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DNA nanostructures acting as DNA machines are described. Specifically, DNA “walkers” assembled on nucleic acid scaffolds and triggered by fuel/ant...
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Switching Photonic and Electrochemical Functions of a DNAzyme by DNA Machines Xiaoqing Liu, Angelica Niazov-Elkan, Fuan Wang, and Itamar Willner Nano Lett., Just Accepted Manuscript • DOI: 10.1021/nl303894h • Publication Date (Web): 30 Nov 2012 Downloaded from http://pubs.acs.org on December 3, 2012

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Switching Photonic and Electrochemical Functions of a DNAzyme by DNA Machines Xiaoqing Liu, Angelica Niazov-Elkan, Fuan Wang, and Itamar Willner* Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.

*Address correspondence to: [email protected] Tel:

+972-2-6585272

Fax:

+972-2-6527715

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ABSTRACT DNA nanostructures acting as DNA machines are described. Specifically, DNA “walkers” assembled on nucleic acid scaffolds and triggered by fuel/anti-fuel strands are activated in solution or on surfaces, e.g., electrodes or semiconductor CdSe/ZnS quantum dots (QDs). The DNA machines led to the switchable formation or dissociation of the hemin/G-quadruplex DNAzyme on the DNA scaffolds. This enabled the chemiluminescence, chemiluminescence resonance energy transfer (CRET), electrochemical, or photoelectrochemical transduction of the switchable states of the different DNA machines.

KEYWORDS: DNA; walker; machine; chemiluminescence; quantum dots (QDs); nanotechnology

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The development of DNA machines attracts substantial research efforts aimed to duplicate macroscopic machinery functions at the molecular level.1 Different molecular machines such as “tweezers”,2 “walkers”,3 “motors”,4 “steppers”,5 “cranes”,6 “catenanes”,7 “rotaxane”,8 “metronomes”,9 “gears”,10 and “spiders”,11 were reported in recent years. The base sequences in the different DNA nanostructures encoded the instructive information for the respective mechanical functions of the systems in the presence of appropriate triggers. Different input fuels and anti-fuels were used to activate the different DNA machines, and these included strand-displacement processes by fuel/anti-fuel strands,12 pH changes,13 metal ion/ligands,14 photoisomerization reactions,15 and chemical reactions with the help of an enzyme or DNAzyme.16 Such DNA machines hold great promise for developing logic gates devices,17 programmed synthesis,18 nanoscale transporters,19 sensors,16c-e,,20 controlling surface properties,13,21 and nanomedicine or diagnostic systems.22 The readout of the molecular mechanical processes is an important issue in developing DNA machines. Fluorescence resonance energy transfer (FRET),2a,14a,14b electrophoretic experiments,3 or fast AFM measurements on surfaces11,19d were implemented to probe the configurations (states) of the different devices. In the present study we address the switching of DNAzyme functions by fueled DNA machines. Specifically, we demonstrate that DNA walker systems on DNA scaffolds switch “ON” and “OFF” the formation or dissociation of the hemin/G-quadruplex DNAzyme nanostructure, respectively, thus enabling the chemiluminescence, chemiluminescence resonance energy transfer (CRET), and the electrochemical or the photoelectrochemical transduction of the walking processes. We introduce new readout signals for probing the mechanical functions of the DNA devices, and particularly interesting are walker devices that illuminate their “walking path” upon mechanical moving. We, also, introduce novel electrochemical and photoelectrochemical readout of the walker operations on surfaces.

RESULTS AND DISCUSSION One of the DNA-walker systems consists of a nucleic acid scaffold, (1), to which three footholds (2), (4) and (5) are hybridized, Figure 1(A). While foothold (2) is functionalized with fluorescein, FAM, the ACS Paragon Plus Environment

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nucleic acid strand (6) acting as the walker is hybridized to foothold (5). The walker unit (6) includes the hemin/G-quadruplex DNAzyme sequence that is caged in the duplex structure with (5) in a catalytically inactive configuration. Treatment of this system with the fuel-strand (7) results in the strand displacement of the walker (6) while forming the energetically stabilized (7)/(5) duplex. The stranddisplacement process allows then the translocation of the walker (6) to foothold (4) through the hybridization of the overhang associated with (6). This process unblocks the G-quadruplex sequence that leads to the formation of the hemin/G-quadruplex DNAzyme. Addition of the anti-fuel strand (8) results in the strand displacement of the fuel-strand associated with (5) to form the energeticallystabilized duplex (7)/(8). The release of (7) from foothold (5) results in the reverse walking step, where the hemin/G-quadruplex strand (6), associated with foothold (4), is separated and binds to foothold (5) due to enhanced energetic base-pair stabilization. The reverse walking process destroys the DNAzyme structure. This bi-directional movement of (6) on the DNA scaffold was then followed by the interaction of the hemin/G-quadruplex with the FAM reporter unit associated with foothold (2). Previous studies have indicated that the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme catalyzes the generation

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chemiluminescence provides the energy for a chemiluminescence resonance energy transfer (CRET) to dyes or QDs.23 Accordingly, the walking process can be followed by this photophysical mechanism. Figure 1(B) shows the luminescence spectrum of the system where the walker (6) is hybridized to foothold (5), upon treatment with H2O2/luminol, in the presence of hemin. A minute chemiluminescence is observed, originating to the inefficient hemin-catalyzed generation of chemiluminescence, and no fluorescence of FAM is detected, Figure 1(B), curve (a). Upon the walkover of (6) to foothold (4) triggered by the fuel-strand (7), and the generation of the hemin/G-quadruplex, the chemiluminescence is activated, and the CRET process leads to the FAM fluorescence at 518 nm, Figure 1(B), curve (b). Also, it should be noted that although the fuel strand (7) is G-rich, it can not form a G-quadruplex, and a control experiment reveals that in the presence of hemin very low chemiluminescence is generated, similar to the background chemiluminescence. By the cyclic translocation of the walker between the ACS Paragon Plus Environment

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footholds (5) and (4), the chemiluminescence and the FAM fluorescence are switched to “OFF” and “ON” states, respectively, Figure 1(B), inset. Also, the FAM dye associated with the DNA scaffold of the DNA “walker” was substituted with the CdSe/ZnS QDs. The “mechanical” formation and dissociation of the G-quadruplexes in the presence of the fuel and anti-fuel strands, respectively, was then used to catalyze the generation of chemiluminescence. The resulting CRET process was used to follow the “mechanical” functions of the molecular device through the CRET-stimulated luminescence of the QDs, Figure 1(C). One important question relates to the mechanism by which the “walker” strand (6) translocates to foothold (4). Namely, does the “walker” perform a concerted intramolecular walkover of (6) using an overhang mechanism of the partially displaced (6) by the fuel (7), or is it a diffusional mechanism whereby (6) is displaced by the fuel (7) to the solution, and the displaced strand rehybridizes to foothold (4) by a diffusional process. To address this issue, we studied the dynamics of walkover of (6) to foothold (4) upon treatment with the fuel strand (7), and constructed a model system that probes the dynamics of binding of (6) to foothold (4) by a diffusional mechanism. To follow the dynamics of walkover in the system we constructed the system shown in Figure 2(A). In this system we modified the walker with the black-hole quencher BHQ-1 to yield the strand (6a). The walkover of (6a) to foothold (4) using the fuel strand (7), and the reverse walkover of (6a) to foothold (5), using the antifuel strand, (8), were then followed by the FRET quenching of the FAM dye by BHQ-1, Figure 2(B). The dynamics of walkover of (6a) to foothold (4) was followed by the time-dependent quenching of FAM, Figure 2(C), curve (a). In parallel, we constructed a model system for probing the diffusional hybridization of (6a) to foothold (4), Figure 2(D). In this system, foothold (5) was initially blocked with the fuel strand (7), and the time-dependent quenching of FAM was monitored upon the injection of the walker (6a) into the solution as a result of hybridization of (6a) to foothold (4), Figure 2(C), curve (b). Clearly the association of (6a) to foothold (4) is substantially faster in the presence of the walker scaffold, implying that the walkover of (6a) to foothold (4) proceeds by an intramolecular, concerted, hangover mechanism, rather than through a diffusional process. It should also be mentioned that a mixed intramolecular/diffusional mechanism may be excluded since the reversible translocation of the walker ACS Paragon Plus Environment

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between the footholds (4)/(5) can be repeated for at least five cycles, without affecting the kinetics of walkover. (For further estimation of the distances existing in the walker assembly that reveals the possible intramolecular hangover hybridization process, see Figure S1, supporting information). A related walker system that makes use of the fact that two G-quadruplex subunits may assemble into a hemin/G-quadruplex catalytic structure, upon triggering the mechanical walking of a DNAzyme subunit on the DNA scaffold, is discussed in Figure S2, supporting information. The DNA walker systems were, then, immobilized on surfaces and the mechanical functions of the DNA assemblies were followed by the switchable electronic or photoelectrochemical outputs of the systems. Previous work demonstrated that the hemin/G-quadruplex exhibited peroxidase-like activity and it electrocatalyzed the reduction of hydrogen peroxide.24 Accordingly, the thiolated nucleic acid scaffold, (9), was assembled on a Au electrode, and the two foothold (4) and (5) were hybridized with the scaffold with a surface coverage of 1.6×1011 molecules cm-2, Figure 3(A). The nucleic acid, (6), that includes the G-quadruplex sequence was hybridized to foothold (5), where the G-quadruplex sequence is caged in an inactive structure, Figure 3(B), curve (a). In the presence of the fuel-strand, (7), strand displacement of (6) proceeds, resulting in the “walk-over” of (6) to foothold (4), a process that deprotects the caged G-quadruplex sequence. The self-assembly of the hemin/G-quadruplex DNAzyme at the electrode surface results in the electrocatalyzed reduction of H2O2, and the resulting amperometric response provides an amperometric readout signal for the mechanical translocation of (6) to foothold (4), Figure 3(B), curve (b). Treatment of the resulting system with the anti-fuel strand, (8), leads to the separation of the hemin/G-quadruplex from (4) and the “caging” of the G-quadruplex sequence in the duplex (5)/(6). As a result, the system lacks electrocatalytic properties toward the reduction of H2O2, Figure 3(B), curve (c). By the cyclic treatment of the system shown in Figure 3(A) with the fuel and the anti-fuel strands, the “mechanical” operations of the DNA device switch reversibly the electrocatalytic functions of the system between “ON” and “OFF” states, respectively, Figure 3(B), inset. The amperometric signals generated by the system provide then a transduction signal for the DNA walker device. In our discussion, we suggest that the walker unit (6) performs a concerted “walk-over” process, ACS Paragon Plus Environment

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where the displacement of (6) from foothold (5) is accompanied by the simultaneous hybridization of the hangover single-strand of (6) to (4), and the sequential formation of the duplex (7) to (5) upon the fueled strand displacement reaction. This mechanism is preferred over a possible displacement of (6) to the solution and its subsequent re-hybridization to foothold (4) through a diffusional path. The concerted walk-over mechanism was supported by a control experiment where the electrode was modified with the scaffold (9) that was functionalized with footholds (4) and (5), where foothold (5) was blocked with the fuel (7), Figure S3, supporting information. The resulting functionalized electrode was interacted with the G-quadruplex sequence (6), 2.5 x 10-10 M, which is 50-fold higher than the concentration that can be generated by the displacement of (6) to the solution. Under these experimental conditions, (6) can only bind to foothold (4) to yield the electrocatalytic hemin/G-quadruplex. We find that this system does not lead to any noticeable electrocatalytic current after 1h, whereas the mechanically-induced transduction of (6) in the presence of the fuel strand proceeds reversibly on the same time-scale. These results clearly imply that the forward/backward “walking” transformations on the DNA scaffold proceed within an intact structure by a concerted mechanism that does not include the separation and uptake of the walker to and from the solution. The walker system was further assembled on a CdSe/ZnS QDs-functionalized electrode, and the resulting photoelectrochemical currents were used as readout signals for the mechanical operation of the molecular device. Since the chemiluminescence generated by the hemin/G-quadruplex can lead to the excitation of the QDs,23 the thiolated nucleic acid (10) was assembled on Au electrodes and the (3)functionalized CdSe/ZnS QDs, the nucleic acid (4), and the nucleic acid (5) were hybridized as footholds onto the DNA scaffold to yield a photocurrent switch without external irradiation, upon activation of DNA walker device, Figure 3(C). Similar to Figure 1 (A), fuel-strand (7) results in the strand displacement of (6), the “walk-over” of (6) to foothold (4), and the concomitant formation of the hemin/G-quadruplex DNAzyme. This leads to the oxidation of luminol by H2O2 and the generation of chemiluminescence. The stimulated chemiluminescence resonance energy transfer (CRET) to the CdSe/ZnS QDs photoexcites the QDs generating the electron-hole pair. Transfer of the conduction band ACS Paragon Plus Environment

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electrons to the electrode and the concomitant scavenging of the valence-band holes by triethanolamine (TEOA) yield a steady-state photocurrent.25 Figure 3(D), curve (a) shows the resulting photocurrent without external irradiation. Treatment of the system with the anti-fuel strand (8) leads to the reverse “walk-over” of (6) to foothold (5) and the caging of the G-quadruplex sequence into a catalytic inactive structure. As a result, the photocurrent generated by the system is blocked, Figure 3(D), curve (b). Control experiments revealed that no photocurrents were generated upon exclusion of the QDs from the system, Figure 3(D), curve (c). These results imply that the currents originate, indeed, from the CRETinduced excitation of the QDs. We thus conclude that the QDs/walker system assembled on the electrode provides a photoelectrochemical device that follows the mechanical functions of the DNA walker. One may, however, utilize the chemiluminescence generated by the hemin/G-quadruplex as an optical readout signal for other molecular DNA machines. Figure 4(A) depicts a hairpin-like structure that is opened and closed by fuel/anti-fuel strands, where the resulting switchable generation of hemin/Gquadruplex DNAzyme provides a readout signal for the DNA machine. The single-stranded nucleic acid (11) includes at its 3' and 5' ends the domains I and II of the hemin/G-quadruplex DNAzyme subunits and region III for complementary base pairing. As a result, the system generates a hairpin-like nanostructure that is stabilized in its stem region by the supramolecular hemin/G-quadruplex formed between the subunits. In this configuration, the hemin/G-quadruplex DNAzyme exists in a catalytically active configuration, leading to the generation of chemiluminescence in the presence of luminol/H2O2, Figure 4(B), curve (a). Treatment of (11) with the fuel-strand (12), a TP53 gene-specific DNA sequence, that is complementary to the single-stranded loop-domain results in the opening of region III and the separation of the two DNAzyme subunits, I and II. This yields a catalytically-inactive structure that generates only low chemiluminescence intensity, attributed to the free hemin in the system, Figure 4(B), curve (b). Further treatment of (11)/(12) structure with the anti-fuel strand, (13), displaces the fuel strand. This process re-assembles the catalytically-active, hairpin-like structure, and leads to the generation of chemiluminescence, Figure 4(B), curve (c). By the cyclic switching of the DNA structure ACS Paragon Plus Environment

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between the hairpin-like structure and the open duplex configuration, the chemiluminescence generated by the molecular DNA device is cycled between ON and OFF states, respectively. Finally, a related molecular DNA device that leads to “ON” and “OFF” switchable chemiluminescence using Hg2+ ions26 as fuel and cysteine as anti-fuel was constructed. The design of the Hg2+/Cysteine switchable chemiluminescence DNA device and the switchable chemiluminescence generated by this system are discussed in Figure S4, supporting information.

CONCLUSIONS The present study demonstrated the versatile use of the hemin/G-quadruplex DNAzyme as a catalyst for the readout of molecular DNA machine functions. Specifically, we demonstrated that the chemiluminescence generated by the hemin/G-quadruplex provides a general means to probe the DNA devices by implementing the chemiluminescence resonance energy transfer (CRET) reactions. Also, the immobilization of the molecular DNA devices on electrode supports or semiconductor QDs allowed the probing of the DNA walker devices through the electrocatalytic functions of the hemin/G-quadruplexes or through the photoelectrochemical DNAzyme-catalyzed generation of photocurrents. These systems present novel electronic or optoelectronic switching devices based on DNA machines. Furthermore, the concept of switching DNAzyme functions by nucleic acid-fueled DNA machines could be of substantial impact in future nanomedicine. For example, a microRNA related to a disease might trigger the walker system to yield a DNAzyme that specifically cleaves and degrades the intracellular m-RNA. Alternatively, as many aptamers bind in a form of G-quadruplexes to harmful proteins or enzymes, one may trigger the walker devices by appropriate biomarkers and lead to the inhibition of these proteins.

EXPERIMENTAL SECTION Materials and Reagents. Core Shell EviDots, CdSe/ZnS Quantum dots in toluene were purchased from Evident Technologies. Bis-[Sulfo-succinimidyl]-Suberate (BS3) was purchased from Thermo Fisher Scientific Inc. Hemin was purchased from Frontier Scientific Inc. Luminol, H2O2, mercury (II) ACS Paragon Plus Environment

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acetate, cysteine, (tris(2-carboxyethyl)phosphine) (TCEP), dithiothreitol (DTT), and triethanolamine (TEOA) were purchased from Sigma-Aldrich. Stock solutions of 1 mM hemin and 250 mM luminol were prepared in DMSO and stored in the dark at -20 °C. Ultrapure water from a NANOpure Diamond (Barnstead Int., Dubuque, IA) source was used through-out the experiments. All oligonucleotides were purchased from Integrated DNA Technologies Inc. (Coralville, IA). The nucleic acids were HPLC-purified and freeze-dried. Stock solutions of 100 µM DNA were prepared with 10 mM phosphate buffer, pH 7.4. The sequences of the oligonucleotides were as follows: (1) 5'-TTC GTT GGA TGA TCA TGC CTT AGT CGA TGC TGA ATT-3' (2) 5'-FAM-TATCAG TCATCCAACGAA-3' (3) 5'-H2N-TATCAG TCATCCAACGAA-3' (4) 5'-GCAAATCGTAATTACTAAGGCATGA-3' (5) 5'-CTGTGCCCGACCAACCCGCCCTACCCAAAGCCTAATTCAGCATCG -3' (6) 5'-TTACGATTTGCTTTGGGTAGGGCGGGTTGGG-3' (6a) 5'-TTACGATTTGCTTTGGGTAGGGCGGGTTGGG-BHQ-1-3' (7) 5'-CCTGCG GATGCGTCTGGCTTTGGGTAGGGCGGGTTGGTCGGGCACAG-3' (8) 5'-CTG TGCCCGACCAACCCGCCCTACCCAAAGCCAGACGCATCCGCAGG-3' (9) 5'-HS-TTTTCATGCCTTAGTCGATGCTGAATT-3' (10) 5'-HS-TTTTTCGTTGGATGATCATGCCTTAGTCGATGCTGAATT-3' (11) 5'-GGGTAGGGTGTTTCCTGACTCAGAGGGGCGGGTTGGG-3' (12) 5'-TGCACCCCTCTGAGTCAGGAAACACGAT-3' (13) 5'-ATCGTGTTTCCTGACTCAGAGGGGTGCA-3' (14) 5'-CGCGAATAGGGTAGGG-3' (15) 5'-TCCGTCCTACCTCCCTATTCGCGTTAATTCAGCATCG-3' (16) 5'-CGGGTTGGGTTAAGTTACTAAGGCATGA-3' (17) 5'-TTCCATGGAGTTGCTGCGCGAATAGGGAGGTAGGACGGA-3' ACS Paragon Plus Environment

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(18) 5'-TCCGTCCTACCTCCCTATTCGCGCAGCAACTCCATGGAA-3' Instrumentation. Light emission experiments were carried out using a photon counting spectrometer (Edinburgh Instruments, FLS 920) equipped with a cooled photomultiplier detection system connected to a computer (F900 v.6.3 software, Edinburgh Instruments). Cyclic voltammetry experiments were performed using a PC-controlled (Autolab GPES software) potentiostat/galvanostat (µAutolab, type III). A gold and platinum wire was used as the working and counter electrode, respectively, and the reference electrode was a Ag/AgCl (saturated KCl) electrode. The gold wires were treated with concentrated H2SO4 and concentrated HNO3 for 10 min separately prior to modification. Photoelectrochemical experiments were carried out using a Keithley Ke617 power supply, equipped with homemade software for current measurement. Gold-coated semi-transparent glass slides (Analytical µ-Systems, Mivitec GmbH, Germany) were used for the photocurrent measurements. The photocurrents were measured between the modified Au working electrode and a graphite rod counter electrode without applying any potential. The gold coated glass sides were cleaned with piranha solution (WARNING: Piranha solution reacts violently with organic materials and should be handled with extreme care) for 1 min., and washed with water thoroughly. Afterwards the electrodes were boiled in hot ethanol for 10 min, slowly cooled down to room temperature, and then were rinsed with water and dried under nitrogen for further modification. Modification of the QDs with DNA. The previously reported method was used to modify the QDs.23 The loading ratio of the oligonucleotides to the QDs is about eight. CRET and Fluorescent Assay of the DNA Machine. The CRET assay using FAM as acceptor for analyzing the DNA walker switching device was performed in 25 mM HEPES (pH 9, 0.4 M NaCl, 0.02 M KCl) that included 3 µM annealed DNA of (1), (2), (4), (5) and (6), or annealed DNA of (1), (2), (14), (15), and (16), 2 µM hemin, 0.15 mM luminol and 1.5 mM H2O2. The CRET assay with QDs as acceptor was performed in 25 mM HEPES (pH 9, 0.4 M NaCl, 0.02 M KCl) that included 1.2 µM DNA of (1), QD modified (3), (4), (5) and (6), 0.8 µM hemin, 0.15 mM luminol and 0.75 mM H2O2. The excitation of FAM for the FRET measurement between FAM and BHQ-1 was performed at 490 nm. ACS Paragon Plus Environment

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The switchable DNA translocation walking processes were triggered upon the addition of the respective fuels and anti-fuels. Cyclic Voltammetry and Photoelectrochemical Assay of DNA machines. For cyclic voltammetry, 70 µl of 2 mM TCEP and 140 µL of 10 µM (4), (5), (6), and (9) were incubated for 0.5 h in 25 mM HEPES (pH 7.4, 0.4 M NaCl, 0.02 M KCl). Then gold wires were modified by their interaction with the diluted DNA, 2 µM, for 12h, followed by their rinsing with HEPES buffer. The electrodes were passivated with 2 mM 6-mercaptohexanol for 2 h, washed with buffer 25 mM HEPES (pH 7.4, 1 M NaCl, 0.02 M KCl), and incubated with 1 µM hemin for 1 h. The switch of the DNA machine was cycled by the alternate addition of the fuel (7) and the anti-fuel (8). The cyclic voltammetry measurements were performed in 25 mM HEPES (pH 7.4, 0.4 M NaCl, 0.02 M KCl) containing 1 µM hemin and 1 mM H2O2. A potential scan from 0 to -0.5 V was employed. For photoelectrochemical measurements, the thiolated DNA sequence (10) was treated with DTT for 2 h, and subsequently separated using a microspin column prior to its linkage to the electrodes. The electrodes were interacted with 0.8 µM (4), (5), (6) and (10), for 1h, washed with HEPES, and then interacted with the (3)-modified QD for 1h, and washed with HEPES and incubated with 0.5 µM hemin solution (pH 7.4) for 0.5 h. The walker was triggered by the addition of (7) and (8), respectively. A 3mL cell containing 25 mM HEPES (pH 9, 0.4 M NaCl, 0.02 M KCl) and 0.5 µM hemin was used for photocurrent measurement. Triethanolamine (TEOA), 10 mM, and luminol, 0.15 mM were subsequently added, after the background current was stabilized, H2O2, 0.75 mM, was added to the cell, and the resulting photocurrents were measured.. Chemiluminescence Assay of the DNAzyme Switch. Switching of the DNAzyme by the strand displacement mechanism was examined in 25 mM HEPES (pH 9, 0.4 M NaCl, 0.02 M KCl) that included 0.5 µM (11), 0.25 µM hemin, 0.5 mM luminol and 30 mM H2O2. The reverse movement was triggered by the addition of (12) and (13), allowing the systems to react for 1 h. Switching of the

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DNAzyme by using of mercury(II) or cysteine was performed in 25 mM HEPES (pH 9, 0.5 M NaNO3, 0.02 M KNO3) that included 0.5 µM DNA, 0.25 µM hemin, 0.5 mM luminol and 30 mM H2O2.

Acknowledgment. This study is supported by the Israel Science Foundation, Israel, and by the Volkswagen Foundation, Germany.

Supporting Information Available: Estimated distances in the walker construct, a switchable walker system consisting of two DNAzyme subunits, a control experiment for the switchable electrocatalytic functions of the walker system on an electrode, and a switchable molecular DNA device that leads to “ON” and “OFF” chemiluminescence using Hg2+ and cysteine as fuels. This material is available free of charge via the Internet at http://pubs.acs.org.

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Figure 1. (A) Probing a reversible DNA walker by the switchable formation of the hemin/G-quadruplex DNAzyme and the DNAzyme-stimulated generation of a CRET signal to the FAM dye or the CdSe/ZnS QDs. (B) and (C) Luminescence spectra corresponding to the FAM system and QDs system, respectively: (a) The walker (6) is in foothold (5). (b) After the fueled walkover of (6) to foothold (4). (c) After the reverse translocation of (6) to foothold (5) using the anti-fuel strand. (d) and (e) Second cycle of moving the walker (6) to foothold (4) and back to foothold (5). The luminescence bands at 420 nm correspond to the DNAzyme generated chemiluminescence in the presence of luminol/H2O2. The bands at λ = 518 nm, in (B) and λ = 615 nm, in (C) correspond to the CRET-induced luminescence of

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FAM and the CdSe/ZnS QDs, respectively. Insets correspond to the cyclic switchable CRET signals of the walker systems.

Figure 2. (A) Switchable translocation of the G-quadruplex walker followed by a FRET. (B) Luminescence spectrum of the systems corresponding to the FRET between the FAM labeled DNA (2) and BHQ-1 labeled walker (6a): (a) the walker (6a) on foothold (5), (b) translocation of walker (6a) to foothold (4) upon the treatment of the system with fuel (7), (c)-(e) cyclic translocation of the walker (6a) to foothold (5), back to (4), and then to foothold (5) using the antifuel and fuel strands, respectively. ACS Paragon Plus Environment

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Inset: Cyclic fluorescence intensities at λ=520 nm upon cyclic the walker (6a) between footholds (5) and (4) using the respective fuel/anti-fuel strands. (C) (a) Time-dependent fluorescence quenching of the FAM dye upon translocation of the walker (6a) from foothold (5) to foothold (4), using the fuel strand (7), according to Figure 2 (A). Arrow indicates time of injection of fuel stand. (b) Time-dependent fluorescence changes upon hybridization of the walker to the system depicted in Figure 1 (D). Arrow indicates time of injection of the walker (6a). (D) Model system for probing the hybridization of the walker from solution to foothold (4). In all experiments the concentrations of the DNA scaffolds corresponded 2.5 × 10-7 M and the concentration of the walker (6a) was 2.5 × 10-7 M.

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Figure 3. Switchable electrochemical transduction of a “DNA walker” associated with an electrode using the hemin/G-quadruplex-walker as reporting electrocatalyst. (B) Cyclic voltammograms corresponding to the “ON”/“OFF” DNAzyme-catalyzed reduction of H2O2 upon: (a) Walker (6) on foothold (5). (b) Fueled translocation of (6) to foothold (4). (c) Reverse anti-fueled translocation of (6) to foothold (5), (d) and (e) Further cycle of fueled/anti-fueled translocation of (6) across footholds (4) and (5), respectively. Inset: Switchable ON/OFF electrocatalytic transduction of the walker translocation across footholds (4) and (5), respectively. (C) Switchable photoelectrochemical transduction of a DNA “walker” associated on an electrode, using the hemin/G-quadruplex generated chemiluminescence, and the subsequent CRET-induced generation of photocurrent, as a readout signal for the walking process. (D) Time-dependent photocurrents upon: (a) The fueled positioning of the walker (6) on foothold (4). ACS Paragon Plus Environment

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(b) The anti-fueled reverse positioning of the walker (6) on foothold (5). (c) Control experiments corresponding to the photocurrent where the CdSe/ZnS QDs are excluded from the scaffold and the DNAzyme (6) is positioned on foothold (4).

Figure 4. Mechanical control of DNA nanostructures and DNAzyme-catalyzed chemiluminescence transduction of the switchable molecular states: (A) Reversible fueled/anti-fueled transformation of a hemin/G-quadruplex bridged hairpin-like configuration and a duplex DNA separating the DNAzyme subunits. (B) Chemiluminescence spectra corresponding to: (a) The hemin/G-quadruplex hairpin-like structure, (b) The duplex DNA structure, (c), (e), and (g) generation of the hemin/G-quadruplex structure by 2nd, 3rd and 4th cycles, (d) and (f) generation of the duplex structure by 2nd and 3rd cycles. Inset: Cyclic “ON” and “OFF” chemiluminescence generated upon the mechanical transformation of the DNA nanostructure between the hemin/G-quadruplex-bridged hairpin and duplex, respectively.

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REFERENCES 1. (a) Krishnan, Y.; Simmel, F. C. Angew. Chem., Int. Ed. 2011, 50, 3124–3156. (b) Bath, J.; Turberfield, A. J. Nat. Nanotechnol. 2007, 2, 275–284. (c) Seeman, N. C. Trends Biochem. Sci. 2005, 30, 119–125. (d) Von Delius, M.; Leigh, D.-A. Chem. Soc. Rev. 2011, 40, 3656–3676. (e) Beissenhirtz, M. K.; Willner, I. Org. Biomol. Chem. 2006, 4, 3392–3401. (f) Niemeyer, C. M.; Adler, M. Angew. Chem., Int. Ed. 2002, 41, 3779-3783. (g) Liu, H.; Liu, D. Chem. Commun. 2009, 2625– 2636. (h) Alberti, P.; Bourdoncle, A.; Saccà, B.; Lacroix, L.; Mergny, J. L. Org. Biomol. Chem. 2006, 4, 3383-3391. 2. (a) Yurke, B.; Turberfield, A. J.; Mills, A. P.; Simmel, F. C.; Neumann, J. L. Nature 2000, 406, 605–608. (b) Chhabra, R.; Sharma, J.; Liu, Y.; Yan, H. Nano Lett. 2006, 6, 978–983. (c) Elbaz, J.; Moshe, M.; Willner, I. Angew.Chem., Int. Ed. 2009, 48, 3834–3837. (d) Elbaz, J.; Wang, Z. G.; Orbach, R.; Willner, I. Nano Lett. 2009, 9, 4510–4514. 3. (a) Sherman, W. B.; Seeman, N. C. Nano Lett. 2004, 4, 1203–1207. (b) Yin, P.; Yan, H.; Daniell, X. G.; Turberfield, A. J.; Reif, J. H. Angew. Chem., Int. Ed. 2004, 43, 4906–4911. (c) You, M.; Chen, Y.; Zhang, X.; Liu, H.; Wang, K.; Wang, R.; Williams, K. W.; Tan, W. Angew. Chem., Int. Ed. 2012, 51, 2457–2460. 4. (a) Venkataraman, S.; Dirks, R. M.; Rothemund, P. W. K.; Winfree, E.; Pierce, N. A.

Nat.

Nanotechnol. 2007, 2, 490-494. (b) Wickham, S. F.; Bath, J.; Katsuda, Y.; Endo, M.; Hidaka, K.; Sugiyama, H.; Turberfield, A. J. Nat. Nanotechnol. 2012, 7, 169-173. (c) Omabegho, T.; Sha, R.; Seeman, N. C. Science 2009, 324, 67–71. (d) Bath, J.; Green, S. J.; Allen, K. E.; Turberfield, A. J. Small 2009, 5, 1513–1516. 5. Wang, Z. G.; Elbaz, J.; Willner, I. Nano Lett. 2011, 11, 304–309. 6. Kufer, S. K.; Puchner, E. M.; Gumpp, H.; Liedl, T.; Gaub, H. E. Science 2008, 319, 594-596.

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7. Elbaz, J.; Wang, Z. G.; Wang, F.; Willner, I. Angew., Chem., Int. Ed. 2012, 51, 2349 –2353. 8. (a) Ackermann, D.; Schmidt, T. L.; Hannam, J. S.; Purohit, C. S.; Heckel, A.; Famulok, M. Nat. Nanotechnol. 2010, 5, 436–442. (b) Lohmann, F.; Ackermann, D.; Famulok, M. J. Am. Chem. Soc. 2012 134, 11884–11887. 9. Buranachai, C.; McKinney, S. A.; Ha, T. Nano Lett. 2006, 6, 496–500. 10. Tian, Y.; Mao, C. J. Am. Chem. Soc. 2004, 126, 11410–11411. 11. Lund, K.; Manzo, A. J.; Dabby, N.; Michelotti, N.; Johnson-Buck, A.; Nangreave, J.; Taylor, S., Pei, R.; Stojanovic, M. N.; Walter, N. G.; Winfree, E.; Yan, H. Nature, 2010, 465, 206–210. 12. (a) Zhang, D. Y.; Seelig, G. Nat. Chem. 2011, 3, 103–113. (b) Hazarika, P.; Ceyhan, B.; Niemeyer, C. M. Angew. Chem., Int. Ed. 2004, 43, 6469–6471. (c) Li, J. J.; Tan, W. Nano Lett. 2002, 2, 315– 318. (d) Turberfield, A. J.; Mitchell, J. C.; Yurke, B.; Mills, A. P.; Blakey, M. I.; Simmel, F. C. Phys. Rev. Lett. 2003, 90, 118102. (e) Alberti, P.; Mergny, J.-L. Proc. Natl. Acad. Sci. USA 2003, 100, 1569–1573. (f) Zhang, Z.; Olsen, E. M.; Kryger, M.; Voigt, N. V.; Tørring, T.; Gültekin, E.; Nielsen, M.; Mohammadzadegan, R.; Andersen, E. S.; Nielsen, M. M.; Kjems, J.; Birkedal, V.; Gothelf, K. V. Angew. Chem., Int. Ed. 2011, 50, 3983–3987 13. (a) Liu, D.; Balasubramanian, S. Angew. Chem., Int. Ed. 2003, 42, 5734 –5736. (b) Shu, W.; Liu, D.; Watari, M.; Riener, C. K.; Strunz, T.; Welland, M. E.; Balasubramanian, S.; McKendry, R. A. J. Am. Chem. Soc. 2005, 127, 17054–17060. (c) Liu, D.; Bruckbauer, A.; Abell, C.; Balasubramanian, S.; Kang, D. J.;Klenerman, D.; Zhou, D. J. Am. Chem. Soc. 2006, 128, 2067–2071. 14. (a) Thomas, J. M.; Yu, H.-Z.; Sen, D. J. Am. Chem. Soc. 2012, 134, 13738–13748. (b) Zhou, C.; Yang, Z.; Liu, D. J. Am. Chem. Soc. 2012, 134, 1416−1418. (c) Li, F.; Zhang, H.; Lai, C.; Li, X. F. ; Le, X. C. Angew. Chem., Int. Ed. 2012, 51, 9317–9320. (d) Sannohe, Y.; Endo, M.; Katsuda, Y.; Hidaka, K.; Sugiyama, H. J. Am. Chem. Soc. 2010, 132, 16311–16313. ACS Paragon Plus Environment

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15. (a) Liu, H.; Xu, Y.; Li, F.; Yang, Y.; Wang, W.; Song, Y.; Liu, D. Angew. Chem., Int. Ed. 2007, 46, 2515–2517. (b) Wang, X.; Huang, J.; Zhou, Y.; Yan, S.; Weng, X.; Wu, X.; Deng, M.; Zhou, X. Angew. Chem., Int. Ed. 2010, 49, 5305–5309. (c) You, M.; Huang, F.; Chen, Z.; Wang, R. W.; Tan, W. ACS Nano, 2012, 6, 7935–7941. (d) Kang, H.; Liu, H.; Phillips, J.-A.; Cao, Z.; Kim, Y.; Chen, Y.; Yang, Z.; Li, J.; Tan, W. Nano Lett. 2009, 9, 2690–2696. (e) Zhou, M.; Liang, X.; Mochizuki, T.; Asanuma, H. Angew. Chem., Int. Ed. 2010, 49, 2167–2170. 16. (a) Tian, Y.; He, Y.; Chen, Y.; Yin, P.; Mao, C. Angew. Chem., Int. Ed. 2005, 44, 4355–4358. (b) Bath, A.; Green, S. J.; Turberfield, A. J. Angew. Chem., Int. Ed. 2005, 44, 4358–4361, (c) Wang, F.; Elbaz, J.; Willner I. J. Am. Chem. Soc. 2012, 134, 5504−5507. (d) Wang, F.; Elbaz, J.; Teller, C.; Willner, I. Angew. Chem., Int. Ed. 2011, 50, 295. (e) Wang, F.; Elbaz, J.; Orbach, R.; Magen, N.; Willner, I. J. Am. Chem. Soc., 2011, 133, 17149–17151. 17. (a) Stojanovic, M. N.; Stefanovic, D. Nat. Biotechnol. 2003, 21, 1069-1074. (b) Song, T.; Liang, H. J. Am. Chem. Soc. 2012, 134, 10803−10806. (c) Jiang, Y.; Liu, N.; Guo, W.; Xia, F.; Jiang, L. J. Am. Chem. Soc., 2012, 134, 15395–15401. (d) Liu, X.; Aizen, R.; Freeman, R.; Yehezkeli, O.; Willner, I. ACS Nano 2012, 6, 3553–3563. 18. (a) Chen, Y.; Mao, C. J. Am. Chem. Soc., 2004, 126, 13240–13241. (b) He, Y.; Liu, D. R. Nat. Nanotechnol. 2010, 5, 778–782. (c) McKee, M. L.; Milnes, P. J.; Bath, J.; Stulz, E.; O’Reilly, R. K.; Turberfield, A. J. J. Am. Chem. Soc., 2012, 134, 1446–1449. 19. (a) Pomerantz, R. T.; Ramjit, R.; Gueroui, Z.; Place, C.; Anikin, M.; Leuba, S.; Zlatanova, J.; McAllister, W. T. Nano Lett. 2005, 5, 1698–1703. Nano Lett. 2005, 5, 1698–1703. (b) Shin, J.-S.; Pierce, N. A. J. Am. Chem. Soc. 2004, 126, 10834–10835. (c) Sahu, S.; LaBean, T. H.; Reif, J. H. Nano Lett. 2008, 8, 3870–3878. (d) Gu, H.; Chao, J.; Xiao, S.-J.; Seeman, N. C. Nature 2010, 465, 202–205. (e) Muscat, R. A.; Bath, J.; Turberfield, A. J. Nano Lett. 2011, 11, 982–987.

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20. (a) Zhu, C.; Wen, Y.; Li, D.; Wang, L.; Song, S.; Fan, C.; Willner, I. Chem. Eur. J. 2009, 15, 11898– 11903. (b) Shlyahovsky, B.; Li, D.; Weizmann, Y.; Nowarski, R.; Kotler, M.; Willner, I. J. Am. Chem. Soc. 2007, 129, 3814–3815. (c) Lu, C.-H.; Wang, F.; Willner, I. J. Am. Chem. Soc., 2012, 134, 10651–10658. (d) Wang, F.; Orbach, R.; Willner, I. Chem. Eur. J. DOI: 10.1002/chem.201201479 21. (a) Xia, F.; Guo, W.; Mao, Y.; Hou, X.; Xue, J.; Xia, H..; Wang, L.; Song ,Y.; Ji, H.; Qi, O.; Wang, Y.; Jiang, L. J. Am. Chem. Soc. 2008, 130, 8345–8350. (b) Wang, S.; Liu, H.; Liu, D.; Ma, X.; Fang, X.; Jiang, L. Angew. Chem. Int. Ed. 2007, 46, 3915–3917. 22. (a) Benenson, Y.; Gil, B; Ben-Dor, U.; Adar, R.; Shapiro, E. Nature 2004, 429, 423–429. (b) Simmel, F. C. Nanomedicine 2007, 2, 817– 830. (c) Modi, S.; Swetha, M. G.; Goswami, D.; Gupta, G. D.; Mayor, S.; Krishnan, Y. Nat. Nanotechnol. 2009, 4, 325–330. (d) Schweller, R. M.; Zimak, J.; Duose, D. Y.; Qutub, A. A.; Hittelman, W. N.; Diehl, M. R. Angew. Chem., Int. Ed. 2012, 51, 9292– 9296. 23. (a) Liu, X.; Freeman, R.; Golub, E.; Willner, I. ACS Nano 2011, 5, 7648– 7655. (b) Golub, E.; Niazov, A.; Freeman, R.; Zatsepin, M.; Willner, I. J. Phys. Chem. C 2012, 116, 13827−13834. 24. Travascio, P.; Li, Y.; Sen, D. Chem. Biol. 1998, 5, 505–517. 25. Wang, F.; Liu, X.; Willner, I. Adv. Mater. 2012, doi: 10.1002/adma.201201772 26. (a) Ono, A.; Togashi, H. Angew. Chem., Int. Ed. 2004, 43, 4300-4302. (b) Miyake, Y.; Togashi, H.; Tashiro, M.; Yamaguchi, H.; Oda, S.; Kudo, M.; Tanaka, Y.; Kondo, Y.; Sawa, R.; Fujimoto, T.; Machinami, T.; Ono, A. J. Am. Chem. Soc. 2006, 128, 2172– 2173. (c) Lee, J. S.; Ulmann, P. A.; Han, M. S.; Mirkin, C. A. Nano Lett. 2008, 8, 529– 533.

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SYNOPSIS TOC DNA "walker" systems operating on nucleic acid scaffolds in solutions or on surfaces lead to the switchable formation or dissociation of the hemin/G-quadruplex DNAzyme, thus allowing the optical, electrochemical or photoelectrochemical transduction of the states of the machines.

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