Abstract: The present invention makes possible the catalytic production of sequence specific oligonucleotides through the use of a specially designed template sequence. The reaction can be made to proceed isothermally in the presence of an excess of nucleoside triphosphates, an agent for polymerization, and a cutting agent. Because the process is catalytic with respect to the template sequence, an unlimited amount of oligonucleotide product can theoretically be generated from a single molecule of template. Where the process is initiated by the presence of a nucleic acid target sequence, the method of the present invention can be used for diagnostic purposes as an amplification method to improve sensitivity. Diagnostic sensitivity can be further enhanced by employing a cascade of these template sequences.

Abstract: The present invention provides a method of transcriptionally modulating the expression of a gene-of-interest. The method comprises contacting a cell which is capable of expressing the gene with an amount of a molecule effective to transcriptionally modulate expression of the gene and thereby affect the level of the protein encoded by the gene which is expressed by the cell. Molecules useful in the practice of the invention are characterized as follows (a) do not naturally occur in the cell, (b) bind to DNA or RNA or bind to a protein through a domain of such protein which is not a ligand binding domain of a receptor which naturally occurs in the cell. Additionally, this invention provides a method for determining whether a molecule known to be a modulator of protein biosynthesis is capable of transcriptionally modulating expression of a gene-of-interest.

Abstract: This invention discloses high-affinity oligonucleotide ligands to complex tissue targets, specifically nucleic acid ligands having the ability to bind to complex tissue targets, and the methods for obtaining such ligands. Tissue targets comprise cells, subcellular components, aggregates or cells, collections of cells, and higher ordered structures. Specifically, nucleic acid ligands to red blood cells ghosts, glioblastomas, and lymphomas are described.

Abstract: A modified DNA sequence encoding full length cystic fibrosis transmembrane conductance regulator protein is provided to facilitate propagation and/or expression of the protein in living cells and in particular, bacterial cells. The modified DNA sequence comprises at least one of the 13 base pair repeat of exon 6b of the normal gene encoding the conductance regulator protein, as one or more normal nucleotides of the 13 base repeat substituted with an alternate nucleotide which, however, continues to code for the corresponding normal amino acid.

Abstract: A method is provided for making synthetic capped RNAs. These compounds serve as substrates for the virally encoded endonuclease associated with influenza virus. We are able to assay for this unique and specific viral activity of cleavage of a capped RNA in vitro. Therefore, screening of inhibitors of this activity is possible. In addition, short non-extendible (due to their length or because of the modification of the 3'-end of the oligo, i.e. 3'-dA) RNAs are potent inhibitors of the cleavage of capped RNAs by influenza endonuclease. Finally, these compounds may be used to investigate viral and cellular mechanisms of transcription/translation or mRNA maturation.

Abstract: A method of assaying genetic sequences comprises introducing double stranded DNA to be assayed into an aqueous buffer medium containing complexes of an anchor DNA strand anchored to a support matrix and hybridized with a reporter DNA strand having a detectable label. A portion of the anchor strand or the reporter strand consists of a selected sequence of bases capable of forming a triple helix or triple strand structure with a portion of particular double stranded DNA. The reporter strand is displaced from the complex upon formation of a triple helix or triple strand structure, and displaced reporter strands are detected to determine the presence of the particular double stranded DNA. Gene probes, anchor/reporter hybrids, selected gene sequences and kits, useful in the assay method, are provided.

Abstract: Described herein are methods for improved partitioning between high and low affinity nucleic acid ligands identified through the SELEX method, termed Flow Cell SELEX. The Flow Cell SELEX method achieves partitioning between high and low affinity nucleic acid ligands using surface plasmon resonance technology. The method of the present invention presents a new and powerful approach to select nucleic acid ligands by providing a partitioning method which 1) enables a significant increase in the efficiency of partitioning from traditional partitioning methods used in SELEX, 2) allows for real time monitoring of the partitioning of the high affinity ligands from the low affinity ligands 3) allows for the ability to select for a nucleic acid ligand having specific kinetic properties, 4) does not rely on radiolabeling or other means of tagging for detection, and 5) allows for use of smaller amounts of target than in traditional methods of SELEX.

Abstract: The present invention relates to the discovery that antisense nucleic acids complimentary to an E6AP gene can be used to regulate cellular p53 levels. In general the invention features E6AP antisense constructs which, by inhibiting E6AP activity, can modulate cellular p53 levels in both p53+ transformed cells and in normal cells. The invention also provides methods for treating papillomavirus (PV) induced condition, methods for regulating cellular p53 levels and methods for regulating cellular proliferation.

Abstract: A method and kits for amplifying and detecting target nucleic acid sequences in a sample is disclosed. The method employs primers which have reactive pair members linked to them. The reactive pair members can be attached to a solid phase and/or detected by labeled conjugate.

Abstract: The present invention relates, in general, to a process of enzymatically synthesizing nucleic acids containing boranophosphonate linkages that are resistant to degradation. The invention further relates to methods of utilizing such nucleic acids in DNA and RNA amplification and sequencing, gene therapy and molecular detection protocols.

Abstract: This invention discloses a method for coevolving products from two or more reactants, along with the nucleic acid that can facilitate the reaction for making the products. The invention further discloses the products and facilitating nucleic acids produced by said method.

Abstract: Amplification oligonucleotides and hybridization assay probes which distinguish Human Immunodeficiency Virus type from other viruses.

Abstract: The invention relates to methods and compositions that are useful for detecting deficiencies in dihydropyrimidine dehydrogenase (DPD) levels in mammals including humans. Cancer patients having a DPD deficiency are at risk of a severe toxic reaction to the commonly used anticancer agent 5-fluorouracil (5-FU). Claimed are DPD genes from human and pig, methods for detecting the level of nucleic acids that encode DPD in a patient, and nucleic acids that are useful as probes for this purpose. Also claimed are methods for expressing DPD in heterologous organisms. Expression vectors that employ a DPD nucleic acid as a selectable marker are also claimed. This selectable marker functions in both prokaryotes and eukaryotes.

Abstract: The present invention is directed to in situ hybridization methods using nucleic acid probes for single copy sequences for detecting chromosomal structural abnormalities in fixed tissue obtained from a patient suspected of having a chromosomal structural abnormality.

Abstract: The invention provides a method of nucleic acid sequence analysis based on repeated cycles of ligation to and cleavage of probes at the terminus of a target polynucleotide. At each such cycle one or more terminal nucleotides are identified and one or more nucleotides are removed from the end of the target polynucleotide, such that further cycles of ligation and cleavage can take place. At each cycle the target sequence is shortened by one or more nucleotides until the nucleotide sequence of the target polynucleotide is determined. The method obviates electrophoretic separation of similarly sized DNA fragments and eliminates the difficulties associated with the detection and analysis of spatially overlapping bands of DNA fragments in a gel, or like medium. The invention further obviates the need to generate DNA fragments from long single stranded templates with a DNA polymerase.

Abstract: Disclosed are compositions and a method for of amplifying nucleic acid sequences useful for detecting the presence of molecules of interest. The method is useful for detecting specific nucleic acids in a sample with high specificity and sensitivity. The method also has an inherently low level of background signal. A preferred form of the method consists of a DNA ligation operation, an amplification operation, and a detection operation. The DNA ligation operation circularizes a specially designed nucleic acid probe molecule. This operation is dependent on hybridization of the probe to a target sequence and forms circular probe molecules in proportion to the amount of target sequence present in a sample. The amplification operation is rolling circle replication of the circularized probe. A single round of amplification using rolling circle replication results in a large amplification of the circularized probe sequences.

Abstract: This invention discloses the use of high-affinity oligonucleotide ligands in flow cytometry diagnostic applications. Specifically, DNA ligands having one or more fluorophore molecules attached are disclosed which are useful in flow cytometry.

Abstract: The present invention provides a novel human chloride channel (HCCP) and polynucleotides which identify and encode HCCP. The invention also provides genetically engineered expression vectors and host cells comprising the nucleic acid sequences encoding HCCP and a method for producing HCCP. The invention also provides for agonists, antibodies, or antagonists specifically binding HCCP, and their use, in the prevention and treatment of diseases associated with expression of HCCP. Additionally, the invention provides for the use of antisense molecules to polynucleotides encoding HCCP for the treatment of diseases associated with the expression of HCCP. The invention also provides diagnostic assays which utilize the polynucleotide, or fragments or the complement thereof, and antibodies specifically binding HCCP.

Abstract: A heteroduplex tracking assay (HTA), a hybridization based method of determining the genetic relationship between two or more viral genomes, for genotyping HCV is disclosed. The HTA for genotyping HCV was developed using single stranded probes derived form the carboxyl terminus of core and part of the E1 for HCV subtypes 1a, 1b, 2a, 2b, and 3a. HTA is more accurate than RFLP for sub-typing HCV and has potential for identifying new variants and is useful for epidemiological studies.

Abstract: The present invention relates to a method of detecting a polynucleotide, comprising hybridizing a polynucleotide of known nucleotide sequence with a nuclease-resistant oligonucleotide primer having a sequence complementary to a part of the polynucleotide, then adding at least one kind of deoxynucleoside triphosphate, DNA polymerase and nuclease thereto, synthesizing a complementary strand being a nucleotide species located adjacent to the 3'-terminal of the primer and complementary to the polynucleotide, followed by decomposition thereof, the synthesis and decomposition of the complementary strand being repeated one or more times, and detecting the resulting pyrophosphoric acid or deoxynucleoside monophosphate. The present invention also includes a detection kit used for this method of detecting a polynucleotide.