Genetic Switches

Loop-based genetic switches represent a ubiquitous regulatory mechanism of transcription present in all kingdoms of life. These switches determine developmental alternatives, such as quiescence versus virulence in bacteriophages, or organ identity in plants. Therefore, studying them offers a unique opportunity to discover fundamental regulatory principles. At their basis is the interaction between proteins bound at distant sites which causes the looping out of the intervening DNA. The looped and unlooped DNA states correspond to the ON/OFF (or viceversa) position of the switch. Investigating the conformations, thermodynamics and kinetics of different repressor-mediated genetic switches, we were able to point out the elements that are essential to make most loop-based genetic switches robust and yet responsive to environmental cues. Some of these essential elements are: (i) modular binding sites with differential affinity for cooperative and tunable protein interactions, (ii) non-specific binding (in addition to specific binding) for synergy and molecular memory, (iii) DNA supercoiling for added stability and switching trigger, (iv) and a protein loop closure that can withstand high torsional stress to maintain the looped switch state in the face of varying torsion on the DNA outside the loop.

Loop formation may be visualized and characterized by several single molecule techniques, including the tethered Particle Motion (TPM) technique and atomic force microscopy (AFM), as the figure below shows