Abstract: A system for analyzing expression levels and activity of a plurality of proteins is provided. A bio-displayed polypeptide binding component associated with a predetermined marker is used to bind the proteins of interest. The predetermined marker components are then amplified and detected in a high throughput manner.

Abstract: The use of protection schemes and solid phase synthesis reactions to generate molecules of core structure M, which have a plurality of moieties, each of which can be individually deprotected or subsequently derivatized are provided. In one process, M is a multifunctional low molecular weight compound, such as a saccharide, aminosugar, deoxysugar, nucleoside, nucleotide, coenzyme, amino acid, lipid, steroid, vitamin, hormone, alkaloid, or small molecule drug. In another process, M is an oligomeric compound, such as an oligosaccharide, oligonucleotide, peptide or protein.

Abstract: Gradient arrays for the analysis of biomolecules are provided. In particular, arrays and methods are provided for analyzing complex protein mixtures, such as the proteome. The arrays provide bifunctional reagents that allow for the separation and isolation of complex protein mixtures. Automated instruments for performing the methods are also provided.

Abstract: Double stranded DNAs, expression vectors and methods for their use are provided in which the intracellular expression of the double stranded DNAs is used to alter the phenotype of a target cell so that the function of a target nucleic acid that includes a nucleotide sequence encoding a motif of interest can be determined using a combinatorial ribozyme library. The members of the library are catalytic RNAs that disrupt the expression of the transcription product of the target nucleic acid. Disruption of transcription product expression results in an altered cell phenotype which is used to determine the function of the target nucleic acid. The specific phenotype or response may be associated with normal cellular processes, or it may contribute to the generation of pathogenesis involved in disease development. The compositions find use in high-throughput screens to assign gene functions.