Tightly bent DNA is the fact of life.  Studying the DNA mechanics in vitro  will enrich our knowledge on how things work in the complex living cells.  Recent experiments from the group of Jon Widom have shown that the elastic properties of DNA depend strongly on its sequence and on the scale of persistence length,  DNA is much more flexible than expected.  We construct various of DNA segments with different length or sequences bounded at each end with a Lac Operator.  We are using the tethered particle method (TPM) to measure the propensity for loop formation and how it depends upon DNA sequence and lengths.

The mechanical properties of the loop can be tuned by changing its sequence and length leading to phenotypic changes in a bacterial population.

One provocative class of examples of transcriptional regulation involve DNA looping. What makes these examples especially intriguing is the way in which DNA mechanics influences the gene expression readout of a wide variety of transcriptional networks.

Using themodynamic models of transcriptional regulation we can quantify the free energy cost of different DNA conformations. We are in the process of measuring the in vivo flexibility of the same DNA sequences we are characterizing in vitro. This is done by using the lac operon as a tool to quantify DNA mechanics. The objectives in this case are multiple, ranging from testing our theoretical models to making the connection between in vivo and in vitro DNA mechanics.