Abstract: Methods for purifying biological macromolecules are provided. Aspects of the subject methods include contacting the biological macromolecule with an exemplary hydroxamate affinity tag to produce a tagged moiety followed by purification of the tagged moiety by immobilized metal affinity chromatography (IMAC). Also provided are kits comprising an exemplary subject hydroxamate affinity tag, an IMAC resin and a metal ion configured for loading onto the resin, wherein the metal ion is capable of binding to a compound containing the hydroxamate affinity tag.

Abstract: Compositions and reagents for molecular profiling using proximity ligation-/>7 situ hybridization (PLISH) are disclosed. In particular, PLISH merges the specificity of proximity ligation, the sensitivity of tiling multiple probes for a target nucleic acid, and the high signal intensity of rolling circle amplification. The probe design capitalizes on the formation of Holliday-like junctions for optimal signal amplification. PLISH provides single molecule resolution and allows for quantitation of a virtually unlimited number of nucleic acids within individual cells. PLISH is also compatible with immunohistochemistry and archival formal-fixed, paraffin-embedded tissue samples.

Abstract: Provided herein is method of screening, comprising: a) combining a nucleic acid-programmed small molecule library with: an enzyme, and a substrate for the enzyme, wherein each of the members of the library comprises a test agent that is linked to an nucleic acid tag that encodes the test agent and the combining results in transferring a chemoselective functional group from the substrate onto at least some of the members of the library; b) isolating the library members onto which the chemoselective functional group has been covalently transferred; and c) amplifying the nucleic acid tags of the library members isolated in step b) to produce an amplification product. Libraries and kits for performing the method are also provided as are compounds and pharmaceutical compositions thereof.

Abstract: The invention provides methods and compositions for protein structure analysis, including substrate binding sites, sites of protein-protein interactions, three dimensional structure analysis, and stability, all with single amino acid resolution. In general, the subject methods involve introduction of cysteine residues, which serve as probes for physical analysis, into a protein by translational misincorporation in vivo. In many embodiments, proteins containing misincorporated cysteine residues are reacted with a crosslinking agent that covalently links misincorporated cysteine residues to a proximal amino acid in the folded protein. These methods, termed “MXLINK” methods, may be used for protein tertiary structure analysis. In other embodiments, cysteine-misincorporated proteins are used in protein footprinting methods, termed “MPAX” or “MSX” methods.

Abstract: The present invention describes templated combinatorial chemical libraries comprised of a plurality of bifunctional molecules having both a chemical compound and a nucleic acid tag that defines the structure of the chemical compound and directs its synthesis. Also described are methods for producing, enriching and in vitro evolution of the bifunctional molecules of such libraries based on the nucleic acid tags and methods for selecting for library compounds having a desired activity.

Abstract: The invention provides methods and compositions for protein structure analysis, including substrate binding sites, sites of protein-protein interactions, three dimensional structure analysis, and stability, all with single amino acid resolution. In general, the subject methods involve introduction of cysteine residues, which serve as probes for physical analysis, into a protein by translational misincorporation in vivo. In many embodiments, proteins containing misincorporated cysteine residues are reacted with a crosslinking agent that covalently links misincorporated cysteine residues to a proximal amino acid in the folded protein. These methods, termed “MXLINK” methods, may be used for protein tertiary structure analysis. In other embodiments, cysteine-misincorporated proteins are used in protein footprinting methods, termed “MPAX” or “MSX” methods.

Abstract: The invention provides methods and compositions for protein structure analysis, including substrate binding sites, sites of protein-protein interactions, three dimensional structure analysis, and stability, all with single amino acid resolution. In general, the subject methods involve introduction of cysteine residues, which serve as probes for physical analysis, into a protein by translational misincorporation in vivo. In many embodiments, proteins containing misincorporated cysteine residues are reacted with a crosslinking agent that covalently links misincorporated cysteine residues to a proximal amino acid in the folded protein. These methods, termed “MXLINK” methods, may be used for protein tertiary structure analysis. In other embodiments, cysteine-misincorporated proteins are used in protein footprinting methods, termed “MPAX” or “MSX” methods.