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Switchable Reconfiguration of a SevenRing Interlocked DNA Catenane Nanostructure Chun-Hua Lu, Alessandro Cecconello, Xiu-Juan Qi, Na Wu, Stefan-S. Jester, Michael Famulok, Michael Matthies, Thorsten Lars Schmidt, and Itamar Willner Nano Lett., Just Accepted Manuscript • DOI: 10.1021/acs.nanolett.5b03280 • Publication Date (Web): 11 Sep 2015 Downloaded from http://pubs.acs.org on September 17, 2015

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Switchable Reconfiguration of a Seven-Ring Interlocked DNA Catenane Nanostructure Chun-Hua Lu,1† Alessandro Cecconello,1† Xiu-Juan Qi,1,2 Na Wu,1 Stefan-Sven Jester,*3 Michael Famulok,4,5 Michael Matthies,6 Thorsten-Lars Schmidt,6 and Itamar Willner*1 1 Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel 2 The Key Laboratory of Analysis and Detection Technology for Food Safety of the MOE, College of Chemistry, Fuzhou University, Fuzhou 350002, China 3 Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, GerhardDomagk-Straße 1, 53121 Bonn, Germany 4 LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany 5 Center of Advanced European Studies and Research (CAESAR), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany 6 Cluster of Excellence Centre for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062 Dresden, Germany *Address correspondence to: [email protected] *Correspondence regarding high-resolution AFM: [email protected] Tel: +972-2-6585272 Fax: +972-2-6527715 † These authors contributed equally.

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Abstract The synthesis, purification and structure characterization of a seven-ring interlocked DNA catenane is described. The design of the seven-ring catenane allows the dynamic reconfiguration of any of the four rings (R1, R3, R4, and R6) on the catenane scaffold, or the simultaneous switching of any combination of two, three or all four rings to yield sixteen different isomeric states of the catenane. The dynamic reconfiguration across the states is achieved by implementing the strand-displacement process in the presence of appropriate fuel/anti-fuel strands, and is probed by fluorescence spectroscopy. Each of the sixteen isomers of the catenane can be transformed into any of the other isomers, thus allowing for 240 dynamic transitions within the system. Key words: Nanobiotechnology, Machine, Switch, Fluorescence, Strand displacement

The design of DNA machines undergoing reversible reconfiguration across distinct states attracts substantial research efforts in recent years.1-5 Different DNA machines acting as “tweezers”,6,7 “shuttles”,8 “walkers”9-12 or “cranes”13 operating in solutions or surfaces14,15 were reported, and the possible applications of these systems for programmed synthesis,16-19 carriers of payloads20 and DNA computing21-26 were discussed. One specific class of reconfigurable DNA machines are interlocked circular DNA catenanes.27-32 Specifically, two,33 three-34 and five-ring35 interlocked catenane nanostructures were synthesized, and their programmed reversible reconfiguration by external triggers was discussed. For example, a three-state two-ring DNA catenane acting as a rotary motor with controlled directionality,36 and a two-state, pH-driven two-ring DNA pendulum37 were reported. Also, catalytic two-ring interlocked DNA catenane systems were assembled, and their reconfiguration across two different “ON”/”OFF” DNAzyme structures was demonstrated.38 Similarly, the synthesis of a

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three-ring DNA catenane undergoing dictated reversible reconfiguration across three distinct states was reported,34 and this dynamic system was applied for the programmed organization of different sized Au nanoparticles, and for controlling plasmonic interactions of Au nanoparticle/fluorophore conjugates associated with the three-ring catenane device.39 The synthesis of higher order, DNA catenane systems is, however, challenging due to the drop in the reaction yields with the increase in number of interlocked rings. Increasing of the number of interlocked DNA rings is interesting since the complexity of reconfigurable states increases with the number of rings. The preparation of two-ring and three-ring interlocked catenanes was based on the ligation of quasi-circularized nucleic acid strands, and on the inter-threading of single strands into the circular DNA structures following by ligation of the quasi-circularized supramolecular structures.36-38 Recently, we reported a method to synthesize a five-ring interlocked DNA catenane system.35 This method is based on the synthesis of two-ring catenanes as subunits, their temporary linking by a “helper” strand followed by inter-threading of a mutual strand into the subunits. The pseudo-circularization of the inter-threaded strand, followed by ligation and the removal of the capping/”helper” units, resulted in a five-ring catenane. The reversible reconfiguration of this system across four states, including the olympiadane DNA structure, was demonstrated, and the programmed geometrical organization of Au nanoparticles by the DNA device was reported. Here we wish to report on the synthesis of a seven-ring interlocked DNA catenane. Besides the synthetic challenge in preparing this macromolecular nanostructure that exhibits a molecular weight of a medium-sized protein, we demonstrate that the system undergoes reversible switchable re-configurations across sixteen states. Figure 1(A) depicts the synthesis of the seven-ring interlocked catenane. In the first step the linear strand L1, L2 and L3 are bridged into a pseudo-circular catenane structure capped by the units C1, C2 and C3, leading, after ligation and purification, to the three-ring interlocked


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catenane R1R2R3. Similarly, the single strand L4 was capped with C4, and after ligation and purification led to the circular DNA R4. The three-ring catenane R1R2R3 and the circular DNA R4 were then interacted with the strands L5, L6 and L7, where L5 includes complementary domains to R2 and R4, respectively, and L6 and L7 include complementary domains to the pseudo-circle L5. To stabilize the supramolecular inter-threaded structure of the pseudo seven-ring catenane we introduced “helper units” H2,5; H4,5,7 and H5,6 that bridge domains of R2L5, R4L5L7 and L5L6, respectively. These “helper units” are aimed to increase the final yield of the seven-ring catenane. The pseudo-interlocked catenated rings were capped by C5, C6 and C7. After ligation followed by separation of the capping and ‘helper” units, the seven-ring interlocked catenane was purified by electrophoresis and further characterized. For the detailed electrophoretic purification of the subunits R1R2R3 and the final electrophoretic purification of the seven-ring catenane see Figure S1, supporting information. The seven-ring interlocked catenane was characterized by ESI mass spectrometry to exhibit a molecular mass of 191288±300 Da consistent with the calculated value 191292 Da. The resulting seven-ring catenane was characterized by AFM analysis in high resolution (HyperDrive) mode. Figure 1(B) and S2, Supporting Information, reveal the existance of 28 seven-ring catenanes displaying the features expected from the geometrical model (see Table S2, Supporting Information). The catenated nanostructure includes two large rings as the ‘body”, R2 and R5, where smaller rings R4, R6 and R7 are interlocked into the ring R5, and smaller rings R1 and R3 are interlocked into large ring R2. This is consistent with the shorter strands L1, L3, L4, L6 and L7 as compared to the initial strands L2 and L5 that generate rings R2 and R5. Figure S1 suggests that the assembly and purification of the S9 structure lacking the complementary strands yielded a single band of high purity, the migration of which corresponds to the size of the seven-ring catenane, supported by the high count of structures


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S9 in the AFM pictures. However, there is also a large population of fragments that appears to correspond either to incorrectly assembled R2/R5 catenanes, or in which the mechanical bond between R2 and R5 was broken after initial correct assembly (16 corresponding to a three-ring catenane, 8 corresponding to a four-ring catenane). Table 1 provides a detailed analysis of the different structures appearing in Figure 1(B) and Figure S2. In both images the majority of the structures consists of the hybridized seven-ring catenane, S9 (see table S2), yet additional fragmented structures that include six-, five-, four-, three-, and two interlocked catenanes, and even separated or single-ring structures (A to G) are observed. Enlarged images of the seven-ring catenane are depicted in Figure 1(B), insets. Also, we note that the denaturing PAGE purification of the seven-ring catenane, prior to hybridization and deposition on the mica surface, excludes the possibility that non interlocked structures exist in the mixture. Thus, the origin of the fragmented structures in the AFM images is at the present unclear, and may originate from fragmentation occurring upon deposition and/or AFM analysis. Nevertheless, the high-yield of the seven-ring catenane confirms the robustness of the assembly. The seven-ring nanostructure may be considered as a “molecular robot”, where the sequences were designed in such a way that the large rings R2 and R5 (body) and ring R7 (head) are non-moveable. In turn, rings R1 and R3 (legs) and R4 and R6 (hands) may undergo strand displacement transitions driven by appropriate fuel strands, Figure 2. Toward this end the “body” ring R5 was tailored to include the rings R4 and R6 on the energetically stabilized domain I and II, and ring R2 was designed to include the energetically-stabilized “leg” rings R3 and R1 on the domains III and IV. In the presence of appropriate fuel strands the “hand(s)” and/or “leg(s)” rings may undergo single or multiple transitions to domain I’, II’, III’ or IV’ to yield different configurations. In the presence of anti-fuel strands, the fuel-strands may be displaced, and the “moving” “hand(s)”/”leg(s)” components may regenerate the original


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configurations. The dynamic reconfigurations of the different “hand(s)’/”leg(s)” components may be followed by labeling the “robot” structure with appropriate fluorophore and quencher units, as outlined in Figure 2. The rings R1 and R3 were labeled with the Cy3-modified nucleic acid and TEX615-modified nucleic acid, respectively. The rings R4 and R6 are labeled with Cy5-modified nucleic acid and Cy5.5-modified nucleic acid, respectively. Similarly, the IAbRQ-functionalized nucleic acid was attached to an identical ring sequence separating domains I/I’; II/II’; III/III’ and IV/IV’ as quencher unit (For the detailed fluorophore- and quencher-modified nucleic acid sequences see Table S1 and Figures S3 and S4, supporting information). Thus, the fuel/anti-fuel transitions of the respective “moving” rings could be followed by the fluorescence intensities of the different fluorophores labeling the seven ring catenated nanostructure. This is exemplified in Figure 2 right with the fuel/anti-fuel induced transitions across the domains I/I’. While the resting of ring R6 on domain I yields a high fluorescence signal of Cy5.5, the fuel-driven transition of R6 to domain I’ leads to a close spatial separation between F1 and the quencher unit (Q), leading to a low fluorescence signal. The reverse anti-fuel-triggered transition of R6 to domain I restores then the original high fluorescence intensity of Cy5.5. The “molecular robot” can exist in 16 states (isomers) of the seven-ring catenanes that can be reversibly switched in the presence of the respective fuel strands and anti-fuel strands, Figure S5. Each of these states (isomers) is then characterized by the fluorescence features of the Cy3, TEX615, Cy5 and Cy5.5 associated with the molecular device. Figure 3 outlines the switchable reconfiguration of state S1 to any of the other 15 states S2-S16. Figure 3(A) shows the selective transitions of each of the rings R4, R6, R1, R3 from state S1 to form the states S2, S3, S4 and S5, respectively. Figure 3(B) shows the selective concomitant transitions of R4/R6, R3/R4, R1/R6, R1/R3, R1/R4 and R3/R6, from state S1 to form the states S6, S7, S8, S9, S10 and S11, respectively. Figure 3(C) shows the concomitant


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transition of the three rings R1/R4/R6, R3/R4/R6, R1/R3/R6 and R1/R3/R4, from state S1 to form the states S12, S13, S14 and S15, respectively. Figure 3(D) depicts the schematic concomitant transition of all four rings R1/R3/R4/R6 from state S1 to form the state S16. The configurations of the respective seven-ring catenane devices are, then, transduced by the fluorescence properties of the four fluorophores (Cy3, TEX615, Cy5 and Cy5.5). Figure 3(E) shows the time-dependent fluorescence changes upon the switchable transitions of two moving ring according to the pathways shown in Figure 3(B). Transition of S1 to S6, by moving rings R4 and R6 results in the time-dependent increase in the fluorescence of Cy5 and the decrease in the fluorescence of Cy5.5, consistent with the spatial separation of Cy5 from the quencher unit and the short distance between Cy5.5 and the quencher unit in configuration S6. The reverse time-dependent fluorescence changes are observed upon the re-configuration S6 to S1. Similarly, the translocation of R3 and R4 results in the transition from state S1 to state S7 leading to the increase of the Cy5 fluorescence, and to the decrease of the TEX615 fluorescence. The reversible reconfiguration of S1 and S8 states is accompanied by an intensified fluorescence of Cy3 and the quenching of Cy5.5 in state S8. Similarly, the reconfiguration of state S1 to S9 and of S1 and S10 is accompanied by intensifying the fluorescence of Cy3 and quenching of the fluorescence of TEX615 (in S9) and by intensifying fluorescence of Cy3 and intensifying fluorescence of Cy5 (in S10). Also, the reconfiguration of S1 to S11 is accompanied by intensifying the fluorescence of TEX615 and quenching of the fluorescence of Cy5.5. Figure 3(F) depicts the time dependent fluorescence changes of the different fluorophores upon the reconfiguration of three of the moving rings associated with S1 to S12, S13, S14 and S15 outlined in Figure 3(C). The reversible reconfiguration of S1 and S12 states is accompanied by an intensified fluorescence of Cy3 and Cy5 and the quenching of Cy5.5 in state S12. Similarly, the reconfiguration of state S1 to S13 and of S1 and S14 is accompanied by intensifying the fluorescence of Cy5 and quenching of


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the fluorescence of TEX615 and Cy5.5 (in S13) and by intensifying fluorescence of Cy3 and quenching fluorescence of Cy5.5 and TEX615 (in S14). Also, the reconfiguration of S1 to S15 is accompanied by intensifying the fluorescence of Cy5 and Cy3 and quenching of the fluorescence of TEX615. For the experimental results confirming the different switchable reconfiguration pathways shown in Figure 3(A) and Figure 3(D) see Figure S6 and Figure S7, supporting information. Also addition transitions are addressed in Figure S8, Figure S9 and Figure S10, supporting information. In conclusion, the present study has demonstrated the synthesis of a seven-ring catenane system that presents “robot” functions of four-moveable rings on the DNA scaffold. The increased number of rings in the seven-ring catenane device provides a means to enhance the complexity of the switchable configurations of the system. The system exists in sixteen distinct states (isomers). Each of these isomers can be transformed into the other fifteen isomer states comprising a total number of 240 transitions between the states, Figure 4. Such complex molecular devices might act as programmed carriers of payloads. By using other triggering stimuli such as pH, ions or light new DNA nanostructures for nanomedicine applications may be envisaged.

Acknowledgement: This research is supported by the MULTI project (No. 317707) of the EC Seventh Framework Programme. TLS is supported by a startup grant of the cfaed and is grateful to M. Mertig for AFM access.

Supporting Information: The sequences for constructing the seven-ring catenane, and the fuel/anti-fuel strands to reconfigure the catenane system across the different states, are provided. The detailed synthesis and purification of the seven-ring catenane are described.


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An additional large-area image that includes the seven-ring catenane structure is presented. The time-dependent fluorescence changes upon the reversible and switchable reconfiguration of the seven-ring catenane across the states S1 to S16 are provided.


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Figure 1. (A) Synthetic route for the preparation of the seven-ring interlocked catenane. (B) AFM image of the seven-ring interlocked catenane. For AFM imaging, all strands were made double -stranded to increase height contrast. Insets: enlarged seven-ring interlocked catenane structures.


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Table 1. Numbers of observed structures S9 and fragments A-H in Figures 1(B) and S2.


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Figure 2. Labeling of the seven-ring interlocked catenane with four fluorophores and quencher units for the monitoring of the reconfiguration of rings, R1, R3, R4, R6 in the presence of the appropriate fuel/anti-fuel strands. Right: The strand-displacement mechanism, in the presence of the fuel/anti-fuel strands, is exemplified for the switchable reconfiguration of ring R6 and the transduction of the ring position by the fluorescence intensities of Cy5.5.


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Figure 3. (A) Reversible reconfiguration of the structure S1 into the structural isomers S2, S3, S4, and S5. (B) Reversible reconfiguration of the structure S1 into the structural isomers S6, S7, S8, S9, S10 and S11 by the programmed reconfiguration of two of the device rings using appropriate fuel/anti-fuel strands. (C) Reversible reconfiguration of the structure S1 into the structural isomers S12, S13, S14 and S15 by the programmed reconfiguration of three rings of the device, using appropriate fuel/anti-fuel strands. (D) Reversible reconfiguration of S1 into the S16 isomer. (E) Time-dependent fluorescence changes of the four fluorophores Cy3, TEX615, Cy5; and Cy5.5 upon the switchable reconfiguration of S1 to the structures S6, S7, S8, S9, S10 and S11 and back, according to (B). (F) Time-dependent fluorescence changes of the four fluorophores Cy3, TEX615, Cy5, and Cy5.5 upon the switchable reconfigurations of S1 to the structures S12, S13, S14 and S15 and back, according to (C).


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Figure 4. Summary of all 240 possible switchable transitions between any of the interlocked seven-ring catenane isomer and the other fifteen isomers.


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A seven-ring interlocked catenane nanostructure undergoes cyclic and reversible transitions across sixteen distinct configurations using the strand displacement mechanism in the presence of tailored fuel and anti-fuel strands.


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