title: DNA molecule provides a computing machine with both data and fuel.
abstract: 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 x 10(12) automata per microl performing 6.6 x 10(10) transitions per second per microl with transition fidelity of 99.9%, dissipating about 5 x 10(-9) W microl as heat at ambient temperature.
authors.affiliation: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Yaakov
authors.initials: Y
authors.lastname: Benenson
authors.forename: Rivka
authors.initials: R
authors.lastname: Adar
authors.forename: Tamar
authors.initials: T
authors.lastname: Paz-Elizur
authors.forename: Zvi
authors.initials: Z
authors.lastname: Livneh
authors.forename: Ehud
authors.initials: E
authors.lastname: Shapiro
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D001331:Automation; D003205:Computing Methodologies; D004247:DNA / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism; D008954:Models, Biological; D010766:Phosphorylation; D012984:Software; D013696:Temperature; D013816:Thermodynamics
chemical_list: D000255:Adenosine Triphosphate; D004247:DNA; C035042:endodeoxyribonuclease FokI; D015252:Deoxyribonucleases, Type II Site-Specific