DNA Nanomachines: Construction, Evolution, and Applications, Notas de estudo de Engenharia de Produção

Baixe DNA Nanomachines: Construction, Evolution, and Applications e outras Notas de estudo em PDF para Engenharia de Produção, somente na Docsity! DNA nanomachines and their functional evolution Huajie Liuw and Dongsheng Liu* Received (in Cambridge. UK) 17th December 2008, Accepted 10th March 2009 First published as an Advance Article on the web 9th April 2009 DOI: 10.1039/b822719e Since the establishment of the Watson–Crick model more than five decades ago, the understandings of DNA structures are well sufficient to enable applications of DNA in designing and assembling two-dimensional (2D) and three-dimensional (3D) structures at the nanoscale. Furthermore, the conformational switchability of DNA also enables the fabrication of nanoscale molecular machines, which can perform movements upon stimuli. In this article, we will summarize the present efforts on constructions of DNA nanomachines based on different driven mechanisms, and further discuss their evolutional processes, in order to find applications and future development directions. Introduction DNA has been seen to play an extraordinary important role in life science more than five decades since the establishment of the Watson–Crick model. Tracing back to its chemical essence, DNA has also received attention in material sciences, especially in nanoscience.1 Based on specific base-pair formation and programmable sequence, DNA nanostructure assembly, pioneered by Seeman et al.2–6 in the 1980s, has now reached the stage of facile fabrication of complicated 2D7–12 and even 3D nanostructures via designed hybridization processes.13–16 However, compared to these static nano- structures, a more challenging aspect in this field is fabricating nanomachines which can perform nanoscale movements in response to external stimuli.17–20 Although protein is the material chosen by Nature to facilitate nanomachines in living beings,21,22 the clearer structures, established synthesis and modification methods and clearer driven mechanisms of DNA nanomachines, have been demonstrated to be of interest for material research as well as theoretical studies. From the first effort to control DNA motion,23 the last decade has witnessed an explosion of interest and effort in this field.24–29 In this review, we have sorted out several basic DNA nanomachine types by driven mechanism. The consequent evolution on the power input method to improve the kinetics of each type is summarized to give a perspective on their development trends. We then highlight the efforts on measuring the mechanical outputs of DNA nanomachines as well as employing these outputs to achieve new functional devices and materials. Through these analyses, we will try to provide some perspectives on the development of DNA nanomachines in the near future. National Centre for NanoScience & Technology, No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China. E-mail: liuds@nanoctr.cn; Fax: +86-10-62656765; Tel: +86-10-82545589 Huajie Liu Dr Huajie Liu received his BS in applied chemistry and MS in inorganic chemistry at Tongji University. From 2005 to 2008, he was a PhD student under the supervision of Prof. Dongsheng Liu at the National Center for Nano- science and Technology. During his PhD period, he worked on developing new control-modes and applications of DNA nanomotors. He is currently working as a postdoctoral fellow with Prof. Kurt V. Gothelf at the University of Aarhus, where his research concentrates on DNA directed assembly of nanomaterials. Dongsheng Liu Professor Dongsheng Liu graduated from the University of Science and Technology of China with a BS degree in 1993. After working in the Institute of Chemistry, Chinese Academy of Sciences for six years, he went to the Hong Kong Polytechnic Uni- versity and finished his PhD there under the supervision of Professor A. S. C. Chan in 2002. He moved to the UK afterwards and worked as a postdoc research associate in NanoIRC and Department of Chemistry, Cambridge University. In 2005, he took the position as a principal investigator in the National Centre for Nano- Science and Technology, China. His researches are mainly focused on using biomolecules to fabricate nanostructures and nanodevices. w Current address: Centre for DNA Nanotechnology at Department of Chemistry and iNANO, University of Aarhus, Denmark. This journal is c The Royal Society of Chemistry 2009 Chem. Commun., 2009, 2625–2636 | 2625 FEATURE ARTICLE www.rsc.org/chemcomm | ChemComm Prototype DNA nanomachines A machine could be defined as any device that uses energy to perform some activity, e.g.mechanical movement. We also use word ‘‘motor’’ to describe a device that converts various forms of energy into kinetic energy for mechanical work. As outlined in an editorial18 by Stoddart: ‘‘organization, the power source, and work of a repetitive nature’’ are the most important characteristics of a molecular machine. From this point of view, the DNA nanomachine could be regarded as a kind of molecular machine that is made up of assembled DNA structures integrated with an external stimuli responding mechanism. Thus all established DNA nanomachines could be sorted into several catalogues by their original driven mechanisms. In the following, we will summarize the variation of each prototype to map their development trends, respectively. DNA nanomachines controlled by ‘‘fuel-strands’’ It is well known that a short DNA strand can be replaced by a longer strand to form a more stable duplex, which is called ‘‘chain-exchange reaction’’ or ‘‘strand-exchange reaction’’. This reaction has been employed to induce motions to DNA-based nanostructures. In 2000, Yurke et al. reported the first hybridization energy-driven DNA nanomachine which resembles a pair of tweezers (Fig. 1).30 Their device is assembled by three single-strands which can form two rigid duplex arms connected by a hinge section and two dangling ends linked to arms. At the ‘‘open’’ state, two ends of the arms are thermodynamically separated. To ‘‘close’’ the tweezers, an additional fourth strand F hybridizes with both dangling ends and pulls the two arms together. The device could be reopened by F’s fully complementary strand F0 because duplex FF0 has a lower free energy (note an overhang section on F is the starting point for FF0 hybridization). The alternating addition of F and F0 will cycle the machine and produce duplex FF0 as waste. Since the machine is powered by competitive hybridization, the authors called the stimuli, DNA F and F0, as ‘‘fuel’’ and ‘‘anti-fuel’’. Overall, one switching is able to generate a force of about 15 pN, with a maximum separation of the arm ends of about 6 nm or 501; FRET and recently sp-FRET31 techniques have been used to monitor the motions. The modifications of this design in following years have led to some variants: an actuator32 and a three-state nanomachine33 that looks like a combination of tweezers and actuator. This fuel-strands strategy has also been employed to drive different DNA assemblies to move: Yan and Seeman proposed a robust DNA nanomachine34 whose motions are between two topological motifs: four-stranded PX and JX2 complexes. The addition of DNA fuels will induce a four-step rotation. A noticeable experimental detail is the use of biotinylated fuel-strands to remove duplex wastes. By covalently linking PX–JX2 machines linearly, the rotations of DNA machines in these arrays could be controlled synchronously and be visualized by atomic force microscopy (AFM). RNA has also been exploited to control this device.35 Extension of this two-state machine to a three-state one has recently been done by the same group.36 In addition to duplexes, DNA can form unusual hybridized structures such as triplexes and quadruplexes. It has been proven by the groups of Tan37 and Mergny38 that the quadruplex–duplex transition could generate mechanical force. Their designs of G-quadruplex-based DNA nano- machines are simpler than that of duplex-based models. In their cases, only one G-rich strand is used to construct the main body of the machine, that is, an intramolecular G-quadruplex. The G-quadruplex state could be switched to the duplex form by adding DNA fuel. Through this transition, the distance between two ends of G-rich strand could be controlled. Hence, we may regard the G-quadruplex and duplex forms as closed and open states, respectively. DNA nanomachines controlled by non-DNA stimuli In principle, the above fuel-strands strategy could be applied to all strand-exchange reaction-powered DNA nanomachines, since, as we have mentioned, hybridization is the common feature of DNA. However, the main disadvantage is these reactions will result in cumulated duplex wastes. These useless duplexes may compete with surrounding nanomachines. And from the point of entropy flow, the accumulation of waste DNA will increase the entropy of the system and will even- tually destroy the machine. To avoid duplex wastes, non-DNA stimuli should also be choices for controlling motions. In fact, this approach has already been proposed in the construction of the first DNA-based nanomechanical device,23 in which case ethidium ions are used as intercalators to induce branch point migration in a tetramobile branched junction structure. Simpler ions than ethidium have also been explored. Mao and Seeman have demonstrated a DNA machine based on a B–Z transition (Fig. 2).39 In the absence of Co(NH3)6 3+ ion, sequence (CG)10 forms normal right-handed B-DNA. This B-DNA can be transformed to left-handed Z-DNA upon the addition of a high concentration of Co(NH3)6 3+ ion. The Fig. 1 DNA tweezers controlled by ‘‘fuel’’ and ‘‘anti-fuel’’ strands. Fuel strand F hybridizes with the dangling ends of the open state machine (shown in blue and green) to pull the tweezers closed. Hybridization with the overhang section of F (red) allows anti-fuel strand F0 to remove F from the tweezers, forming a double-stranded waste product FF0 and allowing the tweezers to open (reprinted with permission from ref. 30; copyright 2000, Nature Publishing Group). 2626 | Chem. Commun., 2009, 2625–2636 This journal is c The Royal Society of Chemistry 2009 their design, two metastable hairpin molecules are used as fuels and the initial machine is a duplex. By mixing the machine and fuels, the duplex will be broken and strand A binds to H1 fuel (State 1), initiating a four-way branch migration in which R is passed from A to H1 (State 2). H2 then binds to the newly exposed sticky ends (State 3) and R-H1 duplex is displaced by R-H2 duplex. The R strand will always move away from the A strand autonomously in the presence of fuels. The motion of this system mimics bacterial pathogens.58 It is intriguing that no preformed track is required and the growing duplex may provide a track for other DNA nanomachines. Enzyme-assisted DNA nanomachines Enzymes are natural catalysts for many DNA-based reactions. It is possible to use enzymatic reactions to control the struc- ture of DNA and make DNA mechanical devices. The first enzyme-assisted DNA nanomachine was reported by Mao’s group in an autonomous DNA motor.59 Their machine consists of two strands (E and F) shown in Fig. 6(a). The E strand contains an RNA-cleaving DNA enzyme. The S strand is a DNA–RNA chimera which is the substrate of the enzyme of E. Upon binding, the machine will be opened by the SE duplex. The DNA enzyme E cleaves its substrate S into two short fragments which have a lower affinity for the E strand than the intact substrate and will, therefore, dissociate from the machine. Its open and closed states transitions could be switched autonomously by the enzymatic reaction. The machine could be temporarily stopped by adding brakes.60 Recently Bishop et al. have Fig. 5 Autonomous DNA nanomachines. (A) DNA ‘‘catalyst’’ system. In this design, machine (catalyst strand) undergoes three continuous steps of motions: hybridization, dehybridization and release. The whole process will repeat unless all fuel strands have been used up (reprinted with permission from ref. 52; copyright 2003, American Physical Society). (B) An autonomous polymerization motor. The metastable fuel hairpins (H1 and H2) do not interact in the absence of the AR complex. Upon mixing, H1 binds to the sticky ends of AR (State 1), initiating a four-way branch migration in which R is passed from A toH1 (State 2).H2 then binds to the newly exposed sticky ends (State 3) and R is passed from H1 to H2 (State 4). In this manner, the R strand is passed back and forth between H1 and H2 hairpins at the living end of the growing polymer, moving away from the A strand (reprinted with permission from ref. 57; copyright 2007, Nature Publishing Group). Fig. 6 Enzyme-assisted DNA nanomachines. (A) An autonomous DNA nanoswitch powered by a DNA enzyme. The E strand contains an RNA-cleaving DNA enzyme and its substrate is an S strand. The cleavage of S will induce the closing of the machine. E will bind with another S strand and open the machine again in the next step (reprinted with permission from ref. 59; copyright 2004; Wiley Inter- science). (B) An enzyme-controlled DNA walker. The track consists of three evenly spaced duplex–DNA anchorages, A, B and C. A special part which is drawn in red is the walker. Initially, A* which carries the walker part will be ligated to B and then the duplex will be cut by endonuclease. The walker part has thus been transported to B. In a similar manner, the walker could be further transported to C (reprinted with permission from ref. 62; copyright 2004; Wiley Interscience). This journal is c The Royal Society of Chemistry 2009 Chem. Commun., 2009, 2625–2636 | 2629 developed a method for improving its efficiency by using the enzyme ribonuclease H to selectively digest waste.61 The enzyme-assisted method could be extended to make DNA walkers. Three different approaches have been reported up to now. One of these is controlled by ligase and endo- nuclease as studied by Yin et al. (Fig. 6(b)).62 This device also contains two components like other DNA walkers: the track and the walker. The track is a long duplex with three short duplex anchorages. The walker part is a six-nucleotide fragment which is always covalently linked to anchorages. Initially, the walker is on anchorage A. A step of this machine could be divided into two half steps: firstly, the walker’s sticky end will complement with anchorage B and be ligated to B by T4 ligase; endonuclease PflM I then recognizes the newly formed reorganization site and cuts the strand. As a model and regardless of the length of the track, this machine could walk autonomously and unidirectionally along a track. The other two examples of enzymatic DNA walkers are similar in walking mechanisms, but with different enzymatic principles. The work done by Mao’s group is based on the DNA enzyme.63 The track in their work is a long duplex with single-stranded DNA–RNA chimera protrudings as anchorages. A DNA enzyme-contained sequence is used as the walker. When the walker binds to a anchorage, it will cut the anchorage and move to the next one. The machines in this case are also autonomous and unidirectional. A striking feature is its ability to move infinitely if anchorages are available. In another approach,64 Bath et al. employed restric- tion endonuclease to cut the anchorages the make the walker move, which will generate the same result as Mao’s design. Evolution of kinetics by changing environment Environmental factors play an important role in the move- ments of DNA nanomachines. For example, a change in pH in solution will induce the motions of i-motif and triplex based DNA nanomotors. The key parts of these proton-driven nanomachines are pH-sensitive DNA segments (C-rich strands) which will be in folded and unfolded states, respec- tively, under different pH values. It is interesting to speculate that if the pH changing in solution could be controlled by a coupled system, the kinetics of proton-driven DNA nano- machines would be managed. In 2005, Liedl and Simmel reported such an approach of controlling an i-motif DNA motor65 by a chemical oscillator. As shown in Fig. 7, strandM (M has the same sequence, except end modifications, with X in Fig. 3) would undergo conformational switches between four- stranded i-motif and single-stranded random coil structures reversibly and periodically, driven by a pH oscillator in a semibatch reactor. The pH oscillator in this case is a variant of the Landolt reaction.66 The alternating oxidation of sulfite and thiosulfate by iodate is accompanied by a periodic production or consumption of protons. This oscillation reaction varies the pH value between 5 and 7 periodically and then leads to DNA conformational switches. A feed solution for the oscillator is pumped slowly and continuously into the system, which also brings a disadvantage as the oscillator will die out after several cycles as a result of the continuous decrease in reactant concentrations. Anyhow, this design of coupling pH oscillator has shed light on making autonomous proton-driven DNA nanomachines. For DNA nanomachines powered by strand-exchange reaction, the output and frame strength of the machines depend on the stability of DNA hybrids, while the quick response relies on hybridization speed. It is difficult to satisfy both requirements simultaneously because usually they will contradict each other. Maruyama’ group developed a cationic copolymer-assisted strategy to solve such a problem using G-quadruplex and DNA tweezer nanomachines as models.67,68 The strategy is partially an extended work of their previous studies on interactions between cationic comb-type copolymers and triplex69 and duplex70 DNA. In those studies, they found poly(L-lysine)-graft-dextran (PLL-g-Dex) copoly- mers have special functions of accelerating strand-exchange reaction while stabilizing DNA hybridization. Similarly, the addition of PLL-g-Dex to the G-quadruplex nanomachine system will increase opening and closing rates by 70- and 40-fold, respectively, while boosting the motion efficiency. For DNA tweezers, the performance could also be improved by PLL-g-Dex copolymers. Non-contact control modes The development of non-contact control modes, such as light- and electricity-control, for stimulating DNA nanomachines is a critical challenge. Non-contact systems offer distinct advantages to contact modes controlled DNA nanomachines in terms of simplifying the experiment by freeing our hands from adding fuels manually and improving the efficiency and precision of the machine by eliminating manual errors, making it possible to perform complicated motions and communicate with other nano-objects. Although light- and electricity- controlled chemical nanomachines have already been achieved,17–20 it is not easy to extend these strategies to DNA-based machines since natural DNA is insensitive to those stimuli. Basically, in terms of non-contact control of Fig. 7 DNA conformational switches between the i-motif and ssDNA driven by a chemical oscillator. In one-half of the reaction cycle, protons produced during the oxidation of sulfite induce the formation of the i-motif. In the other half of the reaction cycle, the oxidation of thiosulfate consumes protons and leads to ssDNA (reprinted with permission from ref. 65; copyright 2005, American Chemical Society). 2630 | Chem. Commun., 2009, 2625–2636 This journal is c The Royal Society of Chemistry 2009 DNA nanomachines, there are only two routes we can evisage: the first route is using artificial DNA strands which contain light or electrical responsive modifications; the second route is switching the environment by external non-contact stimuli. These two routes have both been realized recently. Asanuma’s group reported light-controlled DNA tweezers with covalently tethered azobenzene moieties on the fuel strand.71 Since the azobenzene group is sensitive to light irradiation and its photoresponsive trans- and cis-isomers have different stacking abilities with DNA base-pairs, the stability of azobenzene-containing DNA duplexes and triplexes could be regulated by UV and visible light. They have proved in their previous work that the planar trans-azobenzene could inter- calate between adjacent base-pairs and stabilize the duplex or triplex structure by stacking interactions, whereas the non- planar cis-azobenzene would destabilize it by steric hindrance. In their design of DNA tweezers, 12 azobenzene groups have been incorporated into the fuel strand. Under the alternate irradiation of UV and visible light, azobenzene moieties are in the cis- and trans-configurations, respectively. Therefore, the stability of DNA duplex formed by the tweezer overhangs and fuel strand could be switched. The tweezers will open in UV light and close in visible light. The above route needs specific modifications of DNA strands, which brings difficulty in DNA synthesis. For natural DNA, the second route mentioned above may be more effective. In 2007, our lab first reported an approach of controlling DNA conformational switch between the i-motif and ssDNA structures by light (Fig. 8).72 MGCB is a photo- chromic molecule which could generate a hydroxyl ion under UV light with the reverse process occurring in the dark. By turning on/off the UV light, MGCB molecules produce cycles of pH jumps in solution. Since the DNA conformational switch in our system is pH-sensitive, the coupling of a light- induced pH jump system will realize DNA conformational switches controlled by light. An advantage of this strategy is that we do not need any modifications on DNA. Both ours and Asanuma’s work used light as control signals and so do not produce wastes. Functional evolution of DNA nanomachines What complicated work can DNA nanomachines do is a very interesting question. Basically, there are several requirements for DNA nanomachines to do practical work: (1) the machine’s motion must be stable and powerful; (2) the opera- tion should be simple and clean; (3) the machine should be coupled to the object which is going to be driven. Constructing switchable surface Although a single DNA nanomotor could only generate a force at the pN level, the possibilities for the cooperative motions of many such motors, is clearly of importance. An approach to test this cooperative effect is by immobilizing DNA nanomotors on a surface. Liu and Zhou et al. reported the immobilization of i-motif DNA nanomotors onto defined locations of a microstructured surface to form a microarray.73 Based on the conventional thiol–gold interaction, the authors coupled thiol-modified DNA motors to an Au surface, while the other end of each DNA motor has a fluorophore modification. Then patterns have been constructed on the above DNA monolayer. The results demonstrated that the motor function was maintained on the surface and an on-off optical switch, which is the result of the cooperative work from numerous motors, could be produced by changing pH. The working mechanism is that under different pH values, the distance between the fluoro- phore and Au surface could be switched, leading to different FRET efficiencies. In a similar work, Simmel et al. utilized their improved pH oscillator system to control the pH switch.74 This work realized the autonomous switching of surface optical signals for many cycles. The ability of controlled immobilization of DNA motors on a defined sur- face is an important first step towards the construction of complicated nanodevices. Based on the above work, it is possible to switch the surface function by DNA nanomotors in response to stimuli. Fig. 9 shows the effort of switching surface wettability by three-state i-motif DNA nanomachines.75 The DNA nanomotors were coupled to a gold surface through thiol–Au bonds and a hydrophobic Bodipy-type fluorophore was attached on the other end of the DNA strand. At low pH (state I), DNA motors are in the closed states and hydrophilic phosphate backbones of DNA strands are exposed, leading to a hydro- philic surface. By raising the pH (state II), DNA motors will adopt ssDNA forms and the Bodipy groups will no longer be concealed. Therefore the surface will be switched to hydro- phobic wettability. The state II is not stable for long time since it is a loosely disordered state. The addition of complementary strands of DNA motors could help DNA adopt rigid duplex conformations and make the monolayer be closed packed (state III). At this state the hydrophobic behaviour is stable. It is interesting to note that a rough surface could enhance surface wettability, either hydrophilicity or hydrophobicity.76 Fig. 8 DNA conformational switches between i-motif and ssDNA controlled by light irradiation. Inner cycle: the DNA conformational switch between the i-motif and ssDNA. Outer cycle: the light-induced pH jump. The conformational switch of DNA X is associated with the on and off phases of UV light (reprinted with permission from ref. 72; copyright, 2007, Wiley Interscience). This journal is c The Royal Society of Chemistry 2009 Chem. Commun., 2009, 2625–2636 | 2631 duplex domain contains a N.BbvC IA recognition site which will cause the nicking (scission) of the replicated single strand and the resultant sequence will fold into a G-quadruplex with an intercalated hemin molecule. The complex mimics peroxidase activity and catalyzes an oxidation reaction. The generation of chemiluminescence from this reaction could be detected as an output signal. The obtained G-quadruplex sequences could also be designed to induce nanoparticle aggregation.96 Other work by this group includes constructing sensors for detecting cocaine97 and mercury ions.98 Performing controllable release Controllable collection/release of molecules or nanomaterials is a critical issue for materials science, pharmaceutics, bio- medical applications, and also for constructing hierarchical nanodevices. The feature of generating a nanomechanical output makes DNA nanomachines an ideal tool to trigger such nanoscale processes. The challenge is the conversion of mechanical force to signals for releasing targets. Up to now, two strategies have been explored. The first strategy is the direct utilization of the DNA nanomachines’ force to change the volume of a nanoscale container. Such a controllable DNA nanocontainer system has been developed by our group in 2007 (Fig. 14(a)).99 The device was implemented with the success of immobilization of DNA nanomotors on a surface.73 The most distinctive characteristic of this device is that each i-motif DNA motor in the assembled monolayer is linked to the surface through a single stranded poly-(dA)n spacer (10 r n r 35). The function of spacers in the monolayer is important since they provide a low-density packing domain, which could be regarded as a nanocontainer. By changing pH, the packing density of the upper domain (DNA motors domain) could be switched between high (densely packed i-motif conformations, closed state) and low (loosely packed ssDNAs, open state) states. At open state, small molecules could be released from spacer domains to the outer environment, while at closed state these molecules would be restricted in the nanocontainer protected by the upper closely packed DNA motors. The encapsulation ability of 3D DNA assembled nanostructures100 have been studied by Turberfield’s group Fig. 13 Detecting ssDNA targets by DNA nanomachine. M13 phage ssDNA will hybridize specifically to a hairpin strand and then produce a large amount of G-quadruplex structures. The intercalation of hemin molecules to the G-quadruplex will catalyze an oxidation reaction which will generate chemiluminescence (reprinted with permission from ref. 95; copyright 2006, Wiley Interscience). Fig. 14 DNA nanomachine based nanocontainers. (A) An i-motif DNAmotors controlled nanocontainer. At low pH, the C-rich domain folds into i-motif structure and packs into a membrane impermeable for small molecules on a gold surface. At high pH, the i-motif structures are transformed into ssDNA, making the packing density relatively loose to allow small molecules to diffuse freely (reprinted with permission from ref. 99; copyright 2007, Oxford Journals). (B) A reconfigurable DNA tetrahedron. The tetrahedron is formed by four strands and a hairpin segment has been incorporated into one edge. Based on ‘‘fuel-strands’’ strategy, the hairpin can be switched between open and closed states, leading to a volume change of the tetrahedron (reprinted with permission from ref. 101; copyright 2008, Nature Publishing Group). 2634 | Chem. Commun., 2009, 2625–2636 This journal is c The Royal Society of Chemistry 2009 using rigid DNA tetrahedra.15 The evolution of this strategy has led to reconfigurable DNA tetrahedra whose shapes change precisely and reversibly in response to specific molecular signals.101 As shown in Fig. 14(b), a hairpin segment has been incorporated into one edge of this new reconfigurable DNA tetrahedron. The edge containing hairpin is at its shortest (10 bp, 3.4 nm) when the hairpin is in the closed state. By adding a fuel strand that opens the hairpin, the edge could be extended to its longest state (30 bp, 10.2 nm). This transition will cause a volume change. A tetrahedron with two reconfigurable edges has also been built in this work. The second strategy to control release by DNA nano- machines is to exert force to break substrate–target interactions. Simmel et al. have demonstrated this cyclically binding and releasing thrombins by G-quadruplex based nanomachines.102 It is well known that the G-quadruplex structure has a high binding affinity to the thrombin molecule. Using the same strategy to open G-quadruplex nanomotors, the addition of fuel-strands will disrupt the interactions between the G-quadruplex and thrombin molecules to realize the release of thrombins. The release kinetics has also been studied.103 In a related work done by Sugiyama’s group,104 pH switching has been employed to control the release of the telomere-binding protein TRF 1 which has high affinity towards the i-motif structure; or the release of small G-quadruplex-binding molecules to impede progress of the polymerase. Conclusions and outlook In this review, we have summarized the development of DNA nanomachines in recent decades. The development of this field has demonstrated again the DNA is an important multi- purpose material in nanotechnology other than its biological characteristics. Looking towards the future, the current research on DNA nanomachines is still in its early stages and the most established systems are simple models. We here consider the following issues which might be the most important challenges for future development in this field: (1) experimental and theoretical studies on single DNA nanomachines leading to understanding of energy conversion mechanisms and entropy exchange with the environment; (2) a new power supplying method which could be easily incorporated into current silicon based nanodevices; (3) improvement of the reliability of DNA nanomachines; (4) directionally controllable movements; (5) multi-component DNA nanomachines with clear and interconnected energy transformation and mechanical response; (6) evaluation of biological and medical applications of DNA nanomachines. In summary, the anticipated devel- opment in this field will be fascinating and we believe DNA will play a more important role in nanoscience in the coming decade. Acknowledgements D. L. would like to thank Prof. Xi Zhang in Tsinghua University for helpful discussion and NSFC under grant No. 20725309, NSFC-DFG joint project TRR61 andMOST under grant No 2007CB935902 for financial supports. References 1 N. C. Seeman, Nature, 2003, 421, 427–431. 2 N. C. Seeman, J. Theor. Biol., 1982, 99, 237–247. 3 N. C. Seeman and N. R. Kallenbach, Annu. Rev. Biophys. Biomol. Struct., 1994, 23, 53–86. 4 N. C. Seeman, Angew. Chem., Int. Ed., 1998, 37, 3220–3238. 5 N. C. Seeman, Nano Lett., 2001, 1, 22–26. 6 N. C. Seeman, Chem. Biol., 2003, 10, 1151–1159. 7 E. Winfree, F. R. Liu, L. A. Wenzler and N. C. Seeman, Nature, 1998, 394, 539–544. 8 C. D. Mao, W. Q. Sun and N. C. Seeman, J. Am. Chem. Soc., 1999, 121, 5437–5443. 9 H. Yan, S. H. Park, G. Finkelstein, J. H. Reif and T. H. LaBean, Science, 2003, 301, 1882–1884. 10 P. W. K. Rothemund, Nature, 2006, 440, 297–302. 11 Y. G. Ke, S. Lindsay, Y. Chang, Y. Liu and H. Yan, Science, 2008, 319, 180–183. 12 K. V. Gothelf and T. H. LaBean, Org. Biomol. Chem., 2005, 3, 4023–4037. 13 J. H. Chen and N. C. Seeman, Nature, 1991, 350, 631–633. 14 Y. W. Zhang and N. C. Seeman, J. Am. Chem. Soc., 1994, 116, 1661–1669. 15 R. P. Goodman, I. A. T. Schaap, C. F. Tardin, C. M. Erben, R. M. Berry, C. F. Schmidt and A. J. Turberfield, Science, 2005, 310, 1661–1665. 16 W. M. Shih, J. D. Quispe and G. F. Joyce, Nature, 2004, 427, 618–621. 17 V. Balzani, A. Credi, F. M. Raymo and J. F. Stoddart, Angew. Chem., Int. Ed., 2000, 39, 3348–3391. 18 J. F. Stoddart, Acc. Chem. Res., 2001, 34, 410–411. 19 W. R. Browne and B. L. Feringa, Nat. Nanotechnol., 2006, 1, 25–35. 20 E. R. Kay, D. A. Leigh and F. Zerbetto, Angew. Chem., Int. Ed., 2007, 46, 72–191. 21 M. Schliwa and G. Woehlke, Nature, 2003, 422, 759–765. 22 K. Kinbara and T. Aida, Chem. Rev., 2005, 105, 1377–1400. 23 X. P. Yang, A. V. Vologodskii, B. Liu, B. Kemper and N. C. Seeman, Biopolymers, 1998, 45, 69–83. 24 N. C. Seeman, Trends Biochem. Sci., 2005, 30, 119–125. 25 F. C. Simmel and W. U. Dittmer, Small, 2005, 1, 284–299. 26 P. Alberti, A. Bourdoncle, B. Sacca, L. Lacroix and J.-L. Mergny, Org. Biomol. Chem., 2006, 4, 3383–3391. 27 M. K. Berssenhirtz and I. Willner, Org. Biomol. Chem., 2006, 4, 3392–3401. 28 J. Bath and A. J. Turberfield, Nat. Nanotechnol., 2007, 2, 275–284. 29 T. Liedl, T. L. Sobey and F. C. Simmel, Nano Today, 2007, 2, 36–41. 30 B. Yurke, A. J. Turberfield, A. P. Mills Jr, F. C. Simmel and J. L. Neumann, Nature, 2000, 406, 605–608. 31 B. K. Muller, A. Reuter, F. C. Simmel and D. C. Lamb, Nano Lett., 2006, 6, 2814–2820. 32 F. C. Simmel and B. Yurke, Phys. Rev. E, 2001, 63, 041913. 33 F. C. Simmel and B. Yurke, Appl. Phys. Lett., 2002, 80, 883–885. 34 H. Yan, X. P. Zhang, Z. Y. Shen and N. C. Seeman,Nature, 2002, 415, 62–65. 35 H. Zhong and N. C. Seeman, Nano Lett., 2006, 6, 2899–2903. 36 B. Chakraborty, R. Sha and N. C. Seeman, Proc. Natl. Acad. Sci, USA, 2008, 105, 17245–17249. 37 J. J. Li and W. Tan, Nano Lett., 2002, 2, 315–318. 38 P. Alberti and J.-L. Mergny, Proc. Natl. Acad. Sci, USA, 2003, 100, 1569–1573. 39 C. D. Mao, W. Q. Sun, Z. Y. Shen and N. C. Seeman, Nature, 1999, 397, 144–146. 40 R. P. Fahlman, M. Hsing, C. S. Sporer-Tuhten and D. Sen, Nano Lett., 2003, 3, 1073–1078. 41 D. Miyoshi, H. Karimata, Z.-M. Wang, K. Koumoto and N. Sugimoto, J. Am. Chem. Soc., 2007, 129, 5919–5925. 42 D. Liu and S. Balasubramanian, Angew. Chem., Int. Ed., 2003, 42, 5734–5736. 43 Y. Chen, S.-H. Lee and C. Mao, Angew. Chem., Int. Ed., 2004, 43, 5335–5338. 44 M. Brucale, G. Zuccheri and B. Samori, Org. Biomol. Chem., 2005, 3, 575–577. This journal is c The Royal Society of Chemistry 2009 Chem. Commun., 2009, 2625–2636 | 2635 45 R. Tashiro and H. Sugiyama, J. Am. Chem. Soc., 2005, 127, 2094–2097. 46 V. Viasnoff, A. Meller and H. Isambert, Nano Lett., 2006, 6, 101–104. 47 W. Q. Shen, M. F. Bruist, S. D. Goodman and N. C. Seeman, Angew. Chem., Int. Ed., 2004, 43, 4750–4752. 48 W. B. Sherman and N. C. Seeman, Nano Lett., 2004, 4, 1203–1207. 49 T. H. LaBean, H. Yan, J. Kopatsch, F. R. Liu, E. Winfree, J. H. Reif and N. C. Seeman, J. Am. Chem. Soc., 2000, 122, 1848–1860. 50 J. S. Shin and N. A. Pierce, J. Am. Chem. Soc., 2004, 126, 10834–10835. 51 Y. Tian and C. D. Mao, J. Am. Chem. Soc., 2004, 126, 11410–11411. 52 A. J. Turberfield, J. C. Mitchell, B. Yurke, A. P. Mills Jr, M. I. Blakey and F. C. Simmel, Phys. Rev. Lett., 2003, 90, 118102–11411. 53 S. J. Green, D. Lubrich and A. J. Turberfield, Biophys. J., 2006, 91, 2966–2975. 54 G. Seelig, B. Yurke and E. Winfree, J. Am. Chem. Soc., 2006, 128, 12211–12220. 55 Y. Wang, Y. Zhang and N. P. Ong, Phys. Rev. E, 2005, 72, 051918. 56 D. Y. Zhang, A. J. Turberfield, B. Yurke and E. Winfree, Science, 2007, 318, 1121–1125. 57 S. Venkataraman, R. M. Dirks, P. W. K. Rothemund, E. Winfree and N. A. Pierce, Nat. Nanotechnol., 2007, 2, 490–494. 58 E. Gouin, M. D. Welch and P. Cossart, Curr. Opin. Microbiol., 1999, 8, 35–45. 59 Y. Chen, M. S. Wang and C. D. Mao, Angew. Chem., Int. Ed., 2004, 43, 3554–3557. 60 Y. Chen and C. D. Mao, J. Am. Chem. Soc., 2004, 126, 8626–8627. 61 J. D. Bishop and E. Klavins, Nano Lett., 2007, 7, 2574–2577. 62 P. Yin, H. Yan, X. G. Daniell, A. J. Turberfield and J. H. Reif, Angew. Chem., Int. Ed., 2004, 43, 4906–4911. 63 Y. Tian, Y. He, Y. Chen, P. Yin and C. D. Mao, Angew. Chem., Int. Ed., 2005, 44, 4355–4358. 64 J. Bath, S. J. Green and A. J. Turberfield, Angew. Chem., Int. Ed., 2005, 44, 4358–4361. 65 T. Liedl and F. C. Simmel, Nano Lett., 2005, 5, 1894–1898. 66 V. Gaspar and K. Showalter, J. Am. Chem. Soc., 1987, 109, 4869–4876. 67 N. Makita, S. Inoue, T. Akaike and A. Maruyama, Nucl. Acids Symp. Ser., 2004, 48, 173–174. 68 S. W. Choi, N. Makita, S. Inoue, C. Lesoil, A. Yamayoshi, A. Kano, T. Akaike and A. Maruyama, Nano Lett., 2007, 7, 172–178. 69 A. Maruyama, M. Katoh, T. Ishihara and T. Akaike, Bioconjugate Chem., 1997, 8, 3–6. 70 W. J. Kim, T. Akaike and A. Maruyama, J. Am. Chem. Soc., 2002, 124, 12676–12677. 71 X. Liang, H. Nishioka, N. Takenaka and H. Asanuma, ChemBioChem, 2008, 9, 702–705. 72 H. Liu, Y. Xu, F. Li, Y. Yang, W. Wang, Y. Song and D. Liu, Angew. Chem., Int. Ed., 2007, 46, 2515–2517. 73 D. Liu, A. Bruckbauer, C. Abell, S. Balasubramanian, D.-J. Kang, D. Klenerman and D. Zhou, J. Am. Chem. Soc., 2006, 128, 2067–2071. 74 T. Liedl, M. Olapinski and F. C. Simmel, Nano Lett., 2006, 45, 5007–5010. 75 S. Wang, H. Liu, D. Liu, X. Ma, X. Fang and L. Jiang, Angew. Chem., Int. Ed., 2007, 46, 3915–3917. 76 T. Sun, L. Feng, X. Gao and L. Jiang, Acc. Chem. Res., 2005, 38, 644–652. 77 Z. J. Gartner and D. R. Liu, J. Am. Chem. Soc., 2001, 123, 6961–6963. 78 Z. J. Gartner, B. N. Tse, R. Grubina, J. B. Doyon, T. M. Snyder and D. R. Liu, Science, 2004, 305, 1601–1605. 79 K. V. Gothelf, A. Thomsen, M. Nielsen, E. Clo and R. S. Brown, J. Am. Chem. Soc., 2004, 126, 1044–1046. 80 Y. Chen and C. Mao, J. Am. Chem. Soc., 2004, 126, 13240–13241. 81 S. P. Liao and N. C. Seeman, Science, 2004, 306, 2072–2074. 82 R. Chhabra, J. Sharma, Y. Liu and H. Yan, Nano Lett., 2006, 6, 978–983. 83 C. A. Mirkin, R. L. Letsinger, R. C. Mucic and J. J. Storhoff, Nature, 1996, 382, 607–609. 84 A. P. Alivisatos, K. P. Johnsson, X. G. Peng, T. E. Wilson, C. J. Loweth, M. P. Bruchez and P. G. Schultz,Nature, 1996, 382, 609–611. 85 P. Hazarika, B. Ceyhan and C. M. Niemeyer, Angew. Chem., Int. Ed., 2004, 43, 6469–6471. 86 Y. H. Jung, K.-B. Lee, Y.-G. Kim and I. S. Choi, Angew. Chem., Int. Ed., 2006, 45, 5960–5963. 87 W. Wang, H. Liu, D. Liu, Y. Xu, Y. Yang and D. Zhou, Langmuir, 2007, 23, 11956–11959. 88 J. Sharma, R. Chhabra, H. Yan and Y. Liu, Chem. Commun., 2007, 477–479. 89 Y. Wang, X. Li, X. Liu and T. Li, Chem. Commun., 2007, 4369–4371. 90 W. Shu, D. Liu, M. W. C. K. Riener, T. Strunz, M. E. Welland, S. Balasubramanian and R. A. McKendry, J. Am. Chem. Soc., 2005, 127, 17054–17060. 91 B. Ding and N. C. Seeman, Science, 2006, 314, 1583–1585. 92 C. M. Niemeyer, M. Adler, S. Lenhert, S. Gao, H. Fuchs and L. Chi, ChemBioChem, 2001, 2, 260–264. 93 A. H. Buck, C. J. Campbell, P. Dickinson, C. P. Mountford, H. C. Stoquert, J. G. Terry, S. A. G. Evans, L. M. Keane, T. J. Su, A. R. Mount, A. J. Walton, J. S. Beattie, J. Crain and P. Ghazal, Anal. Chem., 2007, 79, 4724–4728. 94 C. P. Mountford, A. H. Buck, C. J. Campbell, P. Dickinson, E. E. Ferapontova, J. G. Terry, J. S. Beattie, A. J. Walton, P. Ghazal, A. R. Mount and J. Crain, J. Phys. Chem. B, 2008, 112, 2439–2444. 95 Y. Weizmann, M. K. Beissenhirtz, Z. Cheglakov, R. Nowarski, M. Kotler and I. Willner, Angew. Chem., Int. Ed., 2006, 45, 7384–7388. 96 M. K. Beissenhirtz, R. Elnathan, Y. Weizmann and I. Willner, Small, 2007, 3, 375–379. 97 B. Shlyahovsky, D. Li, Y. Weizmann, R. Nowarski, M. Kotler and I. Willner, J. Am. Chem. Soc., 2007, 129, 3814–3815. 98 L. Zhang, C. Feng, Z. Chen, L. Liu, K. Jiang, Q. Li and S. Fan, Nano Lett., 2008, 8, 2564–2569. 99 Y. Mao, D. Liu, S. Wang, S. Luo, W. Wang, Y. Yang, Q. Ouyang and L. Jiang, Nucleic Acids Res., 2007, 35, e33. 100 C. M. Erben, R. P. Goodman and A. J. Turberfield, Angew. Chem., Int. Ed., 2006, 45, 7414–7417. 101 R. P. Goodman, M. Heilemann, S. Doose, C. M. Erben, A. N. Kapanidis and A. J. Turberfield, Nat. Nanotechnol., 2008, 3, 93–96. 102 W. U. Dittmer, A. Reuter and F. C. Simmel, Angew. Chem., Int. Ed., 2004, 43, 3550–3553. 103 A. Reuter, W. U. Dittmer and F. C. Simmel, Eur. Phys. J. E, 2007, 22, 33–40. 104 Y. Xu, Y. Hirao, Y. Nishimura and H. Sugiyama, Bioorg. Med. Chem., 2007, 15, 1275–1279. 2636 | Chem. Commun., 2009, 2625–2636 This journal is c The Royal Society of Chemistry 2009