Abstract: An enzymatic RNA molecule which cleaves mRNA associated with development or maintenance of Burkitt's lymphoma or acute lymphocytic leukemia.

Abstract: The invention provides diagnostic assays for assessing the sensitivity or resistance to DNA damaging agents and microtubule-directed chemotherapeutic drugs of malignant cells in a tumor or tissue. The assay provided involves determining gene expression levels of kinesin genes in the malignant cells, wherein under-expression of kinesin is found in cells resistant to DNA damaging agents and sensitive to microtubule-directed chemotherapeutic drugs, and over-expression of kinesin is found in cells sensitive to DNA damaging agents and resistant to microtubule-directed chemotherapeutic drugs.

Abstract: This invention provides for a novel amplification procedure for nucleic acid. The method uses a mutant RNA polymerase designed to transcribe deoxynucleotides. Using primers that bind to target nucleic acid the primers form polymerase recognition sites that permit transcription of the target in an isothermal and logrithmic manner, with the added advantage of forming multiple single stranded copies, which are readily detected by hybridization assays.

Abstract: This specification relates to the field of molecular biology and provides novel methods and reagents for preserving and protecting the ribonucleic acid (RNA) content of samples from degradation prior to RNA isolation. This preservation may be accomplished without ultra-low temperature storage or disruption of the tissue.

Abstract: Method to produce a more active ribozyme by introducing a modified base into a substrate binding arm of the ribozyme or its catalytic core.

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

Abstract: This invention provides purified telomerase and methods of purifying it. The methods involve the use of several sequential steps, including the use of matrices that bind molecules bearing negative charges, matrices that bind molecules bearing positive charges, intermediate-selectivity matrices, methods that separate molecules based on their size, shape, or buoyant density, and by affinity purification.

Abstract: The present invention provides a method for the rapid simultaneous production of a plurality of single-stranded DNA circles having a predetermined size and nucleotide sequence using pre-designed hairpin oligonucleotides containing complementary sequences for directing ligation to form dumbbell-shaped monomers followed by heat denaturation to yield single-stranded DNA circles.

Abstract: The present invention provides a conditionally replicating viral vector, methods of making, modifying, propagating and selectively packaging, and using such a vector, isolated molecules of specified nucleotide and amino acid sequences relevant to such vectors, a pharmaceutical composition and a host cell comprising such a vector, the use of such a host cell to screen drugs. The methods include the prophylactic and therapeutic treatment of viral infection, in particular HIV infection, and, thus, are also directed to viral vaccines and the treatment of cancer, in particular cancer of viral etiology. Other methods include the use of such conditionally replicating viral vectors in gene therapy and other applications.

Abstract: An enzymatic RNA molecule which cleaves mRNA associated with development or maintenance of lung cancer.

Abstract: The present invention provides a method of treating or preventing the inflammatory response of an inflammatory bowel disease in a subject, comprising administering to the subject an amount of a STAT-4 antisense oligonucleotide effective in treating or preventing the inflammatory response of the inflammatory bowel disease.

Abstract: The present invention relates to a method for introducing molecules in cells by disrupting endosomal and lysosomal membranes using photodynamic treatment, without killing the majority of the cells by the photodynamic treatment. More particularly, this invention includes a method for transferring DNA and/or RNA, such as genes, to cells by photochemically inducing the disruption of endosomes and lysosomes.

Abstract: A method in which a temperature gradient is generated across a “gradient” block, and an apparatus comprising a block across which a temperature gradient can be generated. By setting up such a gradient, multiple reaction mixtures held in wells on the gradient block can be simultaneously run at temperatures which differ only slightly, thereby permitting an optimum temperature for the reaction to be quickly identified. In a preferred embodiment the gradient block is integrated into a thermal cycler used for nucleic acid amplification reactions.

Abstract: Methods for assessing intermolecular interactions in vivo and in vitro are provided. Methods are provided for detecting protein-DNA interactions in vivo, in which a cell having a chimeric guide endonuclease molecule and a target nucleic acid is provided, and cleavage of the target nucleic acid by the chimeric guide endonuclease molecule is monitored. Cleavage by the chimeric guide molecule corresponds to binding of the guide domain to the target nucleic acid, or to a protein associated with the nucleic acid. The methods of the invention are adapted to cleavage of target nucleic acids, amplification of target nucleic acids, detection of target nucleic acids, screening of genomic target nucleic acid sequences for guide binding domains, and screening for modulators of chimeric guide binding domain activity. Also provided are methods for detecting interactions between other molecules, including hormones and receptors, enzymes and substrates, and the like.

Abstract: A method for designing compounds specifically targeting RNA sequences, based on the discovery of short, specific sequences within RNA that are critical to function, using modeling of the compound to effect binding to the nucleotide sequences in the RNA in combination with secondary and/or tertiary structure associated with the minor groove of the RNA in the region of the critical sequences. In the preferred method, computer modeling is used along with analysis of the targeted RNA sequence to design molecules binding to the targeted RNA by covalent or hydrogen binding. Appropriate molecules are synthesized using known methodology that have the required structure and chemical characteristics to specifically bind the critical region of the RNA and thereby inhibit the function of the RNA. Molecules known to bind to RNA can also be modified using this method to increase specificity, and thereby decrease toxicity.

Abstract: Compositions and methods are provided for modulating the expression of TGF-&bgr;. Antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding TGF-&bgr; are preferred. Methods of using these compounds for modulation of TGF-&bgr; expression and for treatment of diseases associated with expression of TGF-&bgr; are also provided. Methods of sensitizing cells to apoptotic stimuli are also provided.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of RECQL4. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding RECQL4. Methods of using these compounds for modulation of RECQL4 expression and for treatment of diseases associated with expression of RECQL4 are provided.

Abstract: Methods and compositions are provided for producing full-length cDNA libraries. In the subject methods, full length first strand cDNAs are isolated using a fusion protein of an eIF-4E domain and an eIF-4G domain separated by a flexible linker. Also provided is the novel fusion protein employed in the subject methods, as well as nucleic acids encoding, and host cells capable of expressing, the same. Finally, kits for use in practicing the subject methods are provided. The subject invention finds use in a variety of applications in which full-length cDNA libraries are employed.

Abstract: Lentiviral vectors modified at the 5′ LTR or both the 5′ and 3′ LTR's are useful in the production of recombinant lentivirus vectors. Such vectors can be produced in the absence of a functional tat gene. Multiple transformation of the host cell with the vector carrying the transgene enhances virus production.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of A20. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding A20. Methods of using these compounds for modulation of A20 expression and for treatment of diseases associated with expression of A20 are provided.

Abstract: A nucleic acid molecule is provided which is initially catalytically inactive but which can complex with a specific co-factor, e.g., a nucleic acid molecule or a non-nucleic acid molecule, to form a catalytically active nucleic acid molecule. The catalytically active nucleic acid molecule can be used to detect the presence of a non-nucleic acid co-factor or of a nucleic acid co-factor using the nucleic acid sequence of the present invention.

Abstract: Methods are provided for the production of nucleic acid ligands against target molecules using a procedure known as Transcription-free Systematic Evolution of Ligands by EXponential enrichment (Transcription-free SELEX). The Transcription-free SELEX method assembles nucleic acid ligands from fragments of synthetic nucleic acids by annealing those fragments to a complementary template, and then ligating the fragments together.

Abstract: Nucleic acids are isolated by adhering a target nucleic acid in a sample to a hydrophobic polymeric solid phase, and applying a nonionic surfactant to the solid phase to remove the target nucleic acid from the solid phase. The solid phase may be made of polyethylene, polypropylene, or polytetrafluoroethylene, and be in the form of a porous matrix. Nonionic surfactants include polyoxyethylene surfactants and polyoxyethylene-co-oxypropylene surfactants. A buffer containing a salt that enhances binding of the nucleic acid to the solid phase may be added to the solid phase with or prior to the sample containing the nucleic acid. When the sample contains cells, the cells are lysed to release contents of the cells as a lysate containing nucleic acids. A kit is formed containing the solid phase and nonionic surfactant, and may also include a flow-through receptacle.

Abstract: This is a method for reproducing in vitro the RNA-dependent RNA polymerase activity associated with hepatitis C virus. The method is characterized in that sequences contained in NS5B are used in the reaction mixture. The terminal nucleotidyl transferase activity, a further property of the NS5B protein, can also be reproduced using this method. The method takes advantage of the fact that the NS5B protein, either purified to apparent homogeneity or present in extracts of overproducing organisms, can catalyze the addition of ribonucleotides to the 3′-termini of exogenous or endogenous RNA molecules. The invention also relates to a composition of matter that comprises sequences contained in NS5B, and to the use of these compositions for the set up of an enzymatic test capable of selecting, for therapeutic purposes, compounds that inhibit the enzymatic activity associated with NS5B.

Abstract: The present invention provides methods for synthesis and therapeutic use of DNA and RNA oligonucleotides and analogs. RNA oligonucleotides are synthesized using a small, circular DNA template which lacks an RNA polymerase promoter sequence. The RNA synthesis is performed by combining a circular single-stranded oligonucleotide template with an effective RNA polymerase and at least two types of ribonucleotide triphosphate to form an RNA oligonucleotide multimer comprising multiple copies of the desired RNA oligonucleotide sequence. Preferably, the RNA oligonucleotide multimer is cleaved to produce RNA oligonucleotides having well-defined ends. Preferred RNA oligonucleotide multimers contain ribozymes capable of both cis (autolytic) and trans cleavage.

Abstract: 2′-deoxy-2′-alkylnucleotides useful for stabilizing enzymatic nucleic acid molecules and antisense molecules.

Abstract: Selective cleavage of single stranded nucleic acids can be effected by contacting the nucleic acid with a zinc finger peptide in dimeric form. Dimerization results from diminution or elimination of zinc from the peptide, such that easily controllable and highly selective cleavage may be realized.

Abstract: Enzymatic nucleic acid molecule containing one or more non-nucleotide mimetics, and having activity to cleave an RNA or DNA molecule.

Abstract: The present invention provides an improved system for linking nucleic acids to one another. In particular, the present invention provides techniques for producing DNA product molecules that may be easily and directly ligated to recipient molecules. The product molecules need not be cleaved with restriction enzymes in order to undergo such ligation. In preferred embodiments of the invention, the DNA product molecules are produced through iterative DNA synthesis reactions, so that the product molecules are amplified products. The invention further provides methods for directed ligation of product molecules (i.e., for selective ligation of certain molecules within a collection of molecules), and also for methods of exon shuffling, in which multiple different product molecules are produced in a single ligation reaction. Preferred embodiments of the invention involve ligation of product molecules encoding functional protein domains, particularly domains naturally found in conserved gene families.

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

Abstract: Vectors and a method for the identification of affector RNA molecules, such as ribozymes, external guide sequences, anti-sense RNA, and triple helix-forming RNA, that inhibit expression of target RNA molecules are disclosed. The method identifies functional affector RNA molecules by screening or selecting for those RNA molecules that inhibit expression of a fusion transcript, which includes the sequence of an RNA molecule of interest, from a library of potential affector RNA molecules. The vectors include a reporter gene encoding the fusion transcript including the RNA molecule of interest and RNA encoding the reporter protein. The vectors also include a second reporter gene encoding a second reporter protein. Expression of the second reporter protein can be used both to detect transformation or transfection of the vector into cells and as a control for effects on the expression of the first reporter protein that are not due to inhibition of expression of the RNA molecule of interest.

Abstract: The present invention relates to an isolated nucleic acid molecule comprising: (i) a primer protion consisting of a contiguous sequence of from 10 to 50 nucleotides capable of hybridizing to (a) the target nucleic acid molecule represented by SEQ ID NO:1, or (b) to the complementary stand thereof; and optional (ii) a further portion comprising from 1 to 25 nucleotides joined to and immediately 5′ to the 5′ end of the primer portion.

Abstract: This invention relates to an isolated nucleic acid fragment encoding an alpha-glucosidase II subunit. The invention also relates to the construction of a chimeric gene encoding all or a portion of the alpha-glucosidase II subunit, in sense or antisense orientation, wherein expression of the chimeric gene results in production of altered levels of the alpha-glucosidase II subunit in a transformed host cell.

Abstract: This invention relates to non-radioactive markers that facilitate the detection and analysis of nascent proteins translated within cellular or cell-free translation systems. Nascent proteins containing these markers can be rapidly and efficiently detected, isolated and analyzed without the handling and disposal problems associated with radioactive reagents. Preferred markers are dipyrrometheneboron difluoride (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) dyes.

Abstract: Disclosed herein are cloning vectors which include: (a) a cloning site which permits the cloning of a nucleic acid in defined orientation; (b) at least one cleavage site adjacent to the cloning site, the cleavage site being rarely-occurring in nucleic acids; and (c) a long region which is located on the side of the cloning site opposite to the cleavage site (b), wherein the long region and the region between the cloning site and the cleavage site (b) contain neither the cloning site nor at least two frequently-occurring cleavage sites.

Abstract: Disclosed is a smooth muscle cell specific promoter, the SM22&agr; gene promoter as well as the murine cDNA and genomic SM22&agr; nucleic acid sequences. Also disclosed are methods of preventing restenosis following balloon angioplasty and methods of treating asthma based on inhibition of smooth muscle cell proliferation by expressing cell cycle control genes, or contraction inhibiting peptides in smooth muscle cells, under the control of the SM22&agr; promoter.

Abstract: The molecules and methods of the present invention provide a means for in vivo production of a trans-spliced molecule in a selected subset of cells. The pre-trans-splicing molecules of the invention are substrates for a trans-splicing reaction between the pre-trans-splicing molecules and a pre-mRNA which is uniquely expressed in the specific target cells. The in vivo trans-splicing reaction provides a novel mRNA which is functional as mRNA or encodes a protein to be expressed in the target cells. The expression product of the mRNA is a protein of therapeutic value to the cell or host organism a toxin which causes killing of the specific cells or a novel protein not normally present in such cells. The invention further provides PTMs that have been genetically engineered for the identification of exon/intron boundaries of pre-mRNA molecules using an exon tagging method.

Abstract: The invention relates to a nucleic acid sequence, called “polyribozyme”, which has an endoribonuclease activity and is capable of inactivating the gene for the capsid protein of a virus, characterized in that it comprises: i) a sequence complementary to at least a part of the gene or its transcript or to its replication intermediates and, includes at distinct sites in this complementary sequence: ii) a plurality of ribozyme catalytic regions; iii) and, optionally, one or more sequences non-complementary to the transcript of the said gene, the said non-complementary sequence(s) being inserted between two consecutive bases of the complementary sequence.

Abstract: This invention provides purified human telomerase and methods of purifying it. The methods involve the use of several sequential steps, including the use of a first matrix that binds molecules bearing negative charges, a matrix that binds molecules bearing positive charges, a second matrix that binds molecules bearing negative charges, an affinity purification step and a matrix that separates molecules according to their size.

Abstract: The invention provides novel DNA polymerases of the &bgr;-family, called &bgr;-type DNA polymerases. Nucleic acids encoding &bgr;-type DNA polymerases are provided, as well as expression vectors and host cells containing the nucleic acid encoding the &bgr;-type DNA polymerases. The invention further relates to methods for synthesizing nucleic acid using &bgr;-type DNA polymerases.

Abstract: The invention describes a method for the isolation of components from samples, particularly large molecular weight DNA from biological samples. The method involves the application of controlled oscillatory mechanical energy to the sample for short periods of time of about 5 to 60 seconds to lyse the sample and release the component(s) from the sample, followed by standard isolation methods. In preferred embodiments, the method includes the use of a spherical particle for applying the mechanical energy.

Abstract: The invention provides novel developmentally-regulated hippocampal genes and polypeptides encoded by those genes. The invention also provides expression vectors, host cells, and antibodies. The invention also provides methods for diagnosing, treating or preventing diseases associated with hippocampus.

Abstract: Eukaryotic RNA polymerase II holoenzymes that contain RNA polymerase II and one or more regulatory proteins are described. These holoenzymes selectively initiate transcription in vitro when supplemented with general transcription factors. The regulatory proteins act positively and negatively to regulate transcription initiation, at least in part, via functional interactions with RNA polymerase II.

Abstract: This specification relates to the field of molecular biology and provides a novel method and reagent for preserving and protecting the ribonucleic acid (RNA) content of tissue samples from degradation prior to RNA isolation. This preservation may be accomplished without ultra-low temperature storage or disruption of the tissue.

Abstract: This invention provides a method for monitoring the transcriptional synthesis of RNA, and to an apparatus therefor. Specifically, the invention resides in monitoring the initiation and termination of a transcription reaction for RNA synthesis, as well as the synthesis of full-length RNA by measuring the fluorescence of a pair of oligonucleotide probes of two types having a base sequence that continuously hybridizes to a part of a base sequence of the RNA synthesized by transcription, the pair of oligonucleotide probes comprising a donor probe labeled with an energy donor fluorescent molecule and an acceptor probe labeled with an energy acceptor fluorescent molecule.