Abstract: This invention relates to agents and conjugates that can be used to detect and isolate target components from complex mixtures such as nucleic acids from biological samples, cells from bodily fluids, and nascent proteins from translation reactions. Agents comprise a detectable moiety bound to a photoreactive moiety. Conjugates comprise agents coupled to substrates by covalent bounds which can be selectively cleaved with the administration of electromagnetic radiation. Targets substances labeled with detectable molecules can be easily identified and separated from a heterologous mixture of substances. Exposure of the conjugate to radiation releases the target in a functional form and completely unaltered. Using photocleavable molecular precursors as the conjugates, label can be incorporated into macromolecules, the nascent macromolecules isolated and the label completely removed.

Abstract: The present invention provides a compound of general formula (I): ##STR1## wherein X represents group (II) or (III): ##STR2## wherein Y represents a leaving group and Z represents an oligonucleotide. The compound can specifically transfer oligonucleotides to cells which specifically recognize a specified saccharide construction. Accordingly, the compound can be used as an antiviral agent or an antitumor agent.

Abstract: The invention relates to modified oligonucleotide primers used to adjust the amplification efficiency of an abundant target without affecting the amplification of other targets in a DNA synthesis reaction. The invention may be used in PCR.TM. or any other primer dependent DNA transcription technology.

Abstract: The methods to synthesize these chemicals in a laboratory are theorized to be related to natural processes that resulted in the creation of primordial life in the early atmosphere of Earth. The theory of the origin of primordial life in the Earth's early atmosphere is derived from an earlier U.S. Disclosure Document entitled "Method and Apparatus to Create Primordial Life from Inanimate Materials" that is substantially repeated in the application.

Abstract: The movement and mixing of microdroplets through microchannels is described employing silicon-based microscale devices, comprising microdroplet transport channels, reaction regions, electrophoresis modules, and radiation detectors. The discrete droplets are differentially heated and propelled through etched channels. Electronic components are fabricated on the same substrate material, allowing sensors and controlling circuitry to be incorporated in the same device.

Abstract: Methods for detecting metastasis of melanoma and breast cancer cells, detecting subclinical metastasis, and monitoring treatment are disclosed. Kits for use in such methods also are disclosed. The methods provide for the detection of nucleic acids corresponding to multiple melanoma or breast cancer specific markers using template dependent amplification processes. Methods using multiple markers provide increased sensitivity over existing methods.

Abstract: The present invention relates to method for isolation of DNA sequences having a target DNA of known sequence which accelerates and simplifies obtaining DNA especially from small amounts of tissue. This method uses polymerase having strand displacement capability, one primer and a circular DNA template.

Abstract: The present invention relates to the cloning of the gene of a thermophilic DNA ligase, from Thermus aquaticus strain HB8, and the use of this ligase for the detection of specific sequences of nucleotides in a variety of nucleic acid samples, and more particularly in those samples containing a DNA sequence characterized by a difference in the nucleic acid sequence from a standard sequence including single nucleic acid base pair changes, deletions, insertions or translocations.

Abstract: A method is disclosed of amplifying the signal of target nucleic acid sequence analyte using a rolling circle replication mechanism and a bidirectional primer. The repeating signal amplification sequence units contain tags which are directly or indirectly detectable. In addition, methods of capturing the tagged complementary nucleic acid sequence of the target nucleic acid sequence onto an array surface and detecting the captured target nucleic acid sequences are disclosed. Kits are also disclosed for enhancing detection of target nucleic acid sequences using a mechanism of rolling circle replication and a bidirectional primer to attach to the complementary nucleic acid sequence of the target nucleic acid sequence a large number of detectable tags.

Abstract: Single-stranded signal primers are modified by linkage to two dyes which form a donor/acceptor dye pair. The two dyes are positioned in sufficiently close spatial proximity on the signal primer that the fluorescence of the first dye is quenched by the second dye. The signal primer may further comprise a restriction endonuclease recognition site (RERS) between the two dyes. As the signal primer is initially single-stranded and remains single-stranded in the absence of target, the restriction endonuclease recognition site is not cleavable or nickable by the restriction endonuclease. In the presence of target, however, signal primer and the restriction endonuclease recognition site are rendered double-stranded and cleavable or nickable by the restriction endonuclease. Cleavage or nicking separates the two dyes and a change in fluorescence due to decreased quenching is detected as an indication of the presence of the target sequence or of target sequence amplification.

Abstract: The invention encompasses tumorigenicity-inhibiting antisense oligonucleotide sequences complementary to mRNA or double-stranded DNA that encodes mammalian DNA methyl transferase. It further encompasses methods for inhibiting tumorigenicity and pharmaceutical composition comprising the tumorigenicity-inhibiting antisense nucleotide.

Abstract: Methods and compositions for the isolation and specific targeting of any single stranded DNA sequence to be acted upon by any desired double stranded DNA genetic element or recognition sequence in a cis-oriented fashion. The invention involves construction of a vector comprised of single stranded sequences that form "stem-loop" structures wherein the "loop" comprises the single stranded target sequence and the "stem" comprises the double stranded "functional" cis-acting genetic elements or recognition sequences. The in vivo formation of this single stranded intermediate (prior to stem-loop folding) is performed by genetic elements which direct the normal DNA replication of any one of a number of prokaryotic and eukaryotic viruses during their life cycles. Constructs containing these replicative functions are used to produce the desired single stranded intermediates. Also included in the stem-loop structure is an appropriate inverted tandem repeat which, forms the "stem" of the stem-loop structure.

Abstract: Method for one-pot deprotection of RNA molecules.

Abstract: Polynucleotides and oligonucleotides for identification of species of the Streptococcus genus and the Enterococcus genus are provided. The polynucleotides and oligonucleotides are useful as probes and primers. Polypeptides expressed by the polynucleotides and oligonucleotides are useful for the preparation of monoclonal and polyclonal antibodies that recognize the polypeptides.

Abstract: A novel class of compounds, exemplified by oligomers comprised of purine, pyrimidine, and other nucleobase monomers are disclosed. The nucleobase oligomers hydrogen bond through Watson/Crick base pairing to complementary nucleic acids, such as DNA and RNA, in an opposing strand. Each internal nucleobases in the oligomer has two attachment sites and is attached to two nucleobases by linkers. Terminating groups may contain reactive functionality, labels, reporters, or nucleic acids. The nucleobase oligomer compounds are useful as sequence specific recognition molecules for complementary nucleic acids. Where the molecule consists of sections of nucleobase oligomer and nucleic acid, the chimera may be an enzyme substrate in cleavage, ligation, and primer extension methods such as PCR and DNA sequencing.

Abstract: A nucleic acid amplifying enzyme having a short reaction time and high fidelity is provided. The enzyme of this invention is a thermostable DNA polymerase having a nucleic acid extension rate of at least 30 bases per second and a 3'-5' exonuclease activity. Also provided are a method and kit for amplifying nucleic acid.

Abstract: This invention relates to polynucleotides encoding Glycoprotein B from the RFHV/KSHV subfamily of gamma herpes viruses, three members of which are characterized in detail. DNA extracts were obtained from Macaque nemestrina and Macaque mulatta monkeys affected with retroperitoneal fibromatosis (RF), and human AIDS patients affected with Kaposi's sarcoma (KS). The extracts were amplified using consensus-degenerate oligonucleotide probes designed from known protein and DNA sequences of gamma herpes viruses. The nucleotide sequences of a 319 base pair fragment are about 76% identical between RFHV1 and KSHV, and about 60-63% identical with the closest related gamma herpes viruses outside the RFHV/KSHV subfamily. Protein sequences encoded within these fragments are are about 91% identical between RFHV1 and KSHV, and <.about.65% identical to that of other gamma herpes viruses.

Abstract: This invention relates to methods for screening nucleic acids for mutations by analyzing nonrandomly fragmented nucleic acids using mass spectrometric techniques and to procedures for improving mass resolution and mass accuracy of these methods of detecting

Abstract: Patched-2 polypeptides and polynucleotides and methods for producing such polypeptides by recombinant techniques are disclosed. Also disclosed are methods for utilizing Patched-2 polypeptides and polynucleotides in therapy, and diagnostic assays for such.

Abstract: This invention relates to an improved process for detecting and quantifying a desired nucleic acid sequence. The process involves synthesizing single stranded RNA, single stranded DNA, double-stranded DNA followed by detection using an electrochemiluminescent labeled binding species.

Abstract: A pesticide composition that includes a metabolite from a fungus selected from homeocarpic basidiomycetes and homeocarpic ascomycetes is described. In one embodiment, the fungus from which the metabolite is derived is one grown under conditions effective to substantially suppress fruiting of the fungus. More particular examples of the invention include pesticide compositions comprising a fungal metabolite derived from a fungus selected from the group Ganoderma spp., Laetiporus spp., Lentinus spp., Morchella spp., and Pleurotus spp.

Abstract: A method of analyzing a DNA molecule is disclosed. In one embodiment the method comprises the steps of exposing a DNA molecule to an effective amount of a chemical modification reagent wherein the reagent converts guanine to 8-hydroxyguanine. The oxidized product is then exposed to a DNA glycosylase enzyme and the DNA molecule is cleaved at the site of the 8-hydroxyguanine. The fragments are then resolved by electrophoresis and the position of guanine residues within the DNA molecule is determined. In a preferred embodiment of the present invention, the modification reagent is a thiazine dye and the enzyme is FPG protein.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of PI3 kinase p110 delta. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding PI3 kinase p110 delta. Methods of using these compounds for modulation of PI3 kinase p110 delta expression and for treatment of diseases associated with expression of PI3 kinase p110 delta are provided.

Abstract: Methods of enzymatic nucleic acid sequencing are provided in which solid-phase capturable chain terminators are employed. In the subject methods, sequencing fragments are generated, where the fragments comprise capturable chain terminators. The fragments are then captured on a solid phase and separated from the remaining components of the sequencing reaction. The fragments are then released from the solid phase, size separated and detected to yield sequencing data from which the sequence of the nucleic acid is determined.

Abstract: Methods and compositions are disclosed which comprise red rice fermentation products, that can be used as natural dietary supplements and/or medicaments for the treatment or prevention of hyperlipidemia and associated disorders and symptoms, such as cardiovascular diseases, cerebrovascular diseases, diabetes, hypertension, obesity, asthenic breathing, chronic headache, chest pain and tightness, limb swelling and distention, loss of appetite and excess expectoration. The methods and compositions are effective in lowering both the serum cholesterol and serum triglyceride levels in humans, and can be used for maintaining cardiovascular health. The invention also encompasses particular Monascus strains that yield fermentation products with the desired biological activities.

Abstract: A computational method maximizing open reading frame length in an assembly consensus sequence is provided. Systems employing the method are also provided.

Abstract: The present invention relates to growing and testing microorganisms in a multitest format which utilizes a gel forming matrix for the rapid screening of clinical and environmental cultures. The present invention is suited for the characterization of commonly encountered microorganisms (e.g., E. coli, S. aureus, etc.), as well as commercially and industrially important organisms from various and diverse environments (e.g., the present invention is particularly suited for the growth and characterization of the actinomycetes and fungi). The present invention is also particularly suited for comparative analysis of phenotypic differences between cell types, including strains of microorganisms that have been designated as the same genus and species, as well as other cell types (e.g., mammalian, insect, and plant cells).

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of G-alpha-i1. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding G-alpha-i1. Methods of using these compounds for modulation of G-alpha-i1 expression and for treatment of diseases associated with expression of G-alpha-i1 are provided.

Abstract: A synthetic nuclease resistant antisense oligodeoxynucleotide capable of selectively modulating expression of human tumor necrosis factor-alpha by targeting exon sequences flanking donor splice sites, thereby regulating expression of TNF-.alpha. in a patient in need of such therapy is provided. In an embodiment either AS-ODN having the sequence set forth in SEQ ID No:4 or SEQ ID No:6 or a combination thereof can be used. The AS-ODN is administered either as the active ingredient in a pharmaceutical composition or by utilizing gene therapy techniques as an expression vector.

Abstract: The present invention is an improved method of making a partially modified PCR product from a DNA fragment with a polymerase chain reaction (PCR). In a standard PCR process, the DNA fragment is combined with starting deoxynucleoside triphosphates, a primer, a buffer and a DNA polymerase in a PCR mixture. The PCR mixture is then reacted in the PCR producing copies of the DNA fragment. The improvement of the present invention is adding an amount of a modifier at any step prior to completion of the PCR process thereby randomly and partially modifying the copies of the DNA fragment as a partially modified PCR product. The partially modified PCR product may then be digested with an enzyme that cuts the partially modified PCR product at unmodified sites thereby producing an array of DNA restriction fragments.

Abstract: tr-.alpha.llb, a soluble, truncated integrin found to be exclusively expressed in tumor cells is provided. An additional truncated integrin, tr-.beta.3, has also been found to be exclusively expressed in tumor cells. Diagnostic compositions including nucleic acid probes and antibodies and methods for detecting the presence of tr-.alpha.llb and tr-.beta.3 to identify the presence of tumor cells in a sample are also provided.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of MDMX. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding MDMX. Methods of using these compounds for modulation of MDMX expression and for treatment of diseases associated with expression of MDMX are provided.

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

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: A method for primer walking cycle sequencing of nucleic acid is provided using a presynthesized set of walking primers wherein the primers have a raised annealing temperature and/or improved annealing properties without increasing sequence complexity.

Abstract: The present invention describes a method of sequencing nucleic acids in which mixtures of oligonucleotide fragments are derived from sequencing reactions using combinations of the 2',3'-dideoxynucleoside 5'-triphosphate or 3' deoxynucleoside 5'-triphosphate terminators and appropriate concentrations of four dNTPs (2'-deoxynucleoside 5' triphosphates, e.g., dATP, dCTP, dGTP, dTTP, dITP, 7-deaza-GTP). These fragments are generated by enzymatic extension of a primer hybridized to the single-stranded template DNA to be sequenced. In contrast to common slab gel sequencing methods, the method of the instant invention does not require precise alignment of the four separation sets of the terminated fragments to permit deduction of the DNA sequence. In addition, the method possesses inherent redundancy in the separations, which facilitates sequence assignment by resolving sequence uncertainties or anomalies.

Abstract: The enzyme 2,3-dihydroxybenzoic acid decarboxylase has industrial applications for the decarboxylation of ring mounted carboxyls, specifically the decarboxylation of 2,3-dihydroxybenzoic acid to catechol. This invention relates to the isolation of a nucleic acid sequence from Aspergillus niger that encodes an enzyme that decarboxylates 2,3-dihydroxybenzoic acid. This invention further discloses the nucleic acid sequence, the protein sequence, vectors comprising the nucleic acid sequence, cells transformed with the nucleic acid sequence, and methods for the production of 2,3-dihydroxybenzoic acid decarboxylase.

Abstract: An improved delivery system for antisense oligonucleotides involves a liposomal composition, comprising a liposome which consists essentially of neutral phospholipids and an antisense oligonucleotide that is entrapped in the liposome and is selected from the group consisting of phosphodiester oligonucleotides, phosphorothioate oligonucleotides, and p-ethoxy oligonucleotides.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of liver glycogen phosphorylase. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding liver glycogen phosphorylase. Methods of using these compounds for modulation of liver glycogen phosphorylase expression and for treatment of diseases associated with expression of liver glycogen phosphorylase are provided.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of Akt-2. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding Akt-2. Methods of using these compounds for modulation of Akt-2 expression and for treatment of diseases associated with expression of Akt-2 are provided.

Abstract: An oligonucleotide analog or an antisense molecule, which is minimally hydrolyzable with an enzyme in vivo, has a high sense strand binding ability, and is easily synthesized, is provided. It is an oligo- or polynucleotide analog containing one or more monomer units being nucleotide analogs of the general formula: ##STR1## where B may be identical or different, and is a pyrimidine or purine nucleic acid base, or a derivative thereof.

Abstract: Amplification primers and methods for specific amplification and detection of a Shiga-like toxin II (SLT-II) target are disclosed. The primer-target binding sequences are useful for amplification and detection of SLT-II target in a variety of amplification and detection reactions.

Abstract: This invention describes compounds active against TNF-.alpha. mRNA. It further describes mRNA molecules capable of conferring stability to RNA in vivo. Possible mRNA molecules to be stabilized include ribozymes, antisense molecules and mRNA encoding polypeptides useful for protein production. The ribozymes and antisense molecules described herein are useful in mammals and plants, particularly suited for viral diseases. Methods of production and methods of use are also described.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of G-alpha-i2. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding G-alpha-i2. Methods of using these compounds for modulation of G-alpha-i2 expression and for treatment of diseases associated with expression of G-alpha-i2 are provided.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of Smad5. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding Smad5. Methods of using these compounds for modulation of Smad5 expression and for treatment of diseases associated with expression of Smad5 are 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, a single base deletion in exon 4, has also been determined. Methods for detecting carriers of the defective vWF gene are also provided.

Abstract: Methods and apparatus in which pressure provides precise control over the timing and preferably synchronization of chemical reactions, particularly enzymatic reactions.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of integrin beta 3. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding integrin beta 3. Methods of using these compounds for modulation of integrin beta 3 expression and for treatment of diseases associated with expression of integrin beta 3 are provided.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of Smad2. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding Smad2. Methods of using these compounds for modulation of Smad2 expression and for treatment of diseases associated with expression of Smad2 are provided.

Abstract: Nucleic acid and protein compositions are provided from B. pertussis which may find use in diagnosis, prevention and therapy of whooping cough. Particularly, an open reading frame encoding filamentous hemagglutinin precursors provided, with the intact protein for the filamentous hemagglutinin portion thereof, can be expressed in a wide variety of hosts, for use in the production of antibodies, for immunodiagnosis or therapy, or as vaccines for prophylactic purposes.