Team:Michigan/Design

Design

While there are many genetic switches for detecting proteins, for example, the lac operon and tet regulators, to our knowledge, every genetic switch is unique to the protein it detects. Aptapaper seeks to create a switch that could have the same logic adapted to any protein, similar to how toehold switches can be adapted and respond to any sequence of trigger RNA. Toehold switches refer to an RNA switch that works by sequestering the ribosomal binding site and start codon in a hairpin, while leaving a portion of what the RNA trigger binds to exposed in a “toehold” region. This toehold region dramatically changes the kinematics of the system, making it much easier for the trigger to bind. After the initial binding, the hairpin is “unzipped” by the trigger1. Exact design specs of the well optimized second generation toehold design are detailed in Figure 1. Because toehold switches can respond to any RNA trigger, Aptapaper attempted to use aptamers in conjunction with toehold switches to allow efficient and sensitive protein sensing. See different design approaches below.