Implementing Arbitrary CRNs Using Strand Displacing Polymerase

The regulation of cellular and molecular processes typically involves complex biochemical networks. Synthetic nucleic acid reaction networks (both enzyme-based and enzyme-free) can be systematically designed to approximate sophisticated biochemical processes. However, most of the prior experimental protocols for reaction networks relied on either strand-displacement hybridization or restriction and exonuclease enzymatic reactions. These resulting synthetic systems usually suffer from either slow rates or leaky reactions. In this work, we propose an alternative architecture to implement arbitrary reaction networks, that is based entirely on strand-displacing polymerase reactions with non-overlapping I/O sequences. We first design a simple protocol that approximates arbitrary unimolecular and bimolecular reactions using polymerase strand displacement reactions. Then we use these fundamental reaction systems as modules to show three large-scale applications of our architecture, including an autocatalytic amplifier, a molecular-scale consensus protocol, and a dynamic oscillatory system.

Duke Scholars

Author John H. Reif Computer Science

Author Xin Song