Analysis and design of a single-molecule DNA nanodevice for thermal band-pass filters

Abstract

We previously proposed, modeled, and experimentally validated a temperature-sensitive single-molecule DNA nanodevice that operates via competitive folding, as a potential platform for implementing a tunable thermal band-pass filter. Due to its peculiar hill-shaped efficiency profile, which differs markedly from the common sigmoidal melting curves observed for isolated DNA folding, this device could be used to control other molecular machines, and thus represents a promising biotechnological advance. Preliminary simulations established the basic feasibility of tuning the device for filter operation. However, the details of the complex dependencies of the peak temperature, width, and maximum value of the efficiency curve on the energetic stabilities of the individual device components, which is essential information for guiding directed design, remained unclear. In this work, an exact closed-form expression for predicting the peak temperature is derived and validated. The scaling behavior of this expression is then exploited to construct an effective algorithm for designing device implementations with target operating characteristics, thereby establishing the algorithmic tractability of tailored device design. This algorithm is then applied to produce a targeted filter design, with detailed simulations of device behavior. Finally, the application of the system model to folding error estimation is also discussed.