Connecting localized DNA strand displacement reactions

• Published in: Nanoscale Vol. 7; no. 30; pp. 12970 - 12978
• Main Authors: Mullor Ruiz, Ismael, Arbona, Jean-Michel, Lad, Amitkumar, Mendoza, Oscar, Aimé, Jean-Pierre, Elezgaray, Juan
• Format: Journal Article
• Language: English
• Published: England 14.08.2015
• Subjects: Asymmetry; Circuits; Constraining; Deoxyribonucleic acid; Design engineering; Displacement; DNA - chemistry; DNA - metabolism; Fluorescent Dyes - chemistry; Kinetics; Nucleic Acid Conformation; Nucleic Acid Hybridization; Platforms; Spectrometry, Fluorescence; Strands
• ISSN: 2040-3364; 2040-3372; 2040-3372
• DOI: 10.1039/C5NR02434J

Logic circuits based on DNA strand displacement reactions have been shown to be versatile enough to compute the square root of four-bit numbers. The implementation of these circuits as a set of bulk reactions faces difficulties which include leaky reactions and intrinsically slow, diffusion-limited reaction rates. In this paper, we consider simple examples of these circuits when they are attached to platforms (DNA origamis). As expected, constraining distances between DNA strands leads to faster reaction rates. However, it also induces side-effects that are not detectable in the solution-phase version of this circuitry. Appropriate design of the system, including protection and asymmetry between input and fuel strands, leads to a reproducible behaviour, at least one order of magnitude faster than the one observed under bulk conditions.