![]() ![]() The fluorescence resonance energy transfer (FRET) between the fluorophore and quencher transduces the configuration of the tweezers. ![]() While the inputs of type I 1 open the tweezers and release the linker, the addressing of the open tweezers with inputs of type I 2 results in the association of the linker to the arms and in the closure of the tweezers. The domains Ia and IIb in the arms I and II provide the recognition sites for the respective inputs. The arms I and II are further bridged by complementary base pairing with the nucleic acid linker IV to form the closed tweezers. The tweezers consist of two nucleic acid arms (I and II) bridged by a “reporter” nucleic acid III that includes at its ends a fluorophore/quencher pair. The general principles of the input-triggered opening or closing of the tweezers and the readout of the tweezers configuration are depicted in Fig. 1 B. Each of the tweezers may exist in the closed configuration “0” or the open structure configuration “1.” Thus, the three tweezers may generate eight different configurations (outputs) two configurations where all three tweezers are closed (000) or open (111), respectively, three configurations consisting of one open tweezers and two closed, and three configurations that include two open tweezers and one closed. ![]() It consists of three tweezers, α, β, γ, and six inputs (pH-acidic or basic Hg 2+ ions or cysteine ligands complexing Hg 2+ ions and two complementary single stranded nucleic acids acting as linker/antilinker units). Results and Discussionįig. 1 A presents the elements of the device. For example, acquired magnetization of a ferromagnetic material reflects its past physical treatment. Such response is found in complex systems. The states are hidden, but they can be unambiguously assigned at each step as shown below, 16 states suffice to fully describe history-dependent response of the system. Therefore we introduce the notion of “state” that, combined with the input, will uniquely determine the output and the next state. These configurations change when inputs are provided however, the next configuration will depend not only on the most recent input but on the past input history. A configuration is deemed an output of the system and is determined by reading out the fluorescence signals of the tweezers. There are eight possible configurations of the three tweezers (open/closed for each). The present study presents unique enzyme-free DNA automata, based on the use of new chemical inputs (Hg 2+/cysteine and H +/OH -) that require detailed design of the recognizing nucleic acids. Previous studies described DNA–protein automata, and the advantages of an all-DNA automata device were theoretically addressed ( 31). Also, programmed nucleic acid structures were used to design DNA machines ( 14– 17), and supramolecular DNA nanostructures performing “walker,” ( 18– 22), “tweezers” ( 23– 26), and “gear” ( 27) functionalities were reported, using nucleic acid strands, aptamer–substrate complexes ( 28), or pH ( 29, 30) as triggers (inputs) for the activation of DNA machinery devices. The use of these logic devices to control gene expression ( 12), and to process intracellular information ( 13), was demonstrated. Indeed, the structural and functional information encoded in biomolecules such as DNA ( 4), DNAzymes ( 5, 6), ribozymes ( 7), DNA/protein hybrids ( 8), and enzymes ( 9) has been implemented to develop logic gates ( 10) and finite automata ( 11). Such a machine is defined as an automaton. The machine processes the inputs depending on its internal state and delivers an output. ![]() We use these properties to operate a molecular assembly of “tweezers” that can be opened or closed by external inputs. In particular, the base sequence in DNA enables recognition and self-assembly. Such combined assemblies hold the promise for future nano-medical and bioengineering applications ( 1– 3). Implementing a finite state machine is quite straightforward.Supramolecular systems that can be instructed by external triggers and interact with biological systems attract growing interest.
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