Abstract: The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei.

Abstract: It has been discovered that any RNA can be targeted for cleavage by RNAase P from eukaryotic cells, for example, human RNAase P, using a suitably designed oligoribonucleotide ("external guide sequence", or EGS) to form a hybrid with the target RNA, thereby creating a substrate for cleavage by RNAase P in vitro. The EGS hydrogen bonds to the targeted RNA to form a partial tRNA like structure including the aminoacyl acceptor stem, the T stem and loop, and part of the D stem. The most efficient EGS with human RNAase P is the EGS in which the anticodon stem and loop was deleted. Modifications can also be made within the T-loop. Methods are also disclosed to randomly select and to express a suitable EGS in vivo to make a selected RNA a target for cleavage by the host cell RNAase P, thus preventing expression of the function of the target RNA. The methods and compositions should be useful to prevent the expression of disease-causing genes in vivo.

Abstract: A process for the categorization of nucleic acid sequences in which said sequences are linked to a population of adaptor molecules each exhibiting specificity for linking to a sequence including a predetermined nucleotide base, categorization of the resulting linked sequences being based upon selection for the base.

Abstract: A process for detecting the presence or absence of a specific nucleic acid sequence or antibody in a sample using an oligonucleotide to bind to the nucleic acid sequence or antibody to be detected, forming double-stranded nucleic acid sequence using the bound oligonucleotide in conjunction with another oligonucleotide or DNA synthesis, synthesizing RNA transcripts from the thus-formed double-stranded nucleic acid sequence, and detecting the existence of the RNA transcripts, and oligonucleotides and kits useful in carrying out such a process.

Abstract: The present invention provides compositions, methods and kits for the detection of genetic polymorphisms or mutations related to Charcot-Marie-Tooth Disease Type 1B. The polymorphism or mutations generally occur in the protein P0 gene in chromosome 1. Also provided are mutant forms of protein P0 and methods for screening compounds to identify compounds that enhance binding between mutant P0 proteins.

Abstract: The present invention provides a novel method for labeling and sequencing nucleic acid molecules, particularly DNA molecules in which an internally labeled, partially extended primer is elongated in a cycled primer extension reaction. An unlabeled DNA primer is contacted with a DNA template in the presence of suboptimal amounts of four dNTPs, one of which is labeled with a detectable marker which may be a fluorescent or visible fluorophor, and infared fluorophor or a radioactive label. This small, labeled primer extension product is then transferred to a new reaction where chain terminated primer extension products for DNA analysis are prepared.

Abstract: The subject invention disclosed herein is a new gene probe biosensor and methods thereof based on surface enhanced Raman scattering (SERS) label detection. The SER gene probe biosensor comprises a support means, a SER gene probe having at least one oligonucleotide strand labeled with at least one SERS label, and a SERS active substrate disposed on the support means and having at least one of the SER gene probes adsorbed thereon. Biotargets such as bacterial and viral DNA, RNA and PNA are detected using a SER gene probe via hybridization to oligonucleotide strands complementary to the SER gene probe. The support means supporting the SERS active substrate includes a fiberoptic probe, an array of fiberoptic probes for performance of multiple assays and a waveguide microsensor array with charge-coupled devices or photodiode arrays.

Abstract: A method of identifying the presence of a known target sequence in nucleic acid contained in a fixed cellular or subcellular biological structure. By adding a stable, reporter-labeled RecA/single-stranded probe complex to the cellular or subcellular structure, the target sequence can be effectively labeled by in situ hybridization, allowing the target sequence to be visualized histologically and microscopically or detected by in situ cytometry or cell sorting flow techniques.

Abstract: A method for detecting and quantifying viral or subviral pathogens in the test sample in which antibodies against a component of the viral or subviral pathogen is immobilized on a substrate. The test sample is placed in contact with the immobilized antibody and then a DNA primer complementary to a fragment or the total genome of the viral or subviral pathogen is permitted to hybridize to the RNA or DNA of the immobilized viral or subviral pathogen. The DNA is then amplified and the amplification products are detected and quantified.

Abstract: Method for screening for familial hemiplegic migraine which comprises searching for the presence of a mutated gene responsible for familial hemiplegic migraine on the chromosome 19, in the region comprised between the microsatellites D19S216 and D19S215, of a family or of an at risk individual, including fetus.

Abstract: A method of synthesis of new and useful single-stranded DNAs which have a stem-loop configuration (ss-slDNA). The method is an in vivo or an in vitro synthesis. Replicating vehicles which produce these ss-slDNAs. The ss-slDNAs are described. Uses for these slDNAs are disclosed. They can be used for introducing random mutations, they lend themselves for replication by a variant of the PCR method. They can also be used for regulating gene function. Other uses are disclosed.

Abstract: Large comb-type branched polynucleotides useful as amplifier molecules in nucleic acid hybridization assays are provided, the polynucleotides comprising: a polynucleotide backbone having at least about 15 multifunctional nucleotides, each of which defines a sidechain site and a first single-stranded oligonucleotide unit that is capable of binding specifically to a first single-stranded polynucleotide sequence of interest; and pendant polynucleotide sidechains extending from said multifunctional nucleotides each comprising iterations of a second single-stranded oligonucleotide unit that is capable of binding specifically to a second single-stranded polynucleotide sequence of interest, the total number of iterations in all sidechains being at least 20. Methods of making these polynucleotides are also provided.

Abstract: The present invention is directed to compositions comprising an oligonucleotide linked to a detectably labeled marker component comprising a fluorophore moiety which comprises a substantially planar, multidentate macrocyclic ligand coordinated to a central atom capable of coordinating with two axial ligands and two polyoxyhydrocarbyl moieties which are attached as axial ligands to the central atom. The present invention is also directed to nucleic acid hybridization and amplification methods employing such compositions.

Abstract: The present invention is directed to methods and reagents for the specific detection and presumptive identification of various bacteria associated with waterborne infectious disease. In particular, this invention relates to methods and reagents for the specific detection and identification of Salmonella and Shigella in environmental samples such as water and sewage.

Abstract: An aqueous composition containing primers for opposing strands of two or more target nucleic acids can be used in polymerase chain reaction to provide simultaneously rapid and efficient amplification and detection of those nucleic acids. The primers for each target DNA differ in length by no more than 5 nucleotides and have a T.sub.m within the range of from about 65.degree. to about 74.degree. C., while the T.sub.m 's are within about 5.degree. C. of each other. Such compositions are useful in diagnostic test kits and methods for amplification and detection of multiple nucleic acids, or in "multiplexing", using multiple capture probes. All of the capture probes have T.sub.m 's which are greater than 50.degree. C. and are within 15.degree. C. of each other.

Abstract: The present invention provides modified oligonucleotide primers that (i) are designed for attachment to a solid support in a manner that does not block the ability to extend the primer from its 3' end, and (ii) incorporate a clearable moiety so that a 3' portion of the primer (linked to an extension product) can be released from an immobilized 5' portion. Upon selective cleavage of the cleavable site, a large portion of the primer fragment remains affixed to the solid support. This enables the release of primer extension products that contain about five or fewer base pairs of the primer sequence, to provide more useful sizing and sequence information per fragment than extension products containing the entire primer.

Abstract: Method and compositions are provided for the determination of telomere length and telomerase activity, as well as the ability to inhibit telomerase activity in the treatment of proliferative diseases. Particularly, primers are elongated under conditions which minimize interference from other genomic sequences, so as to obtain accurate determinations of telomeric length or telomerase activity. In addition, compositions are provided for intracellular inhibition of telomerase activity and means are shown for slowing the loss of telomeric repeats in aging cells.

Abstract: A method of diagnosing cat scratch disease and a method of diagnosing bacillary angiomatosis in a subject by detecting the presence of Rochalimaea henselae or an immunogenically specific determinant thereof in the subject is provided. Also provided is a vaccine comprising an immunogenic amount of a nonpathogenic Rochalimaea henselae or an immunogenically specific determinant thereof and a pharmaceutically acceptable carrier. A method of diagnosing Rochalimaea quintana infection in a subject by detecting the presence of a nucleic acid specific to Rochalimaea quintana in a sample from the subject is provided. A purified heat shock protein of Rochalimaea is provided.

Abstract: The ability to rapidly detect wild polioviruses in clinical specimens is a major concern for the world-wide eradication of polioviruses. Provided is a method of detecting polioviruses of all three serotypes from viral isolates of clinical specimens using a pair of degenerate PCR primers. This primer set, which uses deoxyinosine residues to compensate for third position mismatches at specific positions, recognizes nucleotide sequences near the receptor binding site of polioviruses. These sequences are unique to polioviruses and are absolutely conserved at the amino acid level. As a result, these PCR primers do not recognize nonpoliovirus enteroviruses. All poliovirus serotypes (40 poliovaccine related genotypes and 120 wild poliovirus genotypes from around the world) tested positive. All 14 prototype strains of nonpoliovirus enteroviruses tested negative.

Abstract: The present invention relates to the cloning, sequencing and characterization of a unique human epidermal surface antigen, ESA, and to methods for preparing and using the ESA gene and protein. The ESA gene is mapped to the region 17q11-12, on the long arm of chromosome 17, in the same area as the NF1 locus (the gene for von Recklinghausen neurofibromatosis). The mouse ESA has been located to chromosome 11. ESA mRNA is expressed in cultured keratinocytes and melanocytes, as well as in several carcinoma cell lines. Methods employing the antigen and/or DNA segments in diagnostic and therapeutic methods, including gene therapy, for the treatment of a variety of diseases, including cancer and autoimmunity, are disclosed. Methods for targeting molecules to the suprabasal epidermal cell layer are also presented.