Design Software for DNA-Based Sensing Nano-Architectures

Building on an existing grid computing platform and DNA origami design automation software that leverages such, this Phase II STTR project will produce a CAD (computer-aided design) application for designing DNA nanostructures for a variety of applications. The application, called inSequio, addresses multiple deficits that have blocked advancement in this promising field. It combines an easy-to-use interface, which allows for the specification of complex DNA-based nano-sensor architectures, with an optimization engine that computes the sequence-sets required for reliable self-assembly of specified designs. Among the many enhancements planned for Phase II, we will (1) augment inSequio"s thermodynamics model to support artificial DNA bases; (2) add a reduced model nanoscale dynamics simulator that enables global dynamics calculations; and (3) add a"region of interest"atomistic simulator for active components of the design, which will provide spectroscopic predictions related to optoelectronic sensing, particularly in the THz domain. These new capabilities will provide designers with novel insight into structure functionality during the design process. The project will conclude with a ready-to-use (TRL 9) software application. To demonstrate the utility of the resultant software, a prototype nano-scale molecular sensor for Ricin, composed of dynamic capture and reporting moieties, will be designed, developed and demonstrated.