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Published January 12, 2007 | Supplemental Material
Journal Article Open

A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors

Abstract

A major goal of systems biology is to predict the function of biological networks. Although network topologies have been successfully determined in many cases, the quantitative parameters governing these networks generally have not. Measuring affinities of molecular interactions in high-throughput format remains problematic, especially for transient and low-affinity interactions. We describe a high-throughput microfluidic platform that measures such properties on the basis of mechanical trapping of molecular interactions. With this platform we characterized DNA binding energy landscapes for four eukaryotic transcription factors; these landscapes were used to test basic assumptions about transcription factor binding and to predict their in vivo function.

Additional Information

© 2007 American Association for the Advancement of Science. Received 7 June 2006; accepted 20 November 2006. We thank B. Wold and J. Berger for helpful discussions and K. Kapur and C. Jacobs for help with the document. Supported in part by Defense Advanced Research Projects Agency–Biological Input Output Systems, an NIH Director's Pioneer Award, and Howard Hughes Medical Institute. S.R.Q. holds equity in, is a paid consultant for, and is a co-founder and former director of Fluidigm, which may license the device described in this paper.

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