A jigsaw puzzle : detecting structural changes in ykkCD riboswitch RNA in response to tetracycline binding

Each year in the United States, at least 2 million people become infected with bacteria that are resistant to antibiotics. Approximately 23,000 people die each year as a direct result of these infections, which makes antibiotic resistance an important topic of research. The Gerczei lab is investigating a mechanism of antibiotic resistance that involves the ykkCD riboswitch. This riboswitch was first discovered in Bacilis subtilis, and it specifically recognizes the tetracycline family of antibiotics. When tetracycline is present in the cell, the antibiotic induces synthesis of the riboswitch mRNA which leads to the production of an efflux pump. This pump serves as a transporter protein and pumps the antibiotic out of the cell, rendering the cell resistant to tetracycline. The objective of this project is to detect structural changes occurring within the secondary structure of the ykkCD riboswitch RNA in response to tetracycline binding using nucleic acid footprinting methods. Ultimately, the hope is to use these footprinting techniques to determine the binding site of tetracycline on the RNA and map the structural change caused by tetracycline binding.