Protocol

Protein Arrays: Labeling the Compounds and Probing the Array for Protein-Small Molecule Interactions

This protocol was adapted from "Characterization of Protein Complexes," Chapter 10, in Proteins and Proteomics (ed. Simpson). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2003.

INTRODUCTION

To detect protein interactions with small molecules, a protein microarray is incubated with a fluorescently labeled compound, the array is washed, and stable interactions are identified by scanning the slide for fluorescence. It is often advantageous to label the small molecules indirectly, by covalently linking them to a previously labeled carrier molecule such as BSA. This protocol describes the labeling of BSA with Cy3 or Cy5, the linkage of the small molecule to the labeled BSA, and the probing of protein microarrays with the fluorescently labeled conjugate.