Abstract: Conformationally restricted 3',5'-bridged nucleoside analogues are described herein. The compounds can be prepared by cyclization at C3' and C5' of nucleosides through a linker or linking molecule. The nucleoside bases may be modified or unmodified. The nucleosides can be used as oligonucleotide building blocks or as small molecule pharmaceutical ingredients.

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 present invention relates to polynucleotide and polypeptide molecules for a secreted polypeptide designated zsig15. The polypeptides, and polynucleotides encoding them, may be used for mapping chromosome 19 and markers for tumor growth. The present invention also includes antibodies to the zsig15 polypeptides.

Abstract: The invention describes nucleic acids encoding the PARG protein, including fragments and biologically functional variants thereof. Also included are polypeptides and fragments thereof encoded by such nucleic acids, and antibodies relating thereto. Methods and products for using such nucleic acids and polypeptides also are provided.

Abstract: Methods are provided for preparing a double-stranded cDNA corresponding to the 5' end of an mRNA. In the subject methods, an mRNA is first contacted with an oligo dT primer under first strand cDNA synthesis conditions. Next, the resultant hybrid is contacted with a random primer under first strand cDNA synthesis conditions, such that a cDNA complementary to the 5' end of the mRNA is produced. The resultant hybrid molecule is converted to two different double-stranded cDNAs, a first cDNA comprising the oligo dT primer and a second cDNA lacking the oligo dT primer. The two double-stranded cDNAs are then separated from each other. The subject methods find use in a variety of applications, and find particular use in the synthesis of 5' enriched cDNA libraries. Also provided are cDNA libraries produced by the subject methods, as well as kits for performing the subject methods.

Abstract: The invention describes catalytic nucleic acid based compounds capable of cleaving nucleic acid polymers both in vivo and in vitro. Two embodiments of this invention are compounds with a short stem that does not base pair, a minizyme, and compounds with DNA hybridizing arms and RNA catalytic domain and stem, DNA-armed ribozymes. The compounds of this invention, while nucleotide based may be substituted or modified in the sugar, phosphate, or base. Methods of use and methods of treatment are also described.

Abstract: This invention relates to methods for making polynucleotides of any desired nucleotide sequence by repeating a series of reactions involving assembly of overlapping oligomers, ligation by DNA ligase, and cleavage with a restriction enzyme that cuts so as to add one or more additional nucleotides to a growing polynucleotide. This invention also relates to combining such a method for polynucleotide synthesis with a step employing localized melting of hybridized DNA oligomers, to synthesize an array of polynucleotides of different, defined nucleotide sequence on a substrate, and to the articles for polynucleotide hybridization so made.

Abstract: The invention described here is a method whereby a molecular tag is put on a gene, transcript and protein in a single recombinational event. The protein tag takes the form of a unique peptide that can be recognized by an antibody or other specific reagent, the transcript tag takes the form of the sequence of nucleotides encoding the peptide that can be recognized by a specific polynucleotide probe, and the gene tag takes the form of a larger sequence of nucleotides that includes the peptide-encoding sequence and other associated nucleotide sequences. The central feature of the invention in its essential form is that the tag-creating DNA has a structure such that when it is inserted into an intron within a gene it creates two hybrid introns separated by a new exon encoding the protein tag. A major virtue of the method is that it allows one to identify new proteins or protein-containing structures, and, having done so, to readily identify and analyze the genes encoding those proteins.

Abstract: Compositions and methods are provided for inhibiting the expression of human tumor necrosis factor-.alpha. (TNF-.alpha.). Antisense oligonucleotides targeted to nucleic acids encoding TNF-.alpha. are preferred. Methods of using these oligonucleotides for inhibition of TNF-.alpha. expression and for treatment of diseases, particularly inflammatory and autoimmune diseases, associated with overexpression of TNF-.alpha. are provided.

Abstract: A method of identifying one or a combination of ligands, e.g. oligonucleotides or analogues, that interact specifically with a target, e.g. a DNA or an RNA molecule having a secondary or tertiary structure. One ligand may be pre-reacted to open up the target for interaction with other ligands forming an array on a solid surface.

Abstract: Method for detecting Campylobacter by PCR detection of DNA sequence highly conserved between species lari, coli, jejuni and upsaliensis. Speciation between these four is possible as the PCR product is differentially cleaved by restriction endonucleases.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of MEKK5. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding MEKK5. Methods of using these compounds for modulation of MEKK5 expression and for treatment of diseases associated with expression of MEKK5 are provided.

Abstract: The invention relates generally to the quantitation of virus and viral nucleic acid. The invention relates to methods for quantitating an amount of virus present in a sample, comprising introducing into the sample a composition comprising a genetically tagged viral nucleic acid, isolating said wild type and said tagged nucleic acid, and quantitating said wild type and said tagged nucleic acid. The invention also relates to genetically tagged retroviral nucleic acid comprising a tag sequence, including insertions and deletions.

Abstract: The present invention provides detectably labeled RNA and DNA oligonucleotide multimers useful as diagnostic probes in medical, biological and chemical applications. A method for synthesizing DNA and RNA oligonucleotides, oligonucleotide multimers, and analogs, preferably those that are detectably labeled, is also provided. Oligonucleotide synthesis is performed by combining a circular single-stranded oligonucleotide template with an effective polymerase and at least two types of nucleotide triphosphate, without the addition of auxiliary proteins, to yield an oligonucleotide multimer comprising multiple copies of a repeated oligonucleotide sequence.

Abstract: The present invention relates to compositions of thermostable DNA polymerases derived from the hyperthermophilic eubacteria. In particular, the present invention comprises thermostable DNA polymerases from the hyperthermophilic eubacterium known as Thermotoga neapolitana. The present invention provides methods for utilizing naturally-occurring and non-naturally-occurring forms of T. neopolitana DNA polymerase. The T. neopolitana DNA polymerases of the present invention are used in combination with other compounds, including but not limited to pyrophosphatase and DNA polymerases from other thermophilic or hyperthermophilic organisms.

Abstract: A composition for the transfection of higher eucaryotic cells, comprising complexes of nucleic acid, a substance having an affinity for nucleic acid and optionally an internalizing factor, contains an endosomolytic agent, e.g. a virus or virus component, which may be conjugated. The endosomolytic agent, which is optionally part of the nucleic acid complex, is internalized into the cells together with the complex and releases the contents of the endosomes into the cytoplasm, thereby increasing the gene transfer capacity. Pharmaceutical preparations, transfection kits and methods for introducing nucleic acid into higher eucaryotic cells by treating the cells with the composition are also disclosed.

Abstract: Improvements to nucleic acid fingerprinting are disclosed. The method generates profiles of increased fidelity characteristic of the nucleic acids analyzed. Novel primers and other means are taught. Useful products are disclosed.

Abstract: The invention relates to methods for targeting an exogenous polynucleotide or exogenous complementary polynucleotide pair to a predetermined endogenous DNA target sequence in a target cell by homologous pairing, particularly for altering an endogenous DNA sequence, such as a chromosomal DNA sequence, typically by targeted homologous recombination. In certain embodiments, the invention relates to methods for targeting an exogenous polynucleotide having a linked chemical substituent to a predetermined endogenous DNA sequence in a metabolically active target cell, generating a DNA sequence-specific targeting of one or more chemical substituents in an intact nucleus of a metabolically active target cell, generally for purposes of altering a predetermined endogenous DNA sequence in the cell.

Abstract: Methods for applying graph theory techniques in methods to establish multiplexed assay formats for analyzing polymorphic DNAs are provided. These methods are used for designing and carrying out rapid and efficient processes for distinguishing target polymorphic DNA segments on the basis of variations in sequence and/or length. The methods are thus useful in the design of assays for determining identity, ancestry, predisposition to disease, or the presence or absence of a desired trait; genetic linkage analyses (gene mapping); and drug development.

Abstract: Disclosed is a method for determining a nucleotide sequence of DNA product amplified by polymerase chain reaction not requiring removal of primers and/or 2'-deoxyribonucleoside-5'-triphosphates and/or derivatives thereof, which comprises reacting ribonucleoside-5'-triphosphates comprising ATP, GTP, CTP, UTP and derivatives thereof and one or more of 3'-deoxyribonucleotide-5'-triphosphates comprising 3'-dATP, 3'-dGTP, 3'-dCTP, 3'-dUTP and derivatives thereof in the presence of an RNA polymerase and a DNA product which has been amplified by polymerase chain reaction and contains a promoter sequence for the RNA polymerase to afford a nucleic acid transcription product, separating the obtained nucleic acid transcription product and determining a nucleic acid sequence from the resluting separated fractions.

Abstract: A thermal cycling device comprising a ceramic sample plate, and method of use thereof, is provided.

Abstract: An enzymatic process for hydrolyzing the 7-position acyl ester of certain cephalosporin compounds to the corresponding alcohol is disclosed.

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

Abstract: The present invention relates to a vector for expression of a heterologous protein by a Gram negative bacteria, wherein the vector includes a nucleic acid such as DNA encoding the following: an origin of replication region; optionally and preferably a selection marker; a promoter; an initiation region such as translation initiation region and/or a ribosome binding site, at least one restriction site for insertion of heterologous nucleic acid, e.g. DNA, encoding the heterologous protein, and a transcription terminator. The inventive vector may contain DNA encoding the heterologous protein, e.g., pro-insulin such as pro-insulin with a His tag.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of NF-kappa-B p65 subunit. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding NF-kappa-B p65 subunit. Methods of using these compounds for modulation of NF-kappa-B p65 subunit expression and for treatment of diseases associated with expression of NF-kappa-B p65 subunit are provided.

Abstract: Methods, devices, apparatus and kits for amplifying and detecting nucleic acid are provided. The apparatus is a one or two-tier thermal cycling device that operates in conjunction with a reaction/detection unit. A sample is loaded into a reaction chamber of the device which is then mated with a detection chamber to form the reaction/detection unit. A first heating element of the thermal cycling apparatus applies a desired temperature to the reaction/detection device to amplify target nucleic acid in the sample. The reaction mixture is then transferred to the detection chamber by the second heating element and amplified target nucleic acid is immobilized on a support in the detection chamber. Microprocessor control controls the heat applied by the second element independently of the heat applied by the first element. A detection system associated with the apparatus detects and analyzes the immobilized amplified nucleic acid target.

Abstract: The present invention pertains to a method for sequencing genomes. The method comprises the steps of obtaining nucleic acid material from a genome. Then there is the step of constructing a clone library and one or more probe libraries from the nucleic acid material. Next there is the step of comparing the libraries to form comparisons. Then there is the step of combining the comparisons to construct a map of the clones relative to the genome. Next there is the step of determining the sequence of the genome by means of the map. The present invention also pertains to a system for sequencing a genome. The system comprises a mechanism for obtaining nucleic acid material from a genome. The system also comprises a mechanism for constructing a clone library and one or more probe libraries. The constructing mechanism is in communication with the nucleic acid material from a genome. Additionally, the system comprises a mechanism for comparing said libraries to form comparisons.

Abstract: Methods for simultaneously selecting binding site sequences for multiple DNA-binding proteins are provided. A source of DNA-binding proteins is mixed with oligonucleotide duplexes containing a randomized internal sequence. Bound oligonucleotides are isolated, amplified and analyzed, such as by DNA sequence analysis. The oligonucleotide duplexes are also used to identify and isolate DNA-binding proteins.

Abstract: Methods for determining quantities of nucleic acid sequences in samples undergoing amplification utilize amplification ratio estimates (R*) in operations to accurately perform absolute quantitation even when amplification factors for the target and control sequences undergoing amplification are different, time dependent or vary as a function of starting concentrations of nucleic acid sequences. These operations also take into account conversion efficiencies associated with the conversion of probes upon generation of target or control amplicons, but do not require the explicit calculation of such efficiencies. The operations also recognize that a preferred R* should be determined based on a preferred statistical criterion to improve quantitation. In addition, the use of standard samples having known starting concentrations of target and control sequences therein may enable accurate absolute quantitation without the explicit calculation of amplification ratio estimates.

Abstract: The invention provides a method for isolating nucleic acids encoding proteins comprising a signal peptide, e.g., a secreted protein. The method of the invention comprises isolating an RNA molecule associated with an endoplasmic reticulumn membrane preparation under conditions wherein the RNA is at least partially translated. The invention also provides a library of nucleic acids encoding proteins comprising a signal peptide, individual nucleic acids isolated according to the method of the invention, peptides encoded thereby, pharmaceutical compositions comprising such and kits for performing the method of the invention.

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

Abstract: A novel class of cyclins, referred to as D-type cyclins, of mammalian origin, particularly human origin, DNA and RNA encoding the novel cyclins, and a method of identifying other D-type and non-D type cyclins. Also disclosed are a method of detecting an increased level of a D-type cyclin and a method of inhibiting cell division by interfering with formation of the protein kinase-D type cyclin complex essential for cell cycle start.

Abstract: The invention relates to novel modified oligonucleotides which contain at least one 8-azapurine base and form more stable hybridization complexes with nucleic acids; To a process for their preparation, and to their use as inhibitors of gene expression, as probes for detecting nucleic acids, as aids in molecular biology, and as a pharmaceutical or diagnostic agent.

Abstract: Method of detecting a nucleic acid by converting the nucleic acid into a single-stranded nucleic acid under alkaline conditions, wherein at least one detergent from the group of anionic, non-ionic and zwitterionic detergents is present, adding an immobilizable or immobilized capture probe, hybridizing the capture probe with the nucleic acid under immobilization of the nucleic acid via the capture probe and detecting the amount of synthesized, immobilized hybrid.

Abstract: Amplification primers and methods for specific amplification and detection of a Campylobacter jejuni and C. coli target are disclosed. The primer-target binding sequences are useful for amplification and detection of C jejuni and C. coli target in a variety of amplification and detection reactions.

Abstract: The invention relates to a gene which encodes reverse transcriptase having DNA polymerase activity and substantially no RNase H activity. The invention also relates to vectors containing the gene and hosts transformed with the vectors of the invention. The invention also relates to a method of producing reverse transcriptase having DNA polymerase activity and substantially no RNase H activity by expressing the reverse transcriptase genes of the present invention in a host. The invention also relates to a method of producing cDNA from mRNA using the reverse transcriptase of the invention. The invention also relates to a kit for the preparation of cDNA from mRNA comprising the reverse transcriptase of the invention.

Abstract: A method for the detection of a polynucleotide target sequence is described. The method involves the formation of a covalent or non-covalent bonded pair of nucleotide sequences formed in response to a target polynucleotide sequence, adding nucleotide sequence specific binding proteins each capable of binding one member of the pair of nucleotide sequences, and detecting the specific binding proteins completed to the pair of nucleotide sequences.

Abstract: The present invention relates to a novel advantageous process for amplifying nucleic acids using DNA/PNA primers and a temperature-stable polymerase enzyme.

Abstract: A method of assay of a specific nucleic acid anticipated in a sample, which comprises:a DNA producing step which involves production of a double-stranded DNA having a promoter sequence for an RNA polymerase and the nucleic sequence of the specific nucleic acid (the specific nucleic acid sequence) downstream from the promoter sequence by using the specific nucleic acid in the sample as a template, andan RNA producing and measuring step which involves production of a single-stranded RNA having the specific nucleic acid sequence by the RNA polymerase and measurement of the single-stranded RNA,wherein the RNA producing and measuring step is initiated by adding at least the RNA polymerase, ribonucleoside triphosphates and a probe which is labeled with a fluorescent intercalative dye and is complementary to the single-stranded RNA to the reaction solution after the DNA producing step, involves measurement of the fluorescence intensity of the reaction solution, and is carried out at a constant temperature, and does

Abstract: Mercuric ion is cytotoxic and mutagenic to cells. However, the mechanisms of mercuric ion-induced cytotoxicity are not well understood. Studies have suggested that these effects may be due in part to the alteration and inhibition of a variety of cellular processes including DNA replication, DNA repair, RNA transcription, and protein synthesis. However, prior art studies utilizing whole cells, cell extracts, or purified DNA polymerases to examine these activities are not able to specifically identify the precise mechanism or site of the effect or adequately represent the highly ordered environment in which DNA replication occurs in the intact cell. We disclose a novel method for measuring the activity and fidelity of DNA replication using the complex of proteins called the DNA synthesome, an isolated multiprotein form of DNA polymerase. The DNA synthesome is a highly organized complex of proteins capable of supporting all phases of SV 40 origin-specific DNA replication in vitro.

Abstract: Antisense compounds, compositions and methods are provided for modulating the expression of G-alpha-i3. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding G-alpha-i3. Methods of using these compounds for modulation of G-alpha-i3 expression and for treatment of diseases associated with expression of G-alpha-i3 are provided.

Abstract: A method of forming a macromolecular microgene polymer comprises allowing DNA polymerase to act on oligonucleotides A and B complementary at least partially to each other to effect polymerase chain reaction. According to the present invention, there can be obtained a polymer consisting of a repeating microgene, which is efficiently and simply formed.

Abstract: The present invention relates to a fermentation process for preparing erythritol with high productivity using Trichosporonoides madida DS 911, more specifically, for preparing erythritol by optimizing the culture conditions such as pH, temperature, aeration rate and agitation speed, and by developing the process of fed-batch culture such as feeding strategy of substrate and composition of feeding substrate.

Abstract: Chimeric oligonucleoside compounds, and methods of preparing and formulating the same, are disclosed. The compounds and compositions are useful in activating RNaseH-mediated cleavage of target ribonucleic acid sequences, and in treating disease conditions relating to such sequences.

Abstract: Amplification primers and methods for specific amplification and detection of a Shigella spp. and enteroinvasive strains of Escherichia coli (EIEC) target are disclosed. The primer-target binding sequences are useful for amplification and detection of Shigella and EIEC target in a variety of amplification and detection reactions.

Abstract: The present invention relates to a novel method of identifying cDNA's which encode secreted and membrane-bound proteins. The present invention also relates to a novel method for preparing cDNA libraries enriched for signal sequences. The methods of the invention provide for an improved signal sequence detection system which results, when compared to the prior art, in a greater number of correctly identified signal sequences and less total time required to complete the procedure.

Abstract: This invention features methods, apparatus and kits for performing nucleic acid hybridization and amplification reactions on a support. Such methods and apparatus are useful in diagnostic and therapeutic processes for synthesizing nucleic acid and detecting target nucleic acids in a sample.

Abstract: A molecular sensing apparatus comprises a first electrode (10), a second electrode (12), a first molecule (20), a second molecule (22), and a third molecule (34). The first molecule (20) has a first chain of nucleic bases (30) and a first group (24). The first group (24) is bound to the first electrode (10). The second molecule (22) has a second chain of nucleic bases (32) and a second group (26). The second group (26) is bound to the second electrode (12). The third molecule (34) is bound to the first molecule (20) and the second molecule (22). A method which uses the molecular sensing apparatus is disclosed.

Abstract: A method for the analysis of DNA sequences and PCR products comprises the steps of constructing an oligonucleotide-labeled beadset, and labeled complementary probe, and exposing the beadset and probe to a DNA fragment or PCR product under hybridizing conditions and analyzing the combined sample/beadset by flow cytometry. Flow cytometric measurements are used to classify beads within an exposed beadset to determine the presence of identical or nonidentical sequences within the test sample. The inventive technology enables the rapid analysis of DNA sequences and detection of point mutations, deletions and/or inversions while also reducing the cost and time for performing genetic assays.

Abstract: Disclosed is a process for identifying clones having a specified activity of interest, which process comprises (i) generating one or more expression libraries derived from nucleic acid directly isolated from the environment; and (ii) screening said libraries utilizing an assay system. More particularly, this is a process for identifying clones having a specified activity of interest by (i) generating one or more expression libraries derived from nucleic acid directly or indirectly isolated from the environment; (ii) exposing said libraries to a particular substrate or substrates of interest; and (iii) screening said exposed libraries utilizing a fluorescence activated cell sorter to identify clones which react with the substrate or substrates.