Abstract: Methods are provided for isolation of chromatin fractions of nucleoproteins containing histone H1, H2A, H2B, H3 and H4 proteins and/or histone H1, H2A, H2B, H3 and/or H4 proteins, from intact cells. The methods preserve original patterns of covalent modifications of the histone proteins.

Abstract: A class of antisense agents having a distributed guanidinium peptide nucleic acids (GPNA) backbone which has excellent uptake into mammalian cells, can bind to the target DNA or RNA in a highly sequence specific manner and can resist nucleases and proteases both outside and inside the cell(s) of interest. In one embodiment, either systemic or intratumoral administration of antisense Epidermal Growth Factor Receptor (“EGFR”) GPNA oligonucleotides is believed to downmodulate EGFR levels, thus in turn to reduce head and neck squamous cell carcinoma tumor growth, which has been confirmed to date both in vitro and in vivo.

Abstract: It is intended to provide an artificial mammalian chromosome which is stably held in mammalian cells and allows efficient expression of a target gene carried thereby. Namely, a first cyclic vector containing a mammalian centromere sequence and a selection marker gene and a second cyclic vector containing a functional sequence are transferred into mammalian host cells. Then transformed cells are selected by using the above-described selection marker gene and cells holding an artificial mammalian chromosome are selected from among the transformed cells thus selected. Thus, it is possible to construct an artificial mammalian chromosome which has a mammalian replication origin, the mammalian centromere sequence and the functional sequence, is in a cyclic form, can be replicated in mammalian cells, extrachromosomally held in the host cells and transferred to daughter cells in cell division.

Abstract: The present invention discloses methods and materials for delivering a cargo compound into a cancer cell. Delivery of the cargo compound is accomplished by the use of protein transduction domains derived from cupredoxins. The cargo compound may be a nucleic acid and specifically a DNA, RNA or anti-sense. The invention further discloses methods for treating cancer and diagnosing cancer.

Abstract: The present invention relates to a method for transfection of cells using at least one protein capable of forming nucleoprotein filaments, wherein the protein is initially modified with at least one functional component which influences one or more steps of the transfection, the nucleic acid to be transfected is then loaded with the modified protein, whereby the nucleic acid and the protein form a filament-like complex, and this complex is finally added to the cells to be transfected. The invention further relates to a transfection agent consisting of nucleoprotein filaments (NPF), with at least one nucleoprotein filament-forming protein being modified with at least one functional component for the transfection. Furthermore, the present invention relates to the use of the transfection agent according to the invention for producing a drug for gene therapeutic treatment of humans and animals.

Abstract: There is described a method of isolating nucleotide sequences encoding target peptides from DNA libraries using DNA binding proteins to link the peptide to the sequence which encodes it. DNA libraries are prepared from cells encoding the protein of interest, or from synthetic DNA, and inserted into, or adjacent to, a DNA binding protein in an expression vector to create a chimeric fusion protein. Incorporation of the vector DNA into a carrier package, during expression of the chimeric fusion protein, results in the production of a peptide display carrier package (PDCP) displaying the DNA-bound fusion protein on the external surface of the carrier package. Employment of affinity purification techniques results in the PDCP particles containing sequences encoding the desired peptide to be selected and the desired nucleotide sequences obtained therefrom.

Abstract: The present invention includes compositions, methods and kits for the identification of a polypeptide that binds to a predetermined RNA sequence. The invention comprises, in part, a photoreactive moiety to aid in identification of such a polypeptide.

Abstract: The present invention provides reagents and methods for the introduction of analogues of methyl or acetyl lysine into histone proteins.

Abstract: A therapeutic oligomer-peptide conjugate, and methods of using the conjugate are disclosed. The conjugate includes (a) a substantially uncharged oligonucleotide analog compound having a base sequence that includes a string of bases that are complementary to four or more contiguous cytosine bases in a target nucleic acid region to which the compound is intended to bind, and (b) conjugated to the compound, an arginine-rich peptide effective to enhance the uptake of the compound into target cells. The string of bases in the compound includes at least one inosine base positioned in the string so as to limit the number of contiguous guanine bases in said string to three or fewer. The conjugate has greater cellular uptake than the compound alone, by virtue of the arginine-rich peptide, and substantially greater antisense activity greater activity than the conjugate in the absence of inosine for guanine substitutions.

Abstract: Proteins that interact with c-Fos, nucleic acids encoding them and inhibitors utilizing them as well as methods for detecting an interaction and screening methods utilizing a protein that interacts with c-Fos are provided. Comprehensive analysis of transcription control factor complexes in a mouse brain cDNA library with c-Fos as a bait by using the cotranslation selection and screening of in vitro virus (IVV) and the C-terminal labeling method are conducted, thereby to analyze proteins unknown so far, proteins known so far, but unknown to form a complex with the c-Fos protein, and so forth.

Abstract: Methods are described for improvement of the serum half life of therapeutic nucleic acids by 3? conjugation to useful target proteins, or other large molecules with useful function. In one embodiment, a 3? A, C or G overhang is added to ds-DNA and the primary amines conjugated using biocompatible bifunctional linkers to proteins. The resulting nucleic acid-3?-conjugates are serum nuclease-resistant and retained in vivo for long periods without rapid kidney clearance. Further, the choice of conjugate imparts additional functionality to the nucleic acid -3-conjugate.

Abstract: HNF-4 (hepatocyte nuclear factor 4) is a protein enriched in liver extracts that binds to sites required for the transcription of the transthyretin (TTR) and apolipoprotein CIII (apoCIII) genes (Costa et al., 1989; Costa et al., 1990; Leff et al., 1989). We have purified HNF-4 protein (54 kD) and isolated a cDNA clone encoding the protein. HNF-4 is a member of the steroid hormone receptor superfamily with an unusual amino acid in the conserved “knuckle” of the first zinc finger (DGCKG). This and the fact that HNF-4 does not bind significantly to estrogen, thyroid hormone or glucocorticoid response elements indicate that HNF-4 may represent a new subfamily. HNF-4 binds to its recognition site as a dimer and activates transcription in a sequence-specific fashion in nonhepatic (HeLa) cells. HNF-4 mRNA is present in kidney and intestine as well as liver but is absent in other tissues.

Abstract: The invention provides molecules containing nucleic acid sequences for fragments of LPS-induced TNF-? factor (LITAF) and vectors containing these sequences. Also provided are molecules that contain the peptide sequence SQTWREPGAAGSPFHL, or homologs thereof. Such molecules may be useful in the treatment of diseases that relate to the expression of TNF-?, where treatment involves the modulation of this expression. The invention also provides methods for identifying compounds that inhibit or enhance the transcription of TNF-?.

Abstract: The present invention relates to methods for screening molecules and methods to detect protein-protein interactions and means used therein. More specifically, the present invention relates to methods for screening candidate drugs for treating or detecting MIF (macrophage migration inhibitor factor) related diseases. In certain aspects, the present invention involves detecting MIF/Jab1 (c-Jun activation domain binding protein) interactions as a basis for modulating cellular regulatory pathways and for identifying candidate drugs for MIF-related diseases. The invention also provides methods for the identification of molecules which dissociate or prevent interaction or binding between MIF and Jab1.

Abstract: Isolated nucleic acid sequences encoding mammalian MDM2 binding protein and polypeptide sequences for the mammalian MDM2 binding protein are provided. Also provided are vectors containing these nucleic acid sequences, host cells which express these proteins and antibodies targeted to these proteins. In addition, methods and compositions for modulating the G1 phase of the cell cycle via altering expression and/or activity of a mammalian MDM2 binding protein are provided.

Abstract: As anti-RNA polymerase (RNAP) antibodies are detected with high frequency in patients suffering from cutaneous scleroderma where skin sclerosis progresses rapidly, supervenes scleroderma renal crisis at a high rate, and associates with clinical entities whose prognoses are extremely bad, it is intended to provide a convenient method of detecting an anti-RNAP antibodies, which is extremely useful in diagnosing and classifying clinical entities of scleroderma, and predicting organ failure, in particular scleroderma renal crisis.

Abstract: The present invention provides a human polypeptide homolog of DBF4/ASK1 (for “Activator of S phase kinase”) and polynucleotides which identify and encode DRF1 (for “DBF4 Related Factor 1”). In addition, the invention provides expression vectors, host cells and methods for its production. The invention also provides methods for the identification of DRF1 or DRF1-containing complex agonists/antagonists, useful for the treatment of human diseases and conditions.

Abstract: The present invention provides isolated polypeptides of human p53 that contain mutations. These mutations can be toxic mutations, supertransactivating mutations or tox-suppressor mutations. Further provided by the invention are methods of identifying toxic, supertransactivating, weak transactivating and tox-suppressor mutations as well as methods of identifying compounds that mimic the toxic, supertransactivating and tox-suppressor mutations in human p53. Also provided are methods of inducing toxicity in a cell by administering a polypeptide comprising a supertransactivating or a toxic mutation.

Abstract: The present invention relates to a novel nucleotide sequence and the amino acid sequence encoded therein which comprise a novel gene and protein called Mustang. The present invention also relates to methods and compositions based on these sequences. These sequences are useful in the medical diagnosis, growth and regeneration of bone.

Abstract: The invention relates to the use of a carboxy-terminal fragment of the Ki-67 protein or of an active part, fragment or homologue thereof as a compound that can be used for intracellular transfer and for the introduction in and the release by the cells. The invention further relates to transfer compounds that contain the above-mentioned Ki-67 protein and to the vectors encoding the same. The invention also relates to corresponding pharmaceutical compositions and to the use of the transfer protein as an excipient or active agent in the treatment of diseases.

Abstract: Isolated nucleic acid sequences encoding mammalian MDM2 binding protein and polypeptide sequences for the mammalian MDM2 binding protein are provided. Also provided are vectors containing these nucleic acid sequences, host cells which express these proteins and antibodies targeted to these proteins. In addition, methods and compositions for modulating the G1 phase of the cell cycle via altering expression and/or activity of a mammalian MDM2 binding protein are provided.

Abstract: A nucleic acid sequence required for regulating the autolytic activity of bacteria is provided. Also provided are polypeptides encoded by the gene or mutant gene as well as vector and host cells for expressing these polypeptides. Methods for identifying and using agents which interact with the gene or mutant gene or polypeptides encoded thereby to inhibit bacterial growth and infectivity are also provided.

Abstract: Compositions and methods for the therapy of malignant diseases, such as leukemia and cancer, are disclosed. The compositions comprise one or more of a WT1 polynucleotide, a WT1 polypeptide, an antigen-presenting cell presenting a WT1 polypeptide, an antibody that specifically binds to a WT1 polypeptide; or a T cell that specifically reacts with a WT1 polypeptide. Such compositions may be used, for example, for the prevention and treatment of metastatic diseases.

Abstract: Human RelA-associated inhibitor (RAI) comprises 351 amino acids and is capable of binding to p65, a subunit of the transcription factor NF?B. A process for producing RAI, a cDNA encoding it, a fragment capable of hybridizing selectively to the cDNA sequence, a plasmid for expression and duplication comprising the cDNA, a host cell transformed with the plasmid, an antibody against the polypeptide, a pharmaceutical composition comprising the polypeptide or the antibody against it and a method for diagnosis of diseases using the antibody against the RAI are disclosed.

Abstract: Cloning and characterization of a full length cDNA encoding Sp110 (speckled 110), a novel 110 kDa polypeptide, is disclosed. It is disclosed that Sp110 is a component of the nuclear body, is expressed in leukocytes, and is also expressed in other types of cells, including endothelial cells, smooth muscle cells, liver cells and heart cells, after contact with certain cytokines. The disclosure also includes the following: Sp140 recruits Sp110 to the nuclear body, Sp110 functions as an activator of gene transcription, and Sp110 serves as a nuclear hormone receptor co-activator. Sp110 DNAs, polypeptides, antibodies are disclosed. Also disclosed are Sp110-related screening methods and clinical diagnostic methods.

Abstract: This invention relates to the methylation of histones, in particular to a previously uncharacterised group of histone H3 methylases which comprise a SET domain and which methylate either lysine 4 within the amino tail of histone H3 or within the histone H3 core. Methylation by these methylases, in particular trimethylation, is shown to be important for transcriptional activity.

Abstract: The invention provides fusion protein reporter molecules that can be used to monitor protein modifications (e.g., histone modifications) in living cells, and methods of using the fusion reporter molecules for diagnosing protein-modification-associated disorders (e.g. histone-modification-associated disorders). The invention also provides methods of using the fusion protein reporters to identify candidate pharmaceutical agents that effect protein modification in cells and tissues, thus permitting identification of candidate pharmaceutical agents for treatment of protein-modification-associated disorders.

Abstract: In accordance with the present invention, it has been discovered that various members of the steroid/thyroid superfamily of receptors can interact to form multimeric species comprising a complex of more than one receptor. Accordingly, the interaction of a first receptor species with a second receptor species modulates the ability of the first receptor species to trans-activate transcription of genes maintained under hormone expression control in the presence of the cognate ligand for said first receptor.

Abstract: The present invention provides genomic and cDNA encoding human cytoplasmic polyadenylation element binding protein, expression vectors comprising human cytoplasmic polyadenylation element binding protein cDNA and host cells that contain the expression vectors. Also provided are recombinant human cytoplasmic polyadenylation element binding protein and polypeptides derived thereof.

Abstract: The invention provides isolated Rad2/FEN-1 nucleic acids and their encoded proteins. The present invention provides methods and compositions relating to altering Rad2/FEN-1 concentration and/or composition of plants. The invention further provides recombinant expression cassettes, host cells, transgenic plants, and antibody compositions.

Abstract: The invention provides human polynucleotide sequences that encode transcription factor polypeptides that are termed ALF and SALF, and an alternative C-terminal sequence. The invention includes ALF, SALF and alternative C-terminus polypeptides, peptides, fusion proteins, expression vectors, agonists, antagonists, host cells that overexpress these polypeptides, including transgenic animals, and recombinant knock-out animals that cannot express the relevant RNAs and polypeptides. The invention also provides methods for the detection, diagnosis, screening, and monitoring disorders related to inappropriate expression, production, or activity of ALF and SALF, and provides methods to increase or decrease gene expression with respect to treating disorders related to inappropriate or ineffectual patterns of gene expression.

Abstract: The present invention relates to the discovery of the human nuclear receptor co-repressor gene and the human nuclear receptor co-repressor protein, a molecule that recruits a complex of proteins that alters chromatin structure and mediates transcriptional repression. Novel biological tools, prophylactics, therapeutics, diagnostics, and methods of use of the foregoing are also disclosed.

Abstract: This invention provides methods by which test substances can be screened for their ability to inhibit, enhance or eliminate double minute (DM) or extrachromosomal DNA by micronucleation in cells. This invention also provides a method for inducing maturation or death of a cell having the capacity to generate micronuclei. It also provides a method of treating a disease in a subject, the cells correlated with the disease having DM and extrachromosomal DNA as well as the capacity to generate micronuclei to capture them. Further provided is a method of detecting chromosomal and extrachromosomal DNA in a cell.

Abstract: Compositions and methods of using compositions with a nuclear targeting peptide containing a nonclassical nuclear localization signal to deliver selected molecules to the nucleus of eukaryotic cells are provided. The compositions are useful for gene transfer.

Abstract: The present invention provides novel nucleic acid molecules coding for sigma subunits of Mycobacterium tuberculosis RNA polymerase. It also relates to polypeptides, referred to as SigA and SigB, encoded by such nucleic acid molecules, as well as to vectors and host cells transformed with the said nucleic acid molecules. The invention further provides screening assays for compounds which inhibit the interaction between a sigma subunit and a core RNA polymerase.

Abstract: A method for imaging molecules contained in an array of discrete reaction sites on the surface of a solid support comprises: (i) imaging the array and detecting a first molecule located on the solid support at a known position with respect to the array; (ii) by reference to the first molecule, aligning inspection windows in registration with the discrete reaction sites; and (iii) determining the amount of detectable signal in each window. The method is used to locate the reaction sites accurately on the array, and to correct for any misalignments.

Abstract: A novel growth arrest homeobox gene has been discovered and the nucleotide sequences have been determined in both the rat and the human. The expression of the novel homeobox gene inhibits vascular smooth muscle cell growth. The growth arrest homeobox gene hereinafter referred to as the “Gax gene” and its corresponding proteins are useful in the study of vascular smooth muscle cell proliferation and in the treatment of blood vessel diseases that result from excessive smooth muscle cell proliferation, particularly after balloon angioplasty.

Abstract: This application provides human H37 protein having an amino acid sequence of SEQ ID NO: 1 or NO: 2; human gene encoding the protein; cDNA of the human gene which has a base sequence of SEQ ID NO: 3 or NO: 4; DNA fragment comprising a partial sequence of the cDNA; recombinant vector having the cDNA; antibody against human H37 protein; and a method for controlling the proliferation of cells by introducing the above DNA or antibody into the cells.

Abstract: The invention includes antibiotic pharmaceutical compositions comprising eukaryotic histone H1 protein and methods of using eukaryotic histone H1 protein to kill or to inhibit the growth of microorganisms, including, but not limited to, human pathogenic bacteria. The invention further includes a eukaryotic histone H1-containing animal feed and methods of improving growth of an animal by supplying the feed to the animal. The invention still further includes a kit comprising a eukaryotic histone H1-containing antibiotic pharmaceutical composition and an instructional material which describes the use of the composition. In addition, the invention includes a vaccine comprising a eukaryotic histone H1 protein and a method of vaccinating an animal using the vaccine.

Abstract: The present invention provides an isolated or purified antibody or antigenically-reactive fragment thereof that specifically binds to a C-terminal phosphorylated serine in an H2A histone protein and a product comprising the same. The present invention further provides fusion proteins comprising the isolated or purified antibody or antigenically-reactive fragment thereof. Also provided by the present invention are a method and a kit for determining double-stranded breaks in DNA. The method comprises contacting a sample comprising H2A histone proteins with the isolated or purified antibody or antigenically-reactive fragment thereof and detecting binding of the antibody or fragment thereof to an H2A histone protein in the sample. The detection of the binding of the antibody or fragment thereof to the H2A histone protein indicates the presence of a DNA double-stranded break in DNA.

Abstract: Disclosed are RNA polymerases consisting of a wild type RNA polymerase provided that at least one of amino acids in the wild type RNA polymerase has been modified to enhance its ability for incorporating 3?-deoxyribonucleotides and derivatives thereof in comparison with the corresponding wild type RNA polymerases. Specifically, disclosed are, for example, the RNA polymerases wherein at least one amino acid present in a nucleotide binding sites of the wild type RNA polymerases such as phenylalanine has been replaced with tyrosine. The RNA polymerases of the present invention are a RNA polymerase which exhibits little or no bias for incorporation between ribonucleotides and 3?-deoxyribonucleotide as well as among ribonucleotides having different base groups and among deoxyribonucleotides having. different base groups.

Abstract: The invention provides ssDNA-binding proteins from three species of archaeons, Methanococcus jannaschii, Methanobacter theromoautotrophicum, and Archaeoglobus fulgidus, as well as the ability to identify ssDNA-binding proteins from other archaeons. The proteins help render DNA more accessible to DNA polymerase and are robust reagents for a variety of biotechnical processes, including PCR. The invention further provides nucleic acids encoding such proteins, vectors for transfecting host cells, host cells comprising the vectors, and methods of using the proteins.

Abstract: The invention provides fusion protein reporter molecules that can be used to monitor protein modifications (e.g., histone modifications) in living cells, and methods of using the fusion reporter molecules for diagnosing protein-modification-associated disorders (e.g. histone-modification-associated disorders). The invention also provides methods of using the fusion protein reporters to identify candidate pharmaceutical agents that effect protein modification in cells and tissues, thus permitting identification of candidate pharmaceutical agents for treatment of protein-modification-associated disorders.

Abstract: Methods and compositions for subcellular fractionation of biological samples before proteomic analysis are given. Of particular interest is the separation of DNA binding nuclear proteins.

Abstract: The invention provides compositions and methods for inhibiting degradation of p53, thereby enhancing p53-mediated tumor suppressor activity.

Abstract: The invention encompasses Drosophila Recombination Associated Protein (DRAP) isolated D. melanogaster and a nucleic acid sequence encoding DRAP. The Drosophila Recombination Associated Protein, its homologues from other organisms or active peptides derived therefrom, as well as DNA encoding such protein are useful for homology-dependent pairing of three DNA strands. The combination of strand-transfer and topoisomerase activities associated with DRAP permits directed pairing and cleavage at defined site(s) within DNA. This in turn makes possible the isolation and/or removal of a defined segment of DNA. DRAP is also useful in cloning, genomic cloning and gene mapping, in promoting gene disruptions or “knockout” mutations, in carrying out targeted mutagenesis of specific genes and in generating transgenic animals.

Abstract: The present invention relates to a molecular motor actin binding protein, in particular, to Nuclear Myosin I&bgr; (NMI&bgr;) containing a 16 amino acid N-terminal extension involved in transcription. More particularly, this invention is directed to a molecule with oligonucleotide sequence coding for a protein nuclear Myosin I&bgr; (NMI&bgr;) containing a 16 amino acid N-terminal extension that co-localizes with, and forms functional complexes with, RNA polymerase II. This invention is also directed to polyclonal and monoclonal antibodies to the 16 amino acid N-terminal extension that block in vitro RNA synthesis. This invention is also directed to administration to a cell of polyclonal or monoclonal antibodies to the NMI&bgr; 16 amino acid N-terminal extension sequence or to an epitope within that sequence to inhibit transcription. Other inhibitors are also suitable. This invention may be used to treat illness through targeted inhibition of cell proliferation.

Abstract: This invention relates to a novel protein, termed LBDG3, herein identified as a Nuclear Hormone Receptor Ligand Binding Domain and to the use of this protein and nucleic acid sequence from the encoding genes in the diagnosis, prevention and treatment of disease.

Abstract: The invention describes the LAGE-1 tumor associated gene, including fragments, allelic variants and splice variants thereof. Also included are polypeptides and fragments thereof encoded by such genes, and antibodies relating thereto. Methods and products also are provided for diagnosing and treating conditions characterized by expression of a LAGE-1 gene product.

Abstract: A diagnostic drug and a diagnostic kit for autoimmune diseases including at least one of a polypeptide selected from an HMG-1 family, a polypeptide selected from an HMG-2 family, a fragment thereof which is reactable with an antibody of an autoimmune disease patient, and a method for detecting an antibody of an autoimmune disease patient using the same are provided.