A systems approach to measuring the binding energy landscapes of transcription factors.
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.
Maerkl
Sebastian J
SJ
Biochemistry and Molecular Biophysics Option, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
Quake
Stephen R
SR
D001483:Base Sequence; D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / Q000378:metabolism; D051792:Basic Helix-Loop-Helix Proteins / Q000378:metabolism*; D019295:Computational Biology; D003198:Computer Simulation; D004247:DNA / Q000378:metabolism*; D004271:DNA, Fungal / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism; D024721:E-Box Elements; D015966:Gene Expression Regulation, Fungal; D018257:Helix-Loop-Helix Motifs; D006801:Humans; D046210:Microfluidic Analytical Techniques; D020411:Oligonucleotide Array Sequence Analysis; D011485:Protein Binding; D020033:Protein Isoforms / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid; D012097:Repressor Proteins / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D049490:Systems Biology; D013698:Templates, Genetic; D013816:Thermodynamics; D014157:Transcription Factors / Q000378:metabolism
D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; D051792:Basic Helix-Loop-Helix Proteins; D004247:DNA; D004271:DNA, Fungal; D004268:DNA-Binding Proteins; D020033:Protein Isoforms; D012097:Repressor Proteins; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; C064042:CBF1 protein, S cerevisiae; C106465:MNT protein, human; C060292:PHO4 protein, S cerevisiae