Design, Analysis, and Modeling of Protein-DNA Loops
Thursday, September 20, 2007 - 1:30pm - 2:30pm
DNA looping allows protein transcription factors to act at a distance along DNA. Looping is also a test bed for theories on DNA and protein structure and flexibility. However, most natural DNA loops are not stable enough for structural studies. We have designed and constructed bent DNA molecules that form hyperstable DNA loops anchored by the Lac repressor. Biochemical and fluorescence experiments show that different loop constructs can adopt different conformations, but the shapes of the loops remain uncertain, and the landscape of loop thermodynamics as a function of DNA sequence is not well-explored. We present experimental and theoretical approaches aimed at disentangling the roles of protein and DNA flexibility in this important model system.