid, in vitro diagnostic assays. The unique nature of the sequence makes it possible to clearly discriminate N. gonorrhoeae from other Neisseria species thus eliminating or substantially reducing the number of false positive readings. A 350 base pair N. gonorrhoeae DNA restriction fragment was cloned after subtractive hybridization to Neisseria meningitidis DNA. In further cloning experiments the sequences adjacent to the original 350 base pair fragment were determined. A portion of this sequence was shown to detect 105 of 106 N. gonorrhoeae strains and no other Neisseria species. In addition to use as detection probes, all or portions of the nucleotide sequence can be used as a ligand for the sandwich capture of N. gonorrhoeae sequences and as primers for in vitro amplification of N. gonorrhoeae sequences.

Abstract: A D-arabinitol dehydrogenase enzyme is disclosed. The enzyme is capable of catalyzing the oxidation of D-arabinitol and substantially incapable of catalyzing the oxidation of D-mannitol and is substantially free of other enzymes capable of oxidizing D-mannitol. Also disclosed are methods for determining D-arabinitol. In one embodiment the method comprises the steps of providing in combination (1) a medium suspected of containing D-arabinitol and (2) a D-arabinitol dehydrogenase enzyme and examining the medium for the product of the oxidation of the D-arabinitol. The enzyme utilized is capable of catalyzing the oxidation of D-arabinitol and substantially incapable of catalyzing the oxidation of D-mannitol. Kits for conducting the present method are also disclosed. The D-arabinitol dehydrogenase in purified form has all of the characteristics of a D-arabinitol dehydrogenase which is obtainable from Candida tropicalis ATCC 750 or Candida shehatae.

Abstract: A nucleotide sequence characteristic of Neisseria gonorrhoeae is disclosed. The sequence can be the basis for hybridization type, nucleic acid-based, rapid, in vitro diagnostic assays. The unique nature of the sequence makes it possible to clearly discriminate N. gonorrhoeae from other Neisseria species thus eliminating or substantially reducing the number of false positive readings. A 350 base pair N. gonorrhoeae DNA restriction fragment was cloned after subtractive hybridization to Neisseria meningitidis DNA. In further cloning experiments the sequences adjacent to the original 350 base pair fragment were determined. A portion of this sequence was shown to detect 105 of 106 N. gonorrhoeae strains and no other Neisseria species. In addition to use as detection probes, all or portions of the nucleotide sequence can be used as a ligand for the sandwich capture of N. gonorrhoeae sequences and as primers for in vitro amplification of N. gonorrhoeae sequences.