Dynamic DNA strand displacement circuits

Abstract

Nucleic acids, the NA in DNA and RNA, have long been known to be vitally important molecules within biological cells and organisms. However, they are interesting for more than just their known roles in biology: their predictable Watson-Crick base pairing properties allow nucleic acids to be powerful nanoscale engineering tools. Additionally, nucleic acid-based devices are particularly attractive as biotechnological tools, because nucleic acids naturally exist within all life, and thus nucleic acid devices more easily function in cellular environments. It is for these reasons that nucleic acids have emerged as a frequent star in recent synthetic biology, biotechnology, and nanotechnology research papers. This thesis is a collection of 6 experimental papers, 3 theoretical papers, and 1 review paper that demonstrate and characterize novel nucleic acid-based devices such as catalysts, logic gates, and allosteric switches. Particular effort was placed in ensuring that all the designs are generalizable in sequence and that all the devices are modular in nature; this allows many different components to be integrated into higher-complexity devices. The works presented in this thesis were designed using only non-covalent changes to nucleic acid complexes and structures via Watson-Crick base pairing--i.e. hybridization, branch migration, and dissociation. These three primitives are sufficient to construct an endless variety of circuits and devices, much like how resistors, capacitors, and inductors allow complex electrical circuits. One advantage of devices, reactions, and circuits engineered using only Watson-Crick interactions is their robustness to their environmental conditions. While enzymatic reactions require specific temperatures, salt conditions, and co-factors, nucleic acid hybridization works reliably in a variety of different solutions. These works are not meant to be final, optimized designs for devices, but rather demonstrations of the wide range of possibilities afforded by nucleic acid engineering and of problems that can be practically solved with dynamic nucleic acid devices in the near future.