Journal Article

Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA

Yurke, Bernard, Winfree, Erik, Zhang, David Yu, Turberfield, Andrew J

2007

Overview

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.

• Publisher: American Association for the Advancement of Science,The American Association for the Advancement of Science
• Subject: Animals / Biochemistry / bioengineering / Biological and medical sciences / Biotechnology / Catalysis / Catalysts / Chemical Engineering / chemical reactions / Computers, Molecular / Deoxyribonucleic acid / DNA / DNA - chemistry / electronic circuits / Engineering / Entropy / Equipment Design / Feedback, Physiological / Fluorescence / Fundamental and applied biological sciences. Psychology / Gels / Geometric growth / Growth kinetics / growth models / Industrial applications and implications. Economical aspects / Kinetics / Mice / Molecules / Nanotechnology / Nucleic Acid Hybridization / Nucleic acids / oligonucleotides / Other applications / Rabbits / RNA