Nucleic Acid Enzymes: The Fusion of Self-assembly and Conformational Computing

Macromolecules are the predominant physical substrate supporting information processing in organisms. Two key characteristics— conformational dynamics and self-assembly properties—render macromolecules unique in this context. Both characteristics have been investigated for technical applications. In nature’s information processors selfassembly and conformational switching commonly appear in combination and are typically realised with proteins. At the current state of biotechnology the best candidates for implementing artifical molecular information processing systems that utilise the combination self-assembly and conformational switching are functional nucleic acids. The increasingly realised prevalence of oligonucleotides in intracellular control points towards potential applications. The present paper reviews approaches to integrating the self-assembly and the conformational paradigm with allosterically controlled nucleic acid enzymes. It also introduces a new computational workflow to design functional nucleic acids for information processing. 1 Biomolecular Computing Paradigms With the feature size of solid-state devices approaching nanometer scale molecules are coming increasingly into focus as an alternative material substrate for the implementation of information processing devices. A wide range of approaches to utilizing molecules in computing are under consideration (Fig. 1). The area of molecular electronics investigates possibilities for implementing with organic materials the architectures familiar from silicon-electronics (cf. [1]). Polymer semiconductors and single-molecule transistors are typical research goals. In chemical computing excitable chemical reaction systems with diffusive coupling are investigated for their potential as massively parallel processing media (cf. [2]). And biomolecular computing is concerned with the use of macromolecules and supramolecular systems and in many cases attempts to exploit mechanisms found in nature. The present paper will concentrate on the latter; a recent review covering also the other directions can be found in [3]. Molecular Electronics Biomolecular Computing Chemical Computing Molecular Computing