Abstract
DNAβprotein interactions are fundamental to many biological processes, including the regulation of gene expression. Determining the binding affinities of transcription factors (TFs) to different DNA sequences allows the quantitative modeling of transcriptional regulatory networks and has been a significant technical challenge in molecular biology for many years. A recent paper by Maerkl and Quake1 demonstrated the use of microfluidic technology for the analysis of DNAβprotein interactions. An array of short DNA sequences was spotted onto a glass slide, which was then covered with a microfluidic device allowing each spot to be within a chamber into which the flow of materials was controlled by valves. By trapping the DNAβprotein complexes on the surface and measuring their concentrations microscopically, they could determine the binding affinity to a large number of DNA sequences that were varied systematically. They studied four TFs from the basic helixβloopβhelix family of proteins, all of which bind to Eβbox sites with the consensus CAnnTG (where βnβ can be any base), and showed that variations in affinity for different sites allows each TF to regulate different genes. BioEssays 29:717β721, 2007. Β© 2007 Wiley Periodicals, Inc.