Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA

• Published in: Science (American Association for the Advancement of Science) Vol. 318; no. 5853; pp. 1121 - 1125
• Main Authors: Zhang, David Yu, Turberfield, Andrew J, Yurke, Bernard, Winfree, Erik
• Format: Journal Article
• Language: English
• Published: Washington, DC American Association for the Advancement of Science 16.11.2007; The American Association for the Advancement of Science
• Subjects: Animals; Biochemistry; Biological and medical sciences; Biotechnology; Catalysis; Catalysts; Chemical Engineering; Computers, Molecular; Deoxyribonucleic acid; DNA; DNA - chemistry; Engineering; Entropy; Equipment Design; Feedback, Physiological; Fluorescence; Fundamental and applied biological sciences. Psychology; Gels; Geometric growth; Industrial applications and implications. Economical aspects; Kinetics; Mice; Molecules; Nanotechnology; Nucleic Acid Hybridization; Nucleic acids; Other applications; Rabbits; RNA; Amplification; Cascade circuit; Catalytic reaction; Regulation(control); Biochemical reaction; Network; Entropy; Oligonucleotide; Catalyst
• ISSN: 0036-8075; 1095-9203
• DOI: 10.1126/science.1148532

Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and robust. We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics.