Journal Article

DNA Molecule Provides a Computing Machine with Both Data and Fuel

Benenson, Yaakov, Adar, Rivka, Paz-Elizur, Tamar, Livneh, Zvi, Shapiro, Ehud

2003

Overview

The unique properties of DNA make it a fundamental building block in the fields of supramolecular chemistry, nanotechnology, nano-circuits, molecular switches, molecular devices, and molecular computing. In our recently introduced autonomous molecular automaton, DNA molecules serve as input, output, and software, and the hardware consists of DNA restriction and ligation enzymes using ATP as fuel. In addition to information, DNA stores energy, available on hybridization of complementary strands or hydrolysis of its phosphodiester backbone. Here we show that a single DNA molecule can provide both the input data and all of the necessary fuel for a molecular automaton. Each computational step of the automaton consists of a reversible software molecule/input molecule hybridization followed by an irreversible software-directed cleavage of the input molecule, which drives the computation forward by increasing entropy and releasing heat. The cleavage uses a hitherto unknown capability of the restriction enzyme FokI, which serves as the hardware, to operate on a noncovalent software/input hybrid. In the previous automaton, software/input ligation consumed one software molecule and two ATP molecules per step. As ligation is not performed in this automaton, a fixed amount of software and hardware molecules can, in principle, process any input molecule of any length without external energy supply. Our experiments demonstrate 3 × 1012automata per μ l performing 6.6 × 1010transitions per second per μ l with transition fidelity of 99.9%, dissipating about$5 \\times 10^{-9}\\>W/\\mu l$as heat at ambient temperature.

• Publisher: National Academy of Sciences,National Acad Sciences,The National Academy of Sciences
• Subject: Adenosine Triphosphate - metabolism / Ambient temperature / ATP / Automata / Automation / Computer software / Computing Methodologies / Deoxyribonucleases, Type II Site-Specific - metabolism / Deoxyribonucleic acid / DNA / DNA - chemistry / DNA - metabolism / DNA - physiology / Entropy / Enzymes / Free energy / Heat dissipation / Hybridization / Ligation / Models, Biological / Molecules / Nanotechnology / Oligonucleotides / Phosphorylation / Physical Sciences / Software / Temperature / Thermodynamics