Abstract: A method is provided for mutagenizing nucleic acids and proteins relative to an initial target nucleic acid sequence by the insertion, deletion, or substitution of one or more oligonucleotides during amplification.

Abstract: The present invention provide methods and an apparatus for performing amplification and other enzymatic reactions on nucleic acid molecules that have been printed onto a solid substrate, such as a silicon wafer or glass slide.

Abstract: Specific sequences in the human genome are the sites of strong binding of wild-type p53 protein, but not mutant forms of the protein. These sequences are used diagnostically to detect cells in which the amount of wild-type p53 is diminished. The sequences can also be used to screen for agents which correct for loss of wild-type p53 to DNA in cancer cells.

Abstract: Methods for reducing degradation of polymerase extension products in the presence of formamide, where the polymerase extension products comprise a nonradioactive detection moiety, are disclosed. The methods comprise adding a base, a buffer or a reducing agent to the polymerase extension products. Sequencing methods which generate polymerase extension products comprising a nonradioactive detection moiety are also disclosed, wherein the degradation of the extension products is reduced or eliminated by the addition of a base, a buffer, or a reducing agent. Compositions for reducing degradation of the above polymerase extension products are also disclosed, where the compositions comprise a base, a buffer, or a reducing agent. Kits for performing sequencing methods are also disclosed, wherein the degradation of polymerase extension products is reduced or eliminated. The kits comprise a base, a buffer, or a reducing agent, and instructions.

Abstract: Nucleotide triphosphate probes containing a fluorophore attached to the &bgr;-phosphate and a quencher moiety sufficiently proximal to the fluorophore moiety for use in pyrophosphate detection assays are disclosed. These probes exhibit distinguishable fluorescence characteristics when the fluorophore is attached to the nucleotide through the &ggr;-phosphate and when it is unattached to the nucleotide. The present invention also provides kits and integrated systems for practicing the assays described herein.

Abstract: Human coronary heart disease susceptibility gene (CHD1), some alleles of which are related to susceptibility to coronary heart disease. Germline mutations in the CHD1 gene and their use in the diagnosis of predisposition to coronary heart disease and to metabolic disorders, including hypoalphalipoproteinemia, familial combined hyperlipidemia, insulin resistant syndrome X or multiple metabolic disorder, obesity, diabetes and dyslipidemic hypertension. Presymptomatic therapy of individuals who carry deleterious alleles of the CHD1 gene (including gene therapy, protein replacement therapy, and administration of protein mimetics and inhibitors). The screening of drugs for dyslipidemic therapy.

Abstract: The present invention relates to a thermostable DNA polymerase-associated factor capable of enhancing DNA synthesizing-activity of a DNA polymerase; a thermostable DNA polymerase-associated factor possessing an activity of binding to a DNA polymerase and a method for producing the same; a gene encoding the DNA polymerase-associated factor; a method of DNA synthesis by using a DNA polymerase in the presence of the DNA polymerase-associated factor; and a kit comprising the DNA polymerase-associated factor. According to the present invention, there can be provided in vitro DNA synthesis and a DNA amplification system which are more excellent than conventional techniques by utilizing the DNA polymerase-associated factor of the present invention.

Abstract: The present invention provides a method of identifying a base at a target position in a single-stranded sample DNA sequence wherein an extension primer, which hybridizes to the sample DNA immediately adjacent to the target position, is provided and the sample DNA and extension primer are subjected to a polymerization reaction in the presence of a deoxynucleotide or dideoxynucleotide, whereby the deoxynucleotide or dideoxynucleotide will only become incorporated and release pyrophosphate if it is complementary to the base in the target position. Release of pyrophosphate is detected enzymatically and pyrophosphate detection enzyme(s) are included in the polymerization step.

Abstract: After a photoresist (2) is used to fix a biological sample, in order to obtain a particular biological substance, for example, a certain cell or biopolymer, from the biological sample embedded in the photoresist (2), properties of the photoresist are changed by exposing the portion of the photoresist (2) that covers the biological substance to light L which has an appropriate wavelength. The biological substance embedded in the changed photoresist is collected.

Abstract: The present invention relates to a method of detecting genetic variation in individuals by PCR amplification of the locus of interest, transferring the resulting PCR products to a membrane filter, hybridizing with allele-specific-oligonucleotides (ASOs), and visualizing the results. Such a method is in the field of diagnostics, pharmacogenetics, cancer therapeutics, and drug metabolism. In particular, the present invention relates to the detection of genetic polymorphisms in gene encoding xenobiotics metabolizing enzymes CYP1A1, CYP2D6, CYP3A4, and NAT2.

Abstract: An electrode and method of preparing an electrode by electropolymerizing a film on the conductive working surface of an electrode. The electrode is modified by reductive electropolymerization of a thin film of poly[Ru(vbpy)32+] or poly[Ru(vbpy)32+/vba] (vbpy=4-vinyl-4′methyl-2,2′-bipyridine and vba=p-vinylbenzoic acid) and the electrode is used for the electrochemical detection of aqueous GMP, poly[G], and surface immobilized single-stranded DNA probes. The film is formed from a co-polymer of a mediator such as Ru(vbpy)32+ and a functionalized moiety having a carboxylate group such as p-vinylbenzoic acid. A DNA probe is attached covalently to the carboxylate group via a carbodiimide reaction followed by amidation of an amino-linked single-stranded DNA.

Abstract: The subject invention is a series of methods and systems for using the Surface-Enhanced Raman (SER)-labeled Gene Probe for hybridization, detection and identification of SER-labeled hybridized target oligonucleotide material comprising the steps of immobilizing SER-labeled hybridized target oligonucleotide material on a support means, wherein the SER-labeled hybridized target oligonucleotide material comprise a SER label attached either to a target oligonucleotide of unknown sequence or to a gene probe of known sequence complementary to the target oligonucleotide sequence, the SER label is unique for the target oligonucleotide strands of a particular sequence wherein the SER-labeled oligonucleotide is hybridized to its complementary oligonucleotide strand, then the support means having the SER-labeled hybridized target oligonucleotide material adsorbed thereon is SERS activated with a SERS activating means, then the support means is analyzed.

Abstract: The present invention is based on the discovery and cloning of the human small conductance calcium activated potassium channel type 3 (hKCa3/KCNN3) gene, which is expressed in neuronal cells, skeletal muscle, heart, and lymphocytes. Alterations in the hKCa3/KCNN3 gene or its protein product may enhance susceptibility to schizophrenia and/or bipolar disorder. hKCa3/KCNN3 may be involved in neuropsychiatric, neurological, neuromuscular, and immunological disorders. Substantially purified hKCa3/KNN3 polypeptides and polynucleotides are provided. Antibodies which bind to hKCa3/KCNN3 polypeptides are also disclosed. A method for identifying a compound which affects hKCa3/KCNN3 polynucleotide or polypeptide is provided. A method for diagnosis and determining the prognosis and treatment regimen of a subject having or at risk of having a hKCa3/KCNN3-associated disorder is also provided.

Abstract: Genetic markers associated with programmed cell death were characterized and their extent of polymorphism in normal populations was determined allowing for a method for determining genetic predisposition to SLE and other autoimmune diseases by genotyping. The allelic distribution of these gene markers in a large Mexican American SLE cohort and ethnically matched controls was determined. The results were that bcl-2, Fas-L, and IL-10 loci showed significantly different allelic distribution in SLE patients compared with controls, indicating an association between these gens and SLE. The method allows for determining the presence of these alleles. Alone, the presence of each of these alleles is associated with a moderate increase in SLE risk, while the occurrence of these alles together increases the odds of developing SLE by more than 40-fold.

Abstract: This invention discloses methods for detecting specific nucleic acid sequences, interrogating the identity of a specific base within a sequence, and assaying endonuclease and exonuclease activity. DNA or RNA probes are hybridized to target nucleic acid sequences. Probes that are complementary to the target sequence at each base are depolymerized, while probes which differ from the target at the interrogation position are not depolymerized. The nucleic acid detection systems utilize the pyrophosphorolysis reaction catalyzed by various polymerases to produce deoxyribonucleoside triphosphates or ribonucleoside triphosphates. dNTPs are transformed to ATP by the action of NDPK. The ATP produced by these reactions is detected by luciferase or NADH based detection systems.

Abstract: The present invention relates to genetic mutations in mitochondrial genes that segregate with diabetes mellitus. The invention provides methods for detecting such mutations, as a diagnostic for diabetes mellitus, either before or after the onset of clinical symptoms. Examples of specific mutations in the mitochondrial ATP synthase 8/6 gene and tRNA lysine gene are given. The invention also provides treatments for dysfunctions due to mitochondrial genes that segregate with diabetes mellitus. Cybrid cell lines are described which are useful as model systems for the study of the mitochondrial metabolic disorders that are associated with diabetes mellitus, and for identifying therapeutic compounds and treatments for this disease.

Abstract: The present invention relates generally to the field of diagnostics. More particularly, it concerns the use of methylation-specific PCR in order to identify those males having Fragile X syndrome. The present invention provides a method in which amplification specific for the methylated FMR1 sequence is observed in all individuals with a full mutation, while all normal and premutation individuals show only amplification specific for the unmethylated sequence, thus allowing affected and unaffected males to be distinguished. A full mutation in the presence of mosaicism also may detectable by this method. Thus, methylation-specific PCR is demonstrated as a rapid and reliable tool for the diagnosis of fragile X.

Abstract: A method of detecting a nucleic acid (e.g., DNA, RNA) that contains at least one preselected base (e.g., adenine, guanine, 6-mercaptoguanine, 8-oxo-guanine, and 8-oxo-adenine) comprises (a) reacting the nucleic acid with a transition metal complex capable of oxidizing the preselected base in an oxidation-reduction reaction; (b) detecting the oxidation-reduction reaction; and (c) determining the presence or absence of the nucleic acid from the detected oxidation-reduction reaction at the preselected base. The method may be used in a variety of applications, including DNA sequencing, diagnostic assays, and quantitative analysis.

Abstract: A method for synthesizing a nucleic acid molecule comprising at least one non-canonical nucleoside triphosphate using a mutant polymerase having a reduced discrimination between canonical and non-canonical substrates is disclosed. The method comprises incubating a template nucleic acid in a reaction mixture comprising the mutant nucleic acid polymerase and the appropriate canonical and non-canonical nucleoside triphosphates which are desired substrates for the mutant nucleic acid polymerase. The present invention is also a method of determining the sequence of a nucleic acid molecule using the mutant polymerase to create a nucleic acid molecule comprising at least one non-canonical nucleoside triphosphate.

Abstract: This invention provides methods for the discovery of molecules that target an essential aspect of eukaryotic gene expression--the formation of the mRNA 5' cap m7GpppN. An underlying principle of this invention is the use of a different strains of a test organism that differ only in the composition or source of the essential cap-forming enzymes. The invention provides isogenic yeast strains that derive all their capping activities from fungal sources versus mammalian sources. These strains form the basis of a differential growth inhibition assay to identify molecules that specifically target the fungal capping apparatus. This invention also provides a method to screen in vitro for molecules that inhibit fungal RNA triphosphatase, an essential enzyme that catalyzes the first of three steps in cap synthesis.