DNA molecule provides a computing machine with both data and fuel

Yaakov Benenson*,,, Rivka Adar,, Tamar Paz-Elizur, Zvi Livneh & Ehud Shapiro*,
*Department of Computer Science and Applied Mathematics and Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100 Israel
These authors contributed equally to this work

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 while the hardware consists of DNA restriction and ligation enzymes using ATP as fuel. In addition to information, DNA also stores energy, available upon 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 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 utilizes a hitherto unknown capability of the restriction enzyme FokI, which serves as the hardware, to operate on a non-covalent 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 3x10^12 automata per l performing 6.6x10^10 transitions per s per l with transition fidelity of 99.9%, dissipating about 5x10^-9 W/l as heat at ambient temperature.