Journal Article

Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades

Qian, Lulu, Winfree, Erik

2011

Overview

To construct sophisticated biochemical circuits from scratch, one needs to understand how simple the building blocks can be and how robustly such circuits can scale up. Using a simple DNA reaction mechanism based on a reversible strand displacement process, we experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands. These multilayer circuits include thresholding and catalysis within every logical operation to perform digital signal restoration, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays. The design naturally incorporates other crucial elements for large-scale circuitry, such as general debugging tools, parallel circuit preparation, and an abstraction hierarchy supported by an automated circuit compiler.

• Publisher: American Association for the Advancement of Science,The American Association for the Advancement of Science
• Subject: Abstract logic / Base Sequence / Biochemistry / Biological and medical sciences / Catalysis / catalytic activity / Computer Simulation / Computers, Molecular / Delay circuits / Deoxyribonucleic acid / Digital electronics / Diverse techniques / DNA / DNA - chemistry / DNA - metabolism / DNA, Single-Stranded - chemistry / DNA, Single-Stranded - metabolism / Fluorescence / Fundamental and applied biological sciences. Psychology / Journalism / Kinetics / Logic / Logic circuits / Logic gates / Logical Thinking / Molecular and cellular biology / Nucleic Acid Conformation / Nucleic Acid Hybridization / reaction mechanisms / Threshing