DNA Hairpin Gate: A Renewable DNA Seesaw Motif Using Hairpins

Abstract

In 2011 the DNA seesaw gate motif was introduced. It is a powerful feed-forward DNA nanodevice that can perform digital logic computations. The landmark of that work managed to evaluate moderately large Boolean circuits by cascading multiple DNA seesaw gates. Although the design is robust in solution and scalable, it is designed for one time use and is not reusable. This prevents pursuing important applications such as feedback and sequential digital circuits. We present a novel design for DNA nanodevices that can perform digital logic computations and are furthermore renewable. First, we modified the prior DNA seesaw gate motif into a hairpin. We call the resulting motif a DNA hairpin-seesaw gate. We show the feed-forward digital computation reaction imitates the seesaw gate motif. Second, we added a reporting phase that provides increased scalability to our device. Third, we designed input and fuel extracting hairpins that when added, initiate a renewing process. This results in a renewed functional gate, in its original configuration, which is able to make a new logical computation with new inputs. Finally, we introduced a renewable two-input Boolean logic OR gate. After calculating the output of a certain input set, the circuit is restored and a new set of inputs is introduced to compute the new output. We provide experimental fluorescent data on three repeated rounds of executions of our hairpin gate motif and its restoration, indicating gradual loss of response. Finally, we calculated rate constants of our experimental data by fitting it to a second order reaction model using maximum likelihood estimation method.