Studies on the role of DNA looping in lysogenic gene regulation of bacteriophage lambda

Gene regulation is sufficiently complex that model systems are very important for advancing the field. Bacteriophage lambda is a classic model for understanding how genes are turned on and off by regulatory proteins. Lambda repressor (or CI) is a phage protein that binds to two well-defined regions of DNA (called operators), serving as an activator as well as a repressor. This thesis examines how long-range interactions between operator-bound CI proteins play a role in regulation of the CI gene. My approach was to use a fluorescent protein to measure how specific changes to the CI-binding properties of the two operators alters the amount of CI produced. From this I discovered that long-range interactions between CI proteins bound at the two operators can increase either activation or repression of the CI gene, depending on the pattern of DNA-binding. I used information from the literature to develop a structural model to represent all the configurations in which CI can bind to unlooped or looped operator DNA. Assigning these configurations as either unactivated, unlooped activated, looped activated or repressed, I calculated the probability of each and solved for the activation level of looped DNA relative to unlooped DNA. I finish this thesis with a discussion of the implications of my results and the additional questions they raise.