Abstract: Methods, arrays and kits are provided for rapidly and efficiently identifying and quantifying multiple different activated transcription factors in a biological sample at the same time. In one embodiment, the method includes the step of mixing a library of different transcription factor probes with a sample containing activated transcription factors. The transcription factor probes that have bound to the activated transcription factors may be isolated from the complexes formed between the probes and the activated transcription factors. The bound probes can be identified, for example, by using an array of hybridization probes.

Abstract: Methods, arrays and kits are provided for rapidly and efficiently identifying and quantifying multiple different activated transcription factors in a biological sample at the same time. In one embodiment, the method includes the step of mixing a library of transcription factor probes with a sample containing activated transcription factors. The transcription factor probes that have bound to the activated transcription factors may be isolated from the complexes formed between the probes and the activated transcription factors. The bound probes can be identified, for example, by using an array of hybridization probes.

Abstract: Compositions, kits and methods are provided for isolating and characterizing short-lived proteins. The method comprises: taking a library of cells, each cell in the library expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; modifying a rate of protein expression or degradation by cells in the library; and selecting a population of cells from the library of cells based on the population of cells having different reporter signal intensities than other cells in the library, the difference being indicative of the population of cells expressing shorter lived fusion proteins than the fusion proteins expressed by the other cells in the library; and determining protein sequences of the fusion proteins of the selected population of cells. Also provided are oligonucleotide, protein and antibody arrays derived from short-lived proteins.

Abstract: A library of nucleic acid constructs is provided in which each construct comprises a cis element sequence comprising one or more copies of a cis element to which a transcription factor is capable of binding the cis element sequence varying within the library of constructs, a promoter sequence 3′ relative to the cis element sequence, a reporter sequence 3′ relative to the promoter sequence that comprises a variable sequence that varies within the library and wherein a same cis element sequence is employed with a given reporter sequence within the library of constructs.

Abstract: A method is provided for identifying multiple different activated transcription factors in a cell sample. The method comprises transducing or transfecting a cell sample to comprise a library of constructs. Each construct comprises a cis element sequence including one or more copies of a cis element to which a transcription factor is capable of binding. The cis element sequence varies within the library of constructs and include a promoter sequence 3′ relative to the cis element sequence, and a reporter sequence 3′ relative to the promoter sequence that comprises a variable sequence that varies within the library wherein a same cis element sequence is employed with a given reporter sequence within the library of constructs.

Abstract: A method is provided for screening for agents that affect protein degradation rates, the method comprising: taking a library of cells, the cells expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; contacting the library of cells with a plurality of agents which may affect protein degradation rates; for each agent, selecting cells in the library which express short-lived proteins based on whether the cells have different reporter signal intensities than other cells in the library, the difference being indicative of the selected cells expressing shorter lived fusion proteins than the fusion proteins expressed by the other cells in the library; and characterizing the fusion proteins expressed by the selected cells for each agent.

Abstract: A method is provided for characterizing short-lived proteins, the method comprising: taking a library of cells, each cell in the library expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; modifying a rate of protein expression or degradation by cells in the library; and selecting a population of cells from the library of cells based on the population of cells having different reporter signal intensities than other cells in the library, the difference being indicative of the population of cells expressing shorter lived fusion proteins than the fusion proteins expressed by the other cells in the library; and determining protein sequences of the fusion proteins of the selected population of cells.

Abstract: Method and kits are provided for isolating DNA probes which bind to activated transcription factors, the method comprising: contacting a biological sample with a library of double stranded DNA probes under conditions where DNA probe-transcription factor complexes are formed between the DNA probes and activated transcription factors present in the biological sample; separating DNA probe-transcription factor complexes from non-complexed DNA probes in the library using an agarose gel separation; excising a portion of the agarose gel comprising the separated DNA probe-transcription factor complexes; and isolating the DNA probes from the excised portion of the agarose gel.

Abstract: A method is provided for identifying complexes between a transcription factor and another protein, the method comprising: isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of transcription factor; and identifying which of a plurality of different proteins are present in the isolated transcription factor complexes.

Abstract: Method and kits are provided for screening for transcription factor modulators, the method comprising: forming a plurality of test samples by contacting samples of cells with different agents; and for each test sample, identifying which of a plurality of different activated transcription factors are present by taking a library of double stranded transcription factor probes, the transcription factor probes each comprising a recognition sequence capable of binding to an activated transcription factor, the recognition sequence varying within the library for binding to different activated transcription factors, contacting the different test sample with the library of double stranded DNA probes under conditions where DNA probe-transcription factor complexes are formed between the DNA probes and activated transcription factors present in the test samples, isolating the transcription factor probes from the transcription factor probe-transcription factor complexes formed, and identifying which transcription factor pr

Abstract: Green fluorescent protein (GFP) is widely used as a reporter in determining gene expression and protein localization. The present invention provides fusion proteins with a half life of ten hours or less with several embodiments having half lives of 4 hours or less. Such proteins may be constructed by fusing C-terminal amino acids of the degradation domain of mouse ornithine decarboxylase (MODC), which contains a PEST sequence, to the C-terminal end of an enhanced variant of GFP (EGFP). Fluorescence intensity of the fusion protein in transfected cells is similar to that of EGFP, but the fusion protein, unlike EGFP, is unstable in the presence of cycloheximide. Specific mutations in the MODC region have resulted in mutants with varying half lives, useful for a variety of purposes.

Abstract: Green fluorescent protein (GFP) is widely used as a reporter in determining gene expression and protein localization. The present invention provides fusion proteins with a half life of ten hours or less with several embodiments having half lives of 4 hours or less. Such proteins may be constructed by fusing C-terminal amino acids of the degradation domain of mouse ornithine decarboxylase (MODC), which contains a PEST sequence, to the C-terminal end of an enhanced variant of GFP (EGFP). Fluorescence intensity of the fusion protein in transfected cells is similar to that of EGFP, but the fusion protein, unlike EGFP, is unstable in the presence of cycloheximide. Specific mutations in the MODC region have resulted in mutants with varying half lives, useful for a variety of purposes.

Abstract: A method for in vivo selective targeted degradation of intracellular proteins in situ by inducing in vivo or ex vivo in cells a production of dual-function protein comprising N-terminal domain as well as a C-terminal domain or delivering the dual-function protein. The N-terminal domain of the dual-function protein destabilizes the target protein and directs its degradation when linked to it through a linker between the target protein and between the protein agent of the invention. The protein degradation directing N-terminal domain is a subregion within the first 97 amino acids corresponding to the N-terminus of protein antizyme.

Abstract: Green fluorescent protein (GFP) is widely used as a reporter in determining gene expression and protein localization. The present invention provides fusion proteins with a half life of ten hours or less. Such proteins may be constructed by fusing C-terminal amino acids of the degradation domain of mouse ornithine decarboxylase (MODC), which contains a PEST sequence, to the C-terminal end of an enhanced variant of GFP (EGFP). Fluorescence intensity of the fusion protein in transfected cells is similar to that of EGFP, but the fusion protein, unlike EGFP, is unstable in the presence of cycloheximide. Specific mutations in the MODC region have resulted in mutants with varying half lives, useful for a variety of purposes.

Abstract: The present invention provides fusion protein comprising I.kappa.B and green fluorescent protein. Also provided is DNA encoding this protein and vector expressing such DNA and various methods of using a fusion protein comprising I.kappa.B and green fluorescent protein.

Abstract: The present invention provides fusion protein comprising I.kappa.B and green fluorescent protein. Also provided is DNA encoding this protein and vector expressing such DNA and various methods of using a fusion protein comprising I.kappa.B and green fluorescent protein.

Abstract: A method for selective targeted degradation of intracellular proteins in situ by inducing in cells a production of an agent comprising N-terminal domain as well as a C-terminal domain. The N-terminal domain destabilizes the target protein and directs its degradation when attached to it through the C-terminal domain acting as a linker between the target protein and between the protein agent of the invention. The protein degradation directing N-terminal domain is a subregion within 97 amino acids corresponding to the N-terminus of protein antizyme.