DNA Fuel for Free-Running Nanomachines A. J. Turberfield * and J. C. Mitchell University of Oxford, Department of Physics, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, United Kingdom B. Yurke, A. P. Mills, Jr., † M. I. Blakey, and F.C. Simmel ‡ Bell Laboratories, Lucent Technologies, 600 Mountain Avenue, Murray Hill, New Jersey 07974 (Received 7 August 2002; published 18 March 2003) We describe kinetic control of DNA hybridization: loop complexes are used to inhibit the hybrid- ization of complementary oligonucleotides; rationally designed DNA catalysts are shown to be effective in promoting their hybridization. This is the basis of a strategy for using DNA as a fuel to drive free- running artificial molecular machines. DOI: 10.1103/PhysRevLett.90.118102 PACS numbers: 87.15.He, 81.07.Nb, 81.16.Dn, 81.16.Hc Molecular motors require an energy source. Biological motors typically extract energy from the hydrolysis of nucleoside triphosphates, usually adenosine triphosphate (ATP) (e.g., myosin [1], kinesin [2], dynein [3], DNA processing enzymes [4], ion pumps [5]) or by transport- ing ions down an electrochemical potential gradient across a membrane (e.g., F O ATP synthase [6], the bacte- rial flagellar motor [7]). If their environment is constant (and both energy sources are actively maintained in bio- logical systems), then these motors can run indefinitely. In contrast, most synthetic molecular machines change state in response to changes in external conditions—they act as switches and are closer to regulatory proteins that undergo conformation changes driven by guanosine tri- phosphate hydrolysis [8] than to ATP-driven motors. Such synthetic machines must be clocked around an operat- ing cycle — e.g., by repeated photoisomerization [9] or by cyclic changes of the chemical or electrochemi- cal environment [10]. Some progress towards a unidirec- tional, chemically driven rotor has been reported [11], though the molecule described completes only one third of a revolution. The first molecular device capable of cycling freely under continuous stimulation is light driven [12]: its operating cycle is driven by reversible photoisomerizations and made irreversible by dissipative thermal isomerization. We introduced the use of DNA as a chemical fuel [13] and demonstrated that the free energy of hybridization of complementary oligonucleotides (short strands of DNA) may be used to produce repetitive motion of a molecular machine. The first DNA-fuelled devices [13,14] are clocked around their operating cycle: the machine’s conformation is changed by interaction with a fuel strand, and the change is reversed when the first fuel strand is displaced by a complementary strand (if both components of the DNA fuel are added simulta- neously, they will react directly without affecting the machine). In this Letter, we demonstrate essential ele- ments of kinetic control of hybridization [15] that permit operation of a free-running DNA-fuelled machine. (i) Direct hybridization of the DNA fuel, without involve- ment of the machine, is inhibited by using a protective strand to tie the ends of one or both fuel strands together to form a loop complex. (ii) A rationally designed DNA catalyst (a new class of deoxyribozyme [16]) promotes hybridization of the modified fuel by partially displacing the protective strand and opening the loop. A machine that catalyzes the reaction of DNA fuel in this way will be able to run continuously until the fuel is exhausted. We introduce our discussion of control of DNA hybrid- ization by considering the simple strand-displacement reaction shown in Fig. 1(a). Hybridization between com- plementary strands S and S is inhibited by a protective strand P which has already hybridized to S [17]. Because P is a truncated copy of S, strand displacement can be a b c TET L Q L Q L TAMRA L Q Q L L Q L L Q S P S P S S FIG. 1. Reactions in which the hybridization of two comple- mentary strands is inhibited by a protective strand, already hybridized to one of them. PHYSICAL REVIEW LETTERS week ending 21 MARCH 2003 VOLUME 90, NUMBER 11 118102-1 0031-9007= 03 =90(11)=118102(4)$20.00  2003 The American Physical Society 118102-1