Abstract: The present invention provides methods for high-throughput screening for bioactive compounds, in particular those that bind to RNA sequences involved in the pathogenesis of disease or in regulation of a physiological function. The methods involve measuring the conformation of an RNA target in the presence and absence of test ligands, and identifying as a ligand any test ligand that causes a measurable change in target RNA conformation.

Abstract: Methods are provided for the evolution of proteins of industrial and pharmaceutical interest, including methods for effecting recombination and selection. Compositions produced by these methods are also disclosed.

Abstract: A gene encoding: (a) a protein comprising an amino acid sequence of SEQ ID NO: 2; or (b) a protein having deletion, substitution or addition of at least one amino acid residue in the amino acid sequence of SEQ ID NO: 2, which has a helicase activity.

Abstract: Compositions, and products comprising a MutS homolog which binds to a mismatched region of a duplex DNA molecule in the presence of ADP are provided, as are methods of binding MutS homologs to mismatched DNA in the presence of ADP. The use of MutL homolog derivatives in combination with MutS homologs is also included. Nonhuman mammals which are nullizygous for both Msh2 and p53 are also provided, as are methods of making and using the same.

Abstract: Combinations, called matrices with memories, of matrix materials with remotely addressable or remotely programmable recording devices that contain at least one data storage unit are provided. The matrix materials are those that are used in as supports in solid phase chemical and biochemical syntheses, immunoassays and hybridization reactions. The data storage units are preferably non-volatile antifuse memories. By virtue of this combination, molecules and biological particles, such as phage and viral particles and cells, that are in proximity or in physical contact with the matrix combination can be labeled by programming the memory with identifying information and can be identified by retrieving the stored information. Combinations of matrix materials, memories, and linked molecules and biological materials are also provided.

Abstract: A method and kit are disclosed useful for detecting protein altering mutations in genes. The coding sequence of the gene is PCR amplified with a 5′ primer that contains at its 5′ end a polymerase binding site, a translation initiation site, and an in frame sequence coding for a peptide tag, followed by the in frame 5′ end of the test sequence. The coding sequence for the peptide tag can also be incorporated into the 3′ primer used for PCR. After PCR amplification of the test sequence, the PCR product is used as a template to make mRNA in an in-vitro transcription reaction using an RNA polymerase that recognizes the polymerase binding site incorporated into the 5′ PCR primer. The mRNA is then used as a template to make protein in an in-vitro translation reaction. The protein encoded by the test sequence has at its amino or carboxy terminus a peptide tag that can be used to purify the protein for further analysis.

Abstract: Combinations, called matrices with memories, of matrix materials that are encoded with an optically readable code are provided. The matrix materials are those that are used in as supports in solid phase chemical and biochemical syntheses, immunoassays and hybridization reactions. The matrix materials may additionally include fluophors or other luminescent moieties to produce luminescing matrices with memories. The memories include electronic and optical storage media and also include optical memories, such as bar codes and other machine-readable codes. By virtue of this combination, molecules and biological particles, such as phage and viral particles and cells, that are in proximity or in physical contact with the matrix combination can be labeled by programming the memory with identifying information and can be identified by retrieving the stored information. Combinations of matrix materials, memories, and linked molecules and biological materials are also provided.

Abstract: The present invention relates to methods and compositions for the diagnosis, prevention, and treatment of tumor progression in cells involved in human tumors such as melanomas, breast, gastrointestinal, lung, and bone tumors, various types of skin cancers, and other neoplastic conditions such as leukemias and lymphomas. Genes are identified that are differentially expressed in benign (e.g., non-malignant) tumor cells relative to malignant tumor calls exhibiting a high metastatic potential. Genes are also identified via the ability of their gene products to interact with gene products involved in the progression to, and/or aggressiveness of, neoplastic tumor disease states. The genes and gene products identified can be used diagnostically or for therapeutic intervention.

Abstract: Disclosed are the dbp gene and dbp-derived nucleic acid segments from Borrelia burgdorferi, the etiological agent of Lyme disease, and DNA segments encoding dbp from related borrelias. Also disclosed are decorin binding protein compositions and methods of use. The DBP protein and antigenic epitopes derived therefrom are contemplated for use in the treatment of pathological Borrelia infections, and in particular, for use in the prevention of bacterial adhesion to decorin. DNA segments encoding these proteins and anti-(decorin binding protein) antibodies will also be of use in various screening, diagnostic and therapeutic applications including active and passive immunization and methods for the prevention of Borrelia colonization in an animal. These DNA segments and the peptides derived therefrom are contemplated for use in the preparation of vaccines and, also, for use as carrier proteins in vaccine formulations, and in the formulation of compositions for use in the prevention of Lyme disease.

Abstract: The invention provides methods, compositions, and apparatus for performing sensitive detection of analytes, such as biological macromolecules and other analytes, by labeling a probe molecule with an up-converting label. The up-converting label absorbs radiation from an illumination source and emits radiation at one or more higher frequencies, providing enhanced signal-to-noise ratio and the essential elimination of background sample autofluorescence. The methods, compositions, and apparatus are suitable for the sensitive detection of multiple analytes and for various clinical and environmental sampling techniques.

Abstract: Methods, apparatus and compositions are presented for ligating ligands together which bind to a common receptor. One embodiment includes polynucleotide probes having photoreactive functional groups. The probes are capable of assuming substantially contiguous reactive positions on a target polynucleotide placing the photoreactive group in juxtaposition. Activation of the photoreactive functional groups with radiant energy form a probe reaction product in which the probes are bound to each other.

Abstract: The present invention provides CD36 mutant gene and methods and kits for diagnosing diseases caused by a lipid metabolism abnormality.

Abstract: Fluorescence-based assay methods for detecting biological analytes in a sample. The fluorescence background in these methods is significantly lower than in conventional assay methods. Also provided are methods of attaching nucleic acids to a metallic or metalloid surface.

Abstract: The invention referres to a method for the preparation and selective replication of deoxyribonucleic acid (DNA) from biomaterial using PCR (polymerase chain reaction) for the analysis in time-of-flight mass spectrometers (TOF) with matrix-assisted laser desorption and ionization (MALDI) for determining specific genetic features in biomaterial. The invention consists, in a first step, of replicating the selected DNA segments by the PCR method in the usual unmodified fashion, and in a further enzymatic replication process, to replicate the DNA segments using modified substrates (the nucleic acids used for PCR) and specially prepared primers to such DNA analogs as are especially suitable for ionization by MALDI. Preparation of the primers particularly consists of introducing a charged group, which improves the ionization, and modification of the substrates is used to neutralize the negative charge on the phosphoric acid group of the DNA backbone.

Abstract: This invention provides plasmids that are useful in detecting and determining the DNA-binding activity of sequence-specific DNA-binding molecules. The invention further provides plasmids that are useful in detecting and determining the activity of KNA polymerases in initiating transcription. In particular, the invention relates to plasmids that contain unique restriction sites and cognate nucleotide recognition sequences for sequence-specific DNA-binding molecules. Also provided are methods for using the plasmids disclosed herein.

Abstract: A method is disclosed for producing at least one copy of a pair of complementary single stranded polynucleotides. The method comprises forming, in the presence of nucleoside triphosphates and template dependent polynucleotide polymerase along each of the complementary single stranded polynucleotides, an extension of a polynucleotide primer. The polynucleotide primer is comprised of at least a sequence of 16 nucleotides terminating at its 3′ end in a 2 to 9 nucleotide sequence (S1), which is complementary with the 3′ ends of both of the complementary single stranded polynucleotides. The polynucleotide primer has at least an 8 nucleotide sequence (S2) that is 5′ of S1, where S2 is 50 to 80% complementary to the nucleotide sequences contiguous with the 3′ ends of the complementary single stranded polynucleotides. The extended polynucleotide primer and the single stranded polynucleotides are then dissociated.

Abstract: The present invention is directed to products and methods for storing, separating or analyzing a sample of genetic material. The invention is particularly suited for the separation of a selected genetic material from a sample containing genetic material from multiple sources.

Abstract: The present invention provides for a method for generating a fusion nucleic acid molecule capable of cross-over recombination which comprises: (a) contacting a first pair of primers with a first strand and a second strand of a first nucleic acid molecule and a second pair primers with a first strand and a second strand of a second nucleic acid molecule wherein the primers are suitable for use in a polymerase chain reaction; (b) amplifying the first nucleic acid molecule and the first pair of primers and the second nucleic acid molecule and the second pair of primers under amplification conditions, separately; (c) mixing the amplification products from step (b) and the first primer of the first pair of primers and the second primer of the second pair of primers under hybridization conditions; (d) amplifying the hybridized molecules of step (c) under amplification conditions so as to generate a directed, recombinant fusion nucleic acid molecule capable of cross-over recombination.

Abstract: Combinations, called matrices with memories, of matrix materials that are encoded with an optically readable code are provided. The matrix materials are those that are used in as supports in solid phase chemical and biochemical syntheses, immunoassays and hybridization reactions. The matrix materials may additionally include fluophors or other luminescent moieties to produce luminescing matrices with memories. The memories include electronic and optical storage media and also include optical memories, such as bar codes and other machine-readable codes. By virtue of this combination, molecules and biological particles, such as phage and viral particles and cells, that are in proximity or in physical contact with the matrix combination can be labeled by programming the memory with identifying information and can be identified by retrieving the stored information. Combinations of matrix materials, memories, and linked molecules and biological materials are also provided.

Abstract: A method and a kit for detecting a mutation from a non-mutated sequence of a target polynucleotide in a sample, by using a mismatch binding protein. The method comprises: a) providing non-mutated and mutated target polynucleotide; b) forming duplex of the non-mutated and mutated single strands of the target polynucleotide in a); c) adding a single strand binding protein to the polynucleotide from b); d) incubating the mismatch binding protein with an activating agent; e) adding the incubated mismatch binding protein from d) to the polynucleotide from c), whereby the mismatch binding protein binds to the duplex formed by one non-mutated and one mutated single strand of the target polynucleotide; f) detecting the presence of any mismatch binding protein bound to the target polynucleotide.