Detecting Protein–Small Molecule Interactions Using Fluorous Small-Molecule Microarrays

  • Arturo J. Vegas
  • Angela N. Koehler
Part of the Methods in Molecular Biology book series (MIMB, volume 669)


General binding assays involving microarrays of small molecules can be used to identify small molecule ligands for nearly any protein, even in the absence of knowledge about protein structure or function. Several suitable methods for manufacturing small molecule microarrays (SMMs) exist and different immobilization methods may be more or less preferable for any given application. Here, we describe a protocol for noncovalent and homogenous capture of small molecules using fluorous interactions between small molecules containing fluorocarbon tags and fluorocarbon-coated glass surfaces. These arrays are especially useful for applications that require display of compounds in a specific orientation such as screening biased libraries.

Key words

Small molecule microarrays Fluorous Noncovalent attachment Homogenous display HDAC SAHA Structure-binding relationships 



The authors would like to thank Professor Stuart Schreiber, Dr. James Bradner, Dr. Weiping Tang, Olivia McPherson, Edward F. Greenberg, Dr. Ralph Mazitschek, Dr. Carlos Tassa, Dr. Marvin Yu, and Dr. Philip Yeske for providing materials, technical support, or advice that was relevant to developing this protocol. Work described herein was funded in whole or in part with Federal funds from the National Cancer Institute’s Initiative for Chemical Genetics, National Institutes of Health, under contract no. N01-CO-12400.


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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Arturo J. Vegas
    • 1
    • 2
    • 3
  • Angela N. Koehler
    • 4
  1. 1.Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeUSA
  2. 2.Koch Institute for Integrative Cancer ResearchCambridgeUSA
  3. 3.Department of AnesthesiologyChildren’s Hospital BostonBostonUSA
  4. 4.Broad Institute of Harvard and MITCambridgeUSA

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