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Nucleic Acid Enzymes:
The Fusion of Self-assembly and Conformational Computing
Effirul I. Ramlan and Klaus-Peter Zauner

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 self-assembly and conformational switching commonly appear in combination and are typically realised with proteins. At the current state of biotechnology the best candidates for implementing artificial 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.

Keywords: Molecular computing, allosteric control, ribozymes, deoxyribozymes, logic gates.

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