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Proximity-induced Pattern Operations inReconfigurable DNA Origami Domino ArraySisi Fan, Jin Cheng, Yan Liu, Dongfang Wang, tao luo, Bin

Dai, Chuan Zhang, Daxiang Cui, Yonggang Ke, and Jie SongJ. Am. Chem. Soc., Just Accepted Manuscript • DOI: 10.1021/jacs.0c06061 • Publication Date (Web): 29 Jul 2020

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Proximity-induced Pattern Operations in Reconfigurable DNA Origami Domino ArraySisi Fan1, Jin Cheng1, Yan Liu1, Dongfang Wang1*, Tao Luo1, Bin Dai1, Chuan Zhang2, Daxiang Cui1, Yonggang Ke3*, Jie Song1,4*1 Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.

2 School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China

3 Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 30322, Atlanta, GA, USA

4 Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.

KEYWORDS: reconfigurable DNA origami domino array, dynamic pattern operations, conformational transformation, proximity, molecular control

ABSTRACT: Molecular patterns with nanoscale precision have been used to mimic complex molecular networks. One key challenge in molecular patterns is to perform active pattern operations in controllable systems to fully imitate their complex dynamic behaviors. Here, we present a reconfigurable DNA origami domino array based dynamic pattern operation (DODA DPO) system to perform proximity-induced molecular control for complex pattern operations. The activatable platform of reconfigurable DODA endows a spontaneous cascade of stacking conformational transformation from the “Before” to “After” conformation by a set of “trigger” DNA strands. The conformational transformation further brings the operational pattern units into close proximity to undergo DNA strand displacement cascades to accomplish three different pattern operations of “Writing”, “Erasing” and “Shifting”. Our results also demonstrate the reconfigurable DODA DPO system provides a useful basis to study various molecular control analysis in a fully programmable and controllable fashion.

INTRODUCTIONThe manipulation of molecular systems, which provides

fundamental insights into biochemical and optical-electronic phenomena, can be imitated by programmable assembly of nanomaterials 1. Structural DNA nanotechnology, pioneered by Nadrian C. Seeman in 19822, offers unprecedented opportunities to create molecular patterns by fully controlling over the number, position and orientation of nanoscale objects3-6. Self-assembly of functional interacting components with nanoscale resolution provides an excellent strategy to further unravel the molecular mechanisms behind spatial organization on versatile DNA nanostructures. The attachment of proteins7-11, for example, operation of enzyme cascades12, allows to model complex protein assemblies and examine the effects of spatial organization. The attachment of metal and metal oxide nanoparticles13-14, carbon nanotubes15-16 or gold nanoparticles17-20 allows the construction of complex nanoelectronics or plasmonic circuits. Nonetheless, despite the tremendous amount of achievements in the construction of molecular patterns to provide important structural and functional understandings into the underlying principles, further active pattern operations to fully imitate complex dynamic behaviors in controllable systems is still a key challenge.

Dynamic operation or regulation of the patterns has been progressed with the development of dynamic DNA nanotechnology in the last decades21. Currently, commonly used strategies for the operation of patterns involve two distinct methods. The first one relies on the rearrangement of the guest nano-objects on the static DNA origami, such as DNA cargo-sorting system22-23, DNA navigator system24, signal-triggered translocation of chiroplasmonic nanostructures, etc25-26. The second strategy is based on the dynamic DNA origami nanostructures. The patterns on the DNA origami are operated along with the dynamic behaviors of DNA nanostructures27-32. These dynamic pattern operation systems have been further applied for programmed catalysis, controlled drug-release33, logic gate operations, and sensing. Moreover, further improvement in the ability to control complex pattern operations is still needed to satisfy the needs of more complex and difficult tasks. And it will provide an innovative way to greatly improve the sophistication and functionality of the nanoscale assemblies and devices.

In our previous work34, we have demonstrated the regulation of the patterns can be realized in a reconfigurable DNA origami domino array (DODA). Based on it, we further present a reconfigurable DODA-based dynamic pattern operation (DODA DPO) system to perform proximity-induced

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molecular control for complex pattern operations in this work. We firstly construct the DPO platform of DODA, which endows a spontaneous cascade of stacking conformational

transformation from the “Before” to “After” conformation by a set of “trigger”

Figure 1. Complex pattern operations platform of reconfigurable DODA. (A) Different diagrams showing the transformation of two interconnected DODA units. Transformation of a DODA unit is realized by the addition of a trigger strand, and then causes the subsequent transformation of its neighboring unit. (B) The transformation of the 8 units by 8 units DODA that is used as pattern operations platform. With addition of the trigger strands, the “Before” conformational DODA (left, comprised of grey units) transforms to the “After” conformational DODA (right, comprised of brown units). The schematic in the middle shows an intermediate state during the transformation, the orange-colored units are partially transformed. The transformation reconfigures the computing platform from the standby state (“Before” DODA) to the corresponding operational state (“After” DODA). (C) Complex pattern operations in the reconfigurable DODA platform. The operational state of the “After” DODA enables different pattern operations, including “Writing”, “Erasing” and “Shifting”. Scale bar, 100 nm.

DNA strands. We then use such conformational transformation mechanism to create an activatable platform for DNA strand displacement cascades whereby operations can be stably initialized and then set loose by triggering a change in their proximity thus enabling strand displacement operations to occur. By combination of conformational transformation and conformational transformation induced toehold-mediate strand displacement cascades at close proximity, three different pattern operations of “Writing”, “Erasing” and “Shifting” operations are performed. Our results also demonstrate the reconfigurable DODA-based platform has the potential applications in various molecular control analysis.

RESULTS AND DISCUSSION

Complex pattern operations platform of reconfigurable DODA. Figure 1 shows the DPO platform of reconfigurable DODA. In our group’s previous work32, we report the assembly dynamic transformation of reconfigurable DODA. Different from the static DNA origami reported before35, the reconfigurable DODA is built via self-assembly of dynamic DODA units (Figure S1, the gray ones, also called “anti-junctions”)36-37. After addition of trigger DNA strands, the interconnected modular dynamic units transfer their structural information to neighbors (Figure 1A), resulting the whole DODA nanostructure transforms from one stable conformation - “Before” to another stable conformation - “After” (Figure 1B). The native agarose gel electrophoresis (Figure S2) indicats the successful formation of “Before” and “After” DODA.These two different conformations of DODA have similar size and shape. In order to identify them much more clearly, the loop DNA strands (Figure S3) could perform as a

distinguishable marker. In previous literatures, DNA origami has been applied as platforms to construct molecular patterns to study interactions between gold nanoparticles, organic fluorophores, quantum dots, and proteins. However, these molecular pattern systems can not realize the study of dynamic interactions in a fully programmable and controllable fashion. Satisfactorily, the reconfigurable DODA can provide as an activatable and controllable platform owing to its dynamic transformation behaviors. As shown in Figure 1B, the DODA endows a spontaneous cascade of stacking conformational transformation from the “Before” to “After” conformation by a set of “trigger” DNA strands. The transformation of the DODA provides an activation step to reconfigure the pattern platform from the standby state (“Before” DODA) to the corresponding operational state (“After” DODA). Subsequently, the transformation brings the operational pattern units into close proximity to undergo DNA strand displacement cascades to accomplish three different pattern operations of “Writing”, “Erasing” and “Shifting” at the molecular scale. In this way, the dynamic and controllable pattern operations are realized in a single paltform. According to this principle, a 6×6 lattice in the reconfigurable DODA is selected to perform the “Writing”, “Erasing” and “Shifting” pattern operations (Figure 1C). Note that readout the operated patterns is benefited from simple streptavidin (STV)-biotin interaction. The dots observed by Atomic Force Microscopy (AFM) arise from STV attached biotin-modified DNA strands.

Writing operations. To test the ability of pattern operations in DODA, we firstly demonstrate the writing operations for the pattern changing from “V” to “Y”, in which 3 points are

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written. For the dynamic pattern operation system, it is critical to build pattern operational units for further operations. Herein, we exploit “DNA acrobat” whose toehold stand displacement reaction helps to complete the distinct pattern operations as the pattern operational units. Similar as the work

by Nils G. Walter et. al38, the lengths and sequence domains of the inhibited DNA acrobats and footholds (the track for the toehold strand displacement) are carefully designed to ensure DNA acrobats’ effective and rapid movements (Figure S4). The synthesis and

Figure 2. “Writing” operation in reconfigurable DODA. (A) Illustration for the procedure of “Writing” operation. The inhibited DNA acrobat (formed by W1, W2, W3) and footholds (W4) are incorporated in the “Before” DODA. After “Transformation” and “Execution” procedures, the activated DNA acrobat is subjected to a toehold-mediated strand displacement, leading to the writing of a point. (B) 8% Native PAGE characterization of the DNA strand hybridizations. Lane M: 20bp DNA marker, Lane 1 to 6: W1 (block strand), W2, W3 (DNA walker), W0 (release strand), W4 (foothold), W5 (biotin-modified DNA strand); Lane 7-12: W1 + W3 (hybridization of W1 and W3), W2 + W3 (hybridization of W2 and W3), W1+W2+W3 (hybridization of W1, W2 and W3, inhibited DNA acrobat), W1+W2+W3+W0 (release of W1, activation of inhibited DNA acrobat), W1+W2+W3+W0+W4 (the activated walker W3 hybridizes with foothold W4 through toehold strand displacement reaction). (C) A schematic and an example showing the “Writing” operation. (D) Statistical results of the written points. Source data are provided in Figure S10 and Table S3. Scale bar, 100 nm.

activation of inhibited DNA acrobat in solution are characterized by 8% native PAGE (Polyacrylamide gel electrophoresis), proving the proper sequence designs (Figure 2B). Figure 2A shows the working principle of the “Writing” operation in DODA. Purified “Before” conformational DODA sheets (2 nM) are prepared following a commonly used protocol 35 and then mix with inhibited DNA acrobats (100 nM, hybridization of W1, W2 and W3) together, resulting the inhibited DNA acrobats and footholds located in individual DODA unit between the interconnected DODA units (Figure 2A). At this stage, even the inhibited DNA acrobats are activated by the W0, the distance between the W3 and foothold W4 (~17 nm, 52 nt) is too long for W3 to initiate toehold strand displacement reaction, leading to null “Writing” operation (Figure S8). Therefore, the conformational transformation of DODA can be used to prevent spontaneous progression of the operations until triggered. We thus call the “Before” conformational DODA as the standby state. It also demonstrates the vital role of the conformation transformation for the dynamic and controllable pattern operations. After the conformational transformation bringing the inhibited DNA acrobat to close proximity of strand W4 (from 17.7 nm before the transformation to 5 nm after the transformation) and the subsequent addition of the release strand W0, the inhibited DNA acrobat is activated and the DNA strand W3 binds to the W4 strands via a toehold-mediated strand displacement reaction, making the W2 strand available for the subsequent hybridization with biotin-labeled W5 strand for the visualization of the written pattern. As an illustration of the

“Writing” operation, we design the patterns of transformation from “V” to “Y” (Figure 2C, Figure S6). Following the experimental procedures of writing operation, 3 inhibited DNA acrobats (3 points) (Figure S5) and 3 footholds are incorporated in the “Before” DODA. In AFM images (left and middle ones in Figure 2C, Figure S7 and S9), the inhibited DNA acrobats and footholds are invisible, which mainly resulted from two reasons. Firstly, the flexibility of the inhibited DNA acrobats and footholds could not give enough greater height contrast (compared to the DODA), resulting invisible protrusions. Secondly, the much greater height contrast of the STV attached biotin-staples (forming the “V” patterns) shadows the protrusions of the inhibited DNA acrobats and footholds. After transformation and execution steps, the bright protrusion observed on the AFM image of “Readout” DODA indicates that patterns at the specific sites are written and read successfully (the right one of Figure 2C, Figure S10). Finally, we analyzed the writing efficiency of the 3 points. Over 90% (N=161) of DODAs indicate a successful “Writing” operation. The efficiency of all the three points written in the specific sites is about 28.3%. Two points written is the most common cases (47.3%) (Figure 2D, Table S3). The statistics results also shows the average written points are 1.956 and writing efficiency is 65.2% (Table S3).

Erasing operations. Next, we further demonstrate the “Erasing” operation by designing another kind of inhibited DNA acrobat as the operational pattern units. Here, we show two cases of erasing operation in reconfigurable DODA. The

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first case is the general “Erasing” operation (Figure 3A, 3C-D and 3F) and the other one is the improved “Erasing” operation (Figure 3B, 3E and 3G). As shown in Figure 3A, for the first case, similar as in the writing operation, the inhibited DNA acrobats and the footholds locate in the interconnected “Before” DODA units initially. The distance between them are about 17.7 nm (Figure 3A). After transformation step and addition of the release DNA strand E0, the inhibited DNA acrobats are activated to drop off the biotin-modified DNA strand E3, realizing the “Erasing” operation. In contrast to the writing operation, the inhibited DNA acrobats are designed differently to execute specific erasing operation (Figure S11-S12 and S13A). As an illustration of this erasing operation, we design the transformation of patterns from “X” to “V”, in which 4 bits points are erased (Figure 3D, Figure S14). After incorporating the 4 inhibited DNA acrobats (Figure S13B) into the “Before” DODA, these operational pattern units were visualized both in “Before” and “After” DODA (left and middle ones in Figure 3D, Figure S15 and S17). The vital role of the conformation transformation of DODA is demonstrated in the control experiment in Figure S16. After execution step, the 4 points are erased successfully (the right one in Figure 3D, Figure S18). To evaluate the reliability of erasing operation, we analyze the binding efficiency of the 4 points in the two conformational DODA and theirs final erasing efficiency (Figure 3F).

Figure 3. “Erasing” operation in reconfigurable DODA. (A) Illustration for the procedure of general “Erasing” operation. After “Transformation” and “Execution”, the activated DNA acrobat takes toehold strand displacement, leading to a point erased. In this case of “Erasing” operation, the distance between the inhibited DNA acrobats and footholds is ~17.7 nm when in “Before” conformation. After transformation, the distance shortened to ~5 nm. (B) Illustration for the improved “Erasing” operation. In this case of “Erasing” operation, the

distance between the inhibited DNA acrobats and footholds is ~7.1 nm when in “Before” conformation. After transformation, the distance shortened to ~3.1 nm. This case improves the DPO density of the DODA DPO system. (C) An example showing the general “Erasing” operation (pattern changing from “V” to “Y”). (D) Another example showing the general “Erasing” operation (pattern changing from “U” to “L”) and illustrating the infeasibility of erasing more than three adjacent points (e.g. the five points in black dotted box). (E) An example showing the improved “Erasing” operation. (F) Statistical results of example (in Figure 3C, pattern changing from “V” to “Y”) of the general “Erasing” operation. “Input-standby” (left), “Input-operation” (middle) and “Output-readout” (right). Source data are provided in Figure S15 and Figure S17-S18 and Table S5-S7. (G) Statistical results of example (in Figure 3E) of the improved “Erasing” operation. “Input-standby” (left), “Input-operation” (middle) and “Output-readout” (right). Source data are provided in Figure S34-S36 and Table S10-S12. Scale bars, 100 nm.

As we all know, to realize the erasing operation, it is critical to immobilize the operational pattern units in the operation platform of DODA. Thus, the binging efficiency of the 4 points in “Before” DODA is analyzed firstly. Statistics shows that the binding efficiency of 4 points and 3 points are as high as 70.9% (the left one in Figure 3F). The transformation improves the binding efficiency further (72.5%, the middle one in Figure 3F). The high binding efficiency ensures the erasing operation. More than half of the 4 points can be erased successfully, and the erasing efficiency of 4 points and 3 points is as high as 80.1% (the right one in Figure 3F). These statistic results and more examples (Figure S19-S31) demonstrate high reliability of erasing operation in our designed DODA platform. Notably, based on the working principles of the “Writing” and “Erasing” operations described above, it is infeasible to write or erase more than three adjacent points simultaneously. To demonstrate this issue much more clearly, we design another example in which five adjacent points (the five points in the black dotted box) parallelly locate along the DODA units (Figure 3D). For the first and fifth bits, they could be erased effectively as long as the corresponding footholds are incorporated in their adjacent DODA units. While for the middle three bits (the second, third and fourth ones), they cannot be erased since there are no available locations (occupied by the adjacent inhibited DNA acrobats) to incorporate the corresponding footholds. Consequently, no more than half of the operational sites could be used to perform the pattern operations, decreasing the operational pattern density of the DODA DPO system. To bridge this limitation, we design the second case of improved “Erasing” operation.

For the second case, to increase the operational pattern density of our DODA DPO system, we shorten the distance between the inhibited DNA acrobats and footholds, allowing more operational pattern units pre-input. As illustrated in Figure 3E and Figure S32, 6 inhibited DNA acrobats are incorporated along the DODA units. The distance between inhibited DNA acrobats and the footholds is ~7.1 nm (21 nt) in “Before” DODA. After transformation, the distance shortens to 3.1 nm (Figure S33). The detailed erasing operation is similar with the first case above. To illustrate this case, 6 inhibited DNA acrobats parallelly locate along the DODA units (Figure 3E). The binding and erasing efficiency of 6 points are also analyzed. More than 3 inhibited DNA acrobats can be effectively incorporated in the “Before” DODA, and

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the binding efficiency of 6 points and 5 points is 66.1% (the left one in Figure 3G). The transformation improves the binding efficiency further (68.84%, the middle one in Figure 3G). Such high binding efficiency ensures the erasing operation. The statistical results in Figure 3G indicates the effective erasing operation when increasing the operational pattern density. Of note, to evaluate whether the distance of 7.1 nm is reachable enough for the E2 to take toehold strand displacement reaction, that is, whether the conformational transformation of DODA is still vital for this case of erasing operation, a control experiment of the 6 inhibited acrobats are activated before the conformational transformation is done. The results (Figure S37 and Table S13) show although the distance of 7.1 nm is reachable for E2 to take toehold strand displacement reaction, the erasing efficiency is lower (47.1%) than that of after conformational transformation (61.2%) (Table S14). There results also demonstrate the conformational transformation of DODA is better to realize the DPO.

Figure 4. “Shifting” operation in reconfigurable DODA. (A) Illustration for the procedure of specific “Shifting” operation. After “Transformation” and “Execution” procedures, the activated DNA acrobats take toehold exchange migration, leading to a point shifted. (B) The distinct sequences of designed inhibited DNA acrobat and schematic showing the intended mechanism of toehold exchange migration. (C) 8% Native PAGE characterization of the specific designed inhibited DNA acrobat in solution. Lane M: 20bp DNA marker, Lane 1 to 4: S1 (block strand), S2, S3 (DNA walker), S0 (release strand); Lane 5-8: S1 + S3 (hybridization of S1 and S3), S2 + S3 (hybridization of S2 and S3), S1+S2+S3 (inhibited DNA acrobat, hybridization of S1, S2 and S3), S1+S2+S3+S0 (release of S1, activation of inhibited DNA acrobat). (D) Details of the designed 5 points right shifting in parallel. “1” represents the position of the 5 points. (E) An example showing parallel “Shifting” operation. (F) Statistical results of the shifting efficiency for individual DNA acrobats. Source data are provided in Figure S43 and Table S15. R1 (Right shifting one step for the 2nd DNA acrobat), R2 (Right shifting two steps for the 3rd DNA acrobat), R3 (Right shifting three steps for the 4th DNA acrobat), R4 (Right shifting four steps for the 4th DNA acrobat). (G)

Statistical results of the completion efficiency for individual types of readout. Source data are provided in Figure S43 and Table S16. OPS (One point shifting), PPS (Partial points shifting), APS (All points shifting). Scale bar, 100 nm.

Shifting operation. In addition to “Writing” and “Erasing” operations in the DODA DPO system described above, here we further demonstrate pattern shifting operations in the same platform. The basic concept is similar to the “Writing” and “Erasing” operations (Figure 4A). The pattern shifting is completed by the toehold exchange migration of the inhibited DNA acrobats (Figure S38 and Figure 4C). As depicted in Figure 4B, the activated acrobat S3 undergoes head-over-heels movement over a surface of three stepping footholds by toehold strand displacement. The migration finally accomplishes pattern shifting. The block foothold permits the acrobat to step a definite number, allowing a controllable pattern shifting. Based on the principle, we intend to realize a controllable right shifting in a single DODA (Figure 4D) and thus design the 4 points parallel shifting in DODA (Figure S40). Note that, we design 5 inhibited DNA acrobats and incorporate them in the DODA (Figure S39, 41-42). The first DNA acrobat took 0 step, and the last four DNA acrobats took 1 step, 2 steps, 3 steps and 4 steps, respectively (Figure S40). As proved in Figure 4E, the four DNA acrobats migrate 1 step, 2 steps,3 steps and 4 steps, respectively, realizing 1, 2, 3, and 4 right shifted in parallel. Figure 4F shows the shifting efficiency for individual DNA acrobats. The shifting efficiencies are 83.4%, 50.5%, 34.3% and 32.8% for 1 step, 2 steps, 3 steps, and 4 steps, respectively. With the increase of shifting numbers, the successful shifting efficiency decreases. This result is consistent with the results in Figure 4G, in which most of the readouts are the partial points shifting (PPS). It results from the reversible branch migration of the DNA acrobat S3 which steps between the two competing stepping footholds. The results in Figure S44 of the control experiment (the 5 inhibited robots are activated before transformation) verify the necessity of the DODA conformational transformation for the DPO.

CONCLUSIONS

In summary, our work has shown a reconfigurable DODA DPO system to perform proximity-induced molecular control for complex pattern operations. As a proof-of-principle, three different operations of “Writing”, “Erasing” and “Shifting” are demonstrated. The accomplishment of the DPO benefits from two dynamic behaviors of the reconfigurable DODA-based system. The first one is the conformational transformation of the DODA. The controlled, multistep, long-range transformation of the DODA allows the rearrangement of spatial organization of the patterns. The second one is the conformational transformation induced toehold-mediate strand displacement cascades at close proximity. The valuable feature of our system lies in the combination of the two ideas. We anticipate that the DODA DPO system will provide an innovative way to greatly improve the sophistication and functionality of the nanoscale assemblies and devices. It can

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also be used to control molecular reactions and to further probe unresolved molecular mechanisms in chemical and biological processes.

In contrast to static DNA origami platforms for pattern operations, reconfigurable DODA can transform from “Before” to “After” conformation. The conformational transformation of DODA makes contributions to the DPO in three ways. The first one is the intrinsic transformation of the nanostructures, driving the patterns transformation along with the nanostructures. The second one is the conformational transformation adjust the spatial organization of the operational pattern units. When in “Before” DODA, the distance between operational pattern units is not reachable to interact. While in “After” DODA, the transformation brings the operational pattern units into close proximity to undergo toehold mediate strand displacements. The last one is the transformation mechanism prevents spontaneous progression of the DPO until triggered. That is, the DPO could only be performed after the accurate transformation step. The transformation step activates the DODA platform from the “standby state” to the corresponding “operational state” for DPO.

Reconfigurable DODA-based DPO system can be further developed to include additional features. First, the number of operations units could be further scaled up by enlarging the size of DNA origami. It could be realized by using of long scaffolds 39-40, hierarchical assembly of DNA origami 41-47, surface-assisted large-scale assembly of DNA origami. 48-53, and base-stacking hierarchical assembly30, 54-55, etc. Second, the operation ability could be further improved by immobilizing various operational units to carry out different operations in parallel. Third, the surface-based operation system also enables compartmentalization for faster addressing and other localized operations. Fourth, this system could be further explored for potential applications including chemical synthesis, bioanalysis, and clinic diagnostics by assembling aptamers, small chemicals, metal nanoparticles, and proteins into the DNA acrobats. For instance, in chemical synthesis, desired products can only be assembled if the distance between the chemical groups is reachable enough. Thus, this system can be carefully designed to effectively shorten the distance, allowing the synthesis of desired products from components.

ASSOCIATED CONTENT Supporting InformationThe Supporting Information is available free of charge on the ACS Publications website and includes experimental procedures, and the supporting figures referenced in the manuscript.

AUTHOR INFORMATIONCorresponding Author* [email protected];

* [email protected];

* [email protected]

Notes

The authors declare no competing financial interests

ACKNOWLEDGMENT

We acknowledge the support by the National Natural Science Foundation of China (Nos. 81822024, 11761141006), the Natural Science Foundation of Shanghai, China (Nos. 19520714100, 19ZR1475800), the National Key Research and Development Program of China (Grant No. 2017YFC1200904), and the Project of Shanghai Jiao Tong University (2019QYA03 and YG2017ZD07).

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Table of Contents artwork

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Figure 1. Complex pattern operations platform of reconfigurable DODA. (A) Different diagrams showing the transformation of two interconnected DODA units. Transformation of a DODA unit is realized by the addition

of a trigger strand, and then causes the subsequent transformation of its neighbor-ing unit. (B) The transformation of the 8 units by 8 units DODA that is used as pattern operations platform. With addition of

the trigger strands, the “Before” conformational DODA (left, comprised of grey units) transforms to the “After” conformational DODA (right, comprised of brown units). The schematic in the middle shows an intermediate state during the transformation, the orange-colored units are partially transformed. The transformation reconfigures the computing platform from the standby state (“Before” DODA) to the

corresponding operational state (“After” DODA). (C) Complex pattern operations in the reconfigurable DODA platform. The operational state of the “After” DODA enables different pattern operations, including “Writing”,

“Erasing” and “Shifting”. Scale bar, 100 nm.

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Figure 2. “Writing” operation in reconfigurable DODA. (A) Illustration for the procedure of “Writing” operation. The inhibited DNA acrobat (formed by W1, W2, W3) and footholds (W4) are incorporated in the

“Before” DODA. After “Transformation” and “Execution” procedures, the activated DNA acro-bat is subjected to a toehold-mediated strand displacement, leading to the writing of a point. (B) 8% Native PAGE

characterization of the DNA strand hybridizations. Lane M: 20bp DNA marker, Lane 1 to 6: W1 (block strand), W2, W3 (DNA walker), W0 (release strand), W4 (foothold), W5 (biotin-modified DNA strand); Lane

7-12: W1 + W3 (hybridization of W1 and W3), W2 + W3 (hybridization of W2 and W3), W1+W2+W3 (hybridization of W1, W2 and W3, inhibited DNA acrobat), W1+W2+W3+W0 (release of W1, activation of

inhibited DNA acrobat), W1+W2+W3+W0+W4 (the activated walk-er W3 hybridizes with foothold W4 through toehold strand displacement reaction). (C) A schematic and an example showing the “Writing”

operation. (D) Statistical results of the written points. Source data are provided in Figure S10 and Table S3. Scale bar, 100 nm.

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Figure 3. “Erasing” operation in reconfigurable DODA. (A) Illustration for the procedure of general “Erasing” operation. After “Transformation” and “Execution”, the activated DNA acrobat takes toehold strand dis-

placement, leading to a point erased. In this case of “Erasing” operation, the distance between the inhibited DNA acrobats and footholds is ~17.7 nm when in “Before” conformation. After transformation, the distance

shortened to ~5 nm. (B) Illustration for the improved “Erasing” operation. In this case of “Erasing” operation, the distance between the inhibited DNA acrobats and footholds is ~7.1 nm when in “Before” conformation. After transformation, the distance shortened to ~3.1 nm. This case im-proves the DPO density of the DODA DPO system. (C) An example showing the general “Erasing” operation (pattern

changing from “V” to “Y”). (D) Another example showing the general “Erasing” operation (pat-tern changing from “U” to “L”) and illustrating the infeasibility of erasing more than three adjacent points (e.g. the five

points in black dotted box). (E) An example showing the improved “Erasing” operation. (F) Statistical results of example (in Figure 3C, pattern changing from “V” to “Y”) of the general “Erasing” operation. “Input-

standby” (left), “Input-operation” (middle) and “Output-readout” (right). Source data are provided in Figure S15 and Figure S17-S18 and Table S5-S7. (G) Statistical results of exam-ple (in Figure 3E) of the improved “Erasing” operation. “Input-standby” (left), “Input-operation” (middle) and “Output-readout” (right). Source

data are provided in Figure S34-S36 and Table S10-S12. Scale bars, 100 nm.

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Figure 4. “Shifting” operation in reconfigurable DODA. (A) Illustra-tion for the procedure of specific “Shifting” operation. After “Transfor-mation” and “Execution” procedures, the activated DNA acrobats take toehold

exchange migration, leading to a point shifted. (B) The distinct sequences of designed inhibited DNA acrobat and schematic showing the intended mechanism of toehold exchange migration. (C) 8% Native PAGE

characterization of the specific designed inhibited DNA acrobat in solu-tion. Lane M: 20bp DNA marker, Lane 1 to 4: S1 (block strand), S2, S3 (DNA walker), S0 (release strand); Lane 5-8: S1 + S3 (hybridization of S1 and S3), S2 + S3 (hybridization of S2 and S3), S1+S2+S3 (inhibited DNA acrobat, hybridization of S1, S2 and S3), S1+S2+S3+S0 (release of S1, activation of inhibited DNA acrobat). (D) Details of the designed 5 points right shifting in parallel. “1” represents the position of the 5 points. (E) An example showing parallel “Shifting” operation. (F) Statistical results of the shifting efficiency for individual DNA acrobats. Source data are provided in Figure S43 and Table S15. R1 (Right shifting one step for the 2nd DNA acrobat), R2 (Right

shifting two steps for the 3rd DNA acrobat), R3 (Right shifting three steps for the 4th DNA acrobat), R4 (Right shifting four steps for the 4th DNA acrobat). (G) Statistical results of the completion efficien-cy for

individual types of readout. Source data are provided in Figure S43 and Table S16. OPS (One point shifting), PPS (Partial points shifting), APS (All points shifting). Scale bar, 100 nm.

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reconfigurable dna origami domino array proximity-induced ...1 proximity-induced pattern operations...

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