Research ArticlePrecise Control of Gold Nanoparticles on DNA Origami forLogic Operation

Kuiting Chen,1,2 Xiang Li,1 and Jing Yang 1

1School of Control and Computer Engineering, North China Electric Power University, 102200, China2School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, 430074, China

Correspondence should be addressed to Jing Yang; yjzcdd_2000@ncepu.edu.cn

Received 27 May 2019; Revised 17 July 2019; Accepted 13 September 2019; Published 3 November 2019

Academic Editor: Hassan Karimi-Maleh

Copyright © 2019 Kuiting Chen et al. This is an open access article distributed under the Creative Commons Attribution License,which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Owing to their capacity for accurate structural control and complex programmability, DNA molecules have been extensivelystudied in relation to the construction of nanodevices. However, the existing logic gate sections based on DNA self-assemblywere independent of each other, which hampered the development of large-scale integrated DNA circuits. Herein, we haveexplored a logic operation device with excellent scalability based on assembling and selectively releasing AuNPs on DNAorigami, and have performed YES gate, OR gate, AND gate, and three-input composite gate. In the experiment, the logicoperation result is detected by gel analysis and TEM image. The resolution of the output signals was greatly improved bydetermining the releasing of AuNPs from two-layer honeycomb origami. Our study provides a promising approach for buildingmore complex large-scale DNA logic circuits.

1. Introduction

DNA self-assembly has provided a versatile tool to buildbottom-up nanostructures with predesigned shapes, includ-ing lattices [1], filaments [2], spheres [3], barrels [4], andother complex three-dimensional structures [5–11]. Espe-cially, Rothemund had firstly developed DNA origami,which was fabricated by approximately 200 short single-stranded DNAs (ssDNA) and one long single-strandedM13 scaffold to form complex nanostructures [12], provid-ing a new effective way to design a wide range of artificialnanostructures. DNA origami not only offers an effectiveprotocol to create various nanostructures with diverseshapes and sizes [13–15] but can also serve as a templateto precisely arrange nanoparticles [16–19]. Based on the spe-cific recognition of nucleotide sequence, extended DNAstrands on origami can be regarded as DNA tags to detectand capture functional nanoparticles.

Consequently, various components such as proteins [20–22], quantum dots [23, 24], carbon nanotubes [25, 26], andmetal particles [27–29] can be precisely arranged and manip-

ulated at the specific positions on the DNA origami surfaces.Among various functional particles, owing to its structuraland optical properties, gold nanoparticles (AuNPs) haveattracted more attention from the fields of biosensing andnanodevices [30–38]. For example, Sharma et al. used lipoicacid-modified ssDNA to construct AuNP-DNA conjugateswith a monothiolate-Au linkage [39]. This strategy providesan effective method to fix the size of DNA nanostructures car-rying a discrete number of AuNPs at designed positions.Moreover, Shen et al. developed DNA origami nanomachinesby exploiting the optical property of AuNPs [40]. Althoughthese works revealed that NPs can be well assembled withDNA origami statically, the dynamic operation of anNP/DNA origami device is still a concern for variousresearchers. Our previous study realized a NP/DNA origamisystem, in which AuNPs could be dynamically released froma DNA origami in response to specific DNA signals [41]. Inthis work, the yield of the output structure was not very high,because a monofunctionalized DNA/AuNP conjugate washybridized with one extended strand from the origami tem-plate. Besides, the resolution of the output signals was not very

HindawiJournal of NanomaterialsVolume 2019, Article ID 4890326, 9 pageshttps://doi.org/10.1155/2019/4890326

obvious, resulting from the little molecular weight differencebetween the displaced product and the initial product.

To address these problems, we constructed a logic systembased on the arrangement of AuNPs on two-layer honey-comb origami (TL), in which bifunctionalized AuNPs couldbe logically and dynamically released from DNA origami inresponse to input signals. Using this strategy, “YES,” “OR,”“AND,” and three-input composite logic gates were estab-lished by controlling the releasing of AuNPs from TL ori-gami. In the experiment, the logic operation result isdetected by gel analysis and TEM image. The resolution ofthe output signals was greatly improved by determining thereleasing of AuNPs from TL origami. Our study provides apromising approach for building more complex large-scaleDNA logic circuits.

2. Materials and Methods

2.1. Preparation of DNA Origami. As a computer-aideddesign tool for DNA origami, caDNAno was employed todesign and produce staples. The design drawing of TL isshown in Figure S6. All the sequences of DNA strands(Tables S2 and S3) were exported from caDNAno andsynthetized by Sangon Biotech Co. Ltd. To generate the TLstructure, 2.5 nM of M13mp18 strands were mixed with~200 staples at a ratio of 1: 10 in 1 × TAE buffer (Tris:40mM; acetic acid: 20mM; EDTA: 2mM; and magnesiumacetate: 12.5mM, pH8.0). Composite samples wereannealed from 85°C to room temperature within 16 h [42].It is noteworthy that staples used to form binding sitesshould increase the concentration, so as to ensure the yieldof binding sites. Purified through a 100K ultracentrifugalfilter (MWCO, Amicon, Millipore), which was able toeliminate the excess staple strands, TL was prepared toreact with AuNP (Table S4). The concentration of TL wasdetermined from the optical absorbance at 260 nm.

2.2. Modification of AuNP. Fifteen-nanometer AuNP colloidswere mixed with bis(p-sulfonatophenyl)phenylphosphinedihydrate dipotassium salt (BSPP) and incubated in a shak-ing bed overnight. The treated AuNP solution reacted withthiolated ssDNA, A-SH, or B-SH to form AuNP/DNA conju-gates Au-A or Au-B, respectively. Additionally, oligoethyleneglycols (OEG) were utilized to make surface-unsaturatedAuNPs stable in high concentration magnesium ion. Subse-quently, excess ssDNA strands were removed the same wayas that employed by the TL DNA origami. Finally, freshlyprepared gold conjugates and TL were mixed at a ratio of30: 1, which formed three kinds of AuNP/origami compositestructures: TL-A, TL-B, and TL-AB.

2.3. Loading AuNPs on TL. The mixed solution was incu-bated for two hours at room temperature. After adding trig-ger ssDNA strands, samples were characterized by 1%agarose gel (stained with ethidium bromide) electrophoresisin 0:5 × TBE buffer (45mM Tris, 45mM boric acid, and1mM EDTA; pH8.0) containing 6mM MgCl2 for 1.5 h inan ice-water bath. The target-assembly bands were sliced

out and ground so that a little liquid could be absorbed forTEM imaging.

2.4. TEM Analysis. Two microlitres of target samples weredeposited on a carbon-coated TEM grid (100 mesh, TedPella, Inc.) and dyed by uranyl acetate (Electron Microscopy,Beijing, China). Whereafter, the excess solution was removedby using a piece of filter paper. The grid was stored at roomtemperature to allow drying. TEM images were obtained bya Hitachi H-7650 transmission electron microscope. TEMstatistics were completed manually (Table S5). MATLABwas employed to generate bar graphs and fitting curves.

3. Results and Discussion

The scheme of the logic gate system is depicted in Figure 1(a).The TL origami with dimensions of 130 nm × 14 nm × 6 nmprovided a template for the nanodevice, in which DNA-coated AuNPs could bind on by hybridizing with extendedDNA staples. Six AuNP-binding sites, composed of twoextended ssDNA per site, were evenly distributed on theTL’s surface with a distance of ~21 nm between every twosites. Extended sequences LogA and LogB were arrangedalternately on these sites. In other words, every TL-A orTL-B was able to bind three gold particles, respectively,and TL-AB was able to bind six AuNPs. The TL structureis described in Figure S3, including an unfolding map, across-section profile, all the sequences of the staples, andthe specific locations of the binding sites. Typical TEMimages of TL are shown in Figure S7. Besides, two types of15 nm AuNPs were modified with thiolated ssDNA, A-SH,or B-SH, which were marked as Au-A or Au-B, respectively.Figure 1(b) illustrates components of the logic gate device bygel images. Lane 1 indicates bare AuNPs without modifiedDNA strands, whose band has more mobility than thatof Au-A or Au-B (lane 2 and lane 3, respectively). As areference for TL running in lane 5, M13mp18 ran in lane 4.Both of them could be observed under UV light after beingstained by ethidium bromide (EB).

In the logic gate system, logic operations were completedby inputting ssDNA which could displace AuNPs arrangedon the TL’s surface selectively and programmably. The addi-tion of a trigger strand was equivalent to a logical input, withpossible states of adding or not adding (0 or 1, respectively).Then, we defined AuNPs-bound-on TL structure as the orig-inal state (0), while the AuNP-free TL structure was definedas the triggered state (1).

In YES gate A, Au-A was set as the potential released par-ticle. When input strand A∗ was presented, extended staplesLogA preferentially hybridized to A∗ owing to the 5 nt longtoehold (Figure S1). As a result, Au-A was released.Comparing lane 6 and lane 7, we could easily observe thedisappearance of TL-A in the output area of lane 7, onaccount of the perfect displacement of Au-A. Interestingly,in the UV image, we found that a triggered structureexhibited a faster movement by getting rid of Au-A.Furthermore, without the influence of gold nanoparticles,DNA origami appeared much more brightly. To furtherstudy the effect of strand A∗, we performed a concentration-

2 Journal of Nanomaterials

Original state

Triggered state

AuNP

A-SH/B-SH

Origami

Extended staple

ReporterYESA⁎/B⁎

(a)

Outputarea

ExcessAuNPs

(b)

100 nm

(c)

100 nm

(d)

0 1 2 3 4 5 6 >6Number of AuNPs bound on per TL

0

50

100

150

200

250

Cou

nts

01

(e)

0 1 2 3 4 5 6 >6Number of AuNPs bound on per TL

0

20

40

60

80

100

120

140

160

180

Coun

ts

01

(f)

Figure 1: (a) Scheme of YES gate. (b) Gel electrophoresis analysis. Lane 1: AuNP without DNAmodification. Lane 2: AuNPmodified with A-SH. Lane 3: AuNP modified with B-SH. Lane 4: M13. Lane 5: TL origami. Lane 6: TL origami mixed with Au-A (TL-A). Lane 7: sample afteradding A∗ to lane 6. Lane 8: TL origami mixed with Au-B (TL-B). Lane 9: sample after adding B∗ to lane 8. (c, d) TEM images of Au-B-boundTL (TL-B) and Au-B-released TL. (e) Distribution histograms of YES gate A: blue bars indicate TL-A and gray bars indicate TL; solid linesrepresent curve fitting. (f) Distribution histograms of YES gate B: green bars indicate TL-B and gray bars indicate TL; solid lines representcurve fitting.

3Journal of Nanomaterials

gradient experiment. As shown in Figure S2, with theincrease of the concentration of A∗, the replacement effectbecame better. Logic gate B was a little different from gateA in hybridization and displacement details. As shown inFigure S1, there were two toeholds in the hybrid structureof B-SH and LogB. Both 3′-end and 5′-end toeholds couldbe recognized by B∗, leading to the strand displacement.The reactions similar to Au-A displacement occurred inlane 8 and lane 9. Profiting from the two-time toehold, thedisplacement efficiency of B∗ was higher than that of A∗,which was especially evident in the 4.5μM band (Figure S3).Furthermore, Figures 1(c) and 1(d) demonstrated severaltimes the TEM images of Au-B-bound TL (TL-B) and Au-B-released TL.

In order to quantitatively analyze the diversity of logicgate structures, we statistically counted all the TEMimages, plotted bar graphs, and fitted curves utilizingMATLAB. Representational TEM images are displayed inFigure S8 (YES gate A) and Figure S9 (YES gate B). Thenumerical information of the statistical results is listed inTable S1. By statistical counting, the distribution histogramsof various products are shown in Figure 1(e) (YES gate A)and Figure 1(f) (YES gate B). The narrower Gaussiandistribution observed by TEM indicated the higherhomogeneity of the sample. In Figure 1(e), blue barsrepresent the original state, whose peak corresponded to“3” on the abscissa, and the theoretical value of the numberof AuNPs bound on per TL. Gray bars indicated thetriggered state. It could be observed that 92.8% of TLs werenot connected with AuNPs. Characteristics similar toFigure 1(e) were obtained in Figure 1(f). Particularly, 3-AuNPs-bound-on TL structures accounted for 79.4% in theoriginal state sample and the AuNP-free TL occupied92.6% of the triggered state.

It was worth mentioning that different products from theoriginal or triggered state samples had conformed to differentdistribution laws. The histograms from the original statesamples were fit with Gaussian distribution, while the trig-gered state samples were fit with exponential distribution.These results demonstrated well the selective release ofAuNPs from the DNA origami. (The truth tables of YES gateA and YES gate B are listed in Table 1.)

Owing to the superior scalability of our computingsystem, the AND logic gate was also established via combin-ing YES gate A and YES gate B. In the construction of theAND gate, TL origami with six alternately-arranged bindingsites was obtained as described above. Au-A and Au-B weresimultaneously assembled on TL (TL-AB).

As illustrated in Figure 2(a), the AuNPs were releasedwhen A∗ and B∗ were added, and the true output was definedby AuNP-free TL. Evidently, by displacing Au-A with A∗,

TL-B was gained. Similarly, TL-A could be obtained sepa-rately by adding B∗ which was capable of untying Au-B. Inthe output area of the gel result (Figure 2(b)), because a nano-particle has little effect on band migration, the bands of TL-AB, TL-B, and TL-A were almost displayed at the same hor-izontal position. Only when Au-A and Au-B were simulta-neously disassembled would the band disappear. Histogramstatistics of TEM images described a matching result inFigure 2(c). The peak moved to “0” when both A∗ and B∗

were added to the system. Moreover, the distribution of pur-ple bars representing an input-free state positioned a peak at~“5,” rather than at the theoretical value of “6.” We guessedthat intermolecular repulsion and steric hindrance affectedthe perfect assembly of TL-AB. Besides, we also guessed that,when Au-A or Au-B was separated, the particle spacingincreased, which facilitated the rehybridization of excessAuNPs to the corresponding binding sites. The statisticalresult of the histogram supported these guesses: when eitherA∗ or B∗ was added into the system separately, which shouldhave led to three AuNPs unbound, peaks identically shiftedfrom “5” to “3,” instead of “2” or less. Representative TEMimages of various output products are displayed inFigures 2(d) and S10. The truth table of AND gate is listedin Table 2.

To fabricate the OR gate, we altered the trigger ssDNAfor TL-B. As illustrated in Figure 3(a), TL-B could be dis-assembled by both bst and bAu. Concretely, bst recognizedthe toehold region of the extended staple (light green) andcould form a 12-pair-long complementary double-strandstructure, which left a 3-pair-long unstable double-strandconnection between the staple strand and B-SH. Due tothe instability of the 3-pair complementary structure, Au-Bwas detached from TL, thereby reporting the output as “1.”The trigger strand bAu worked similarly: it detected the toe-hold of B-SH (orange) and preferentially displaced B-SH fromLogB, so as to rid Au-B of the TL template. The detailedsequences are portrayed in Figure S1. Then, the logic ORgate system was characterized by gel electrophoresis(Figure 3(b)). When bst or bAu, respectively, reacted withthe original conjugate, or both of them simultaneouslyparticipated in the reaction, the band indicating TL-Bdisappeared in the output area. Furthermore, concentrationgradient experiments for the trigger strand were performedand the results are exhibited in Figure S4 and Figure S5. Itwas reasonable that bAu consumed more than bst in general,as a result of excessive Au-B in the solution. Statisticaldistribution of the TEM images agreed with the rules of ORlogic. Peak migration occurred when either bst or bAu wasadded into the system as well as when both of these triggerstrands were added. Typical TEM images of the outputscaused by diverse inputs are shown in Figures 3(d) and S11.The truth table of OR gate is listed in Table 3.

To develop the capacity of the logic device for large-scaleoperations and to verify the extensibility of this capacity, athree-input composite logic gate was constructed throughuniting YES gate A and OR gate. Figure 4(a) is the schemeof the composite gate. Au-A and Au-B were simultaneouslyassembled on TL (TL-AB), which was identical in the prepa-ration of the AND gate. Subsequently, three input strands

Table 1: Truth table of YES gate A and YES gate B.

Input Output Input OutputA∗ Au-free TL B∗ Au-free TL

1 1 1 1

0 0 0 0

4 Journal of Nanomaterials

(A∗, bst and bAu) were utilized to unbind the AuNPs on TL.In the same way, we defined a Au-free TL as a true outputand marked it as “1” in the truth table. Interestingly, the com-

posite gate circuit could be the equivalent of an OR gate witha switch control, where A∗ was regarded as the switching var-iable, while bst and bAu constituted a logical variable. First,when A∗ was absent from the system, no matter how bstand bAu were used as input, there was no true output.As illustrated in Figure 4(b), if the values of A∗ were 0,bands representing AuNPs-binging-on-TL products alwaysappeared in the output area (lanes 1-4, Figure 4(b)). Then, A∗

was added into the solution, leading to a logic rule which wasconcordant with the OR gate. Bands vanished in the outputarea of the gel image as long as bst, bAu, or both of them wereadded into the system (lanes 6-8, Figure 4(b)). The truth tableof the composite gate is listed in Table 4.

ReporterANDA⁎

A⁎

AA

A A AB B B

A

BBB

B⁎

B⁎

A⁎ and B⁎

(a)

0 0 0 1

0 0 1 10 1 0 11 2 3 4

A⁎

B⁎

OutputareaExcessAuNPs

(b)

1 2 3 4 5 6 >6Number of AuNPs bound on per TL

0

0010

0111

50

100

150

200Co

unts

(c)

00 10 01 11

200 nm 200 nm 200 nm 200 nm

(d)

Figure 2: (a) Scheme of AND gate. (b) Gel electrophoresis analysis. Lane 1: TL attached by Au-A and Au-B (TL-AB, original state sample).Lane 2: sample after adding A∗ to lane 1. Lane 3: sample after adding B∗ to lane 1. Lane 4: sample after simultaneously adding A∗ and B∗ tolane 1. (c) Distribution histograms of AND gate: purple bars indicate TL-AB; blue bars indicate TL-B caused by the displacement of Au-Afrom TL-AB; pink bars indicate TL-A caused by the displacement of Au-B from TL-AB; gray bars indicate TL; solid lines represent curvefitting. (d) TEM images of various output structures.

Table 2: Truth table of AND gate.

Input 1 Input 2 OutputA∗ B∗ Au-free TL

0 0 0

1 0 0

0 1 0

1 1 1

5Journal of Nanomaterials

4. Conclusions

To sum up, we have successfully explored a logic operationdevice with excellent scalability based on assembling andselectively releasing AuNPs on DNA origami. In the comput-ing process, the arrangement of AuNPs on DNA origami wascontrolled by specific DNA signals, which realized the logicoperations. Using this strategy, we performed YES gate, ORgate, AND gate, and three-input composite gate through

Reporter

bst

bAu

B B

BB

BOR

B

B

bst

bst and bAu

bAu

(a)

Output

ExcessAuNPs

1 2 3 400

10

01

11

bstbAu

(b)

0 1 2 3 4 5 6 >6Number of AuNPs bound on per TL

0

20

40

60

80

100

120

140

160

Coun

ts

01

01

(c)

00 10 01 11

(d)

Figure 3: (a) Scheme of the OR gate. (b) Gel electrophoresis analysis. Lane 1: TL attached by Au-B (TL-B, original state sample). Lane 2:sample after adding bst to lane 1. Lane 3: sample after adding bAu to lane 1. Lane 4: sample after simultaneously adding bst and bAu tolane 1. (c) Distribution histograms of OR gate: grass green bars indicate TL-B; bottle green bars indicate TL resulting from the addition ofbst; orange bars indicate TL caused by the addition of bAu; gray bars indicate TL; solid lines represent curve fitting. (d) TEM images ofvarious output structures.

Table 3: Truth table of OR gate.

Input 1 Input 2 Outputbst bAu Au-free TL

0 0 0

1 0 1

0 1 1

1 1 1

6 Journal of Nanomaterials

DNA strand displacement. The models were confirmed bygel electrophoresis and TEM images including statistical dis-tribution of specific structures. It is worthmentioning that weestablished a progressive relationship between different logicgates. For example, we obtained AND gate by combining twoYES gates and three-input composite gate by combining YESgate and OR gate. These processes have proved that this strat-egy has outstanding scalability and splicing.

Moreover, compared with previous work, the true outputwas distinguished by determining that there were AuNPs onDNA origami or not, which allowed us to read the output sig-

nal by observing whether the band disappeared in a rela-tively large-scale output area instead of comparing subtledissimilarities in migration. That is to say, the resolution ofthe logic nanodevice is greatly improved. In addition, as aresult of abandoning the 15 nm particle, which was used asa marker in the previous computing system, we amelioratedthe utilization rate of AuNP as an effective information.Finally, our prototype provides a promising approach forbuilding a multibit arithmetic unit taking biomolecules asthe material and could inspire advanced designs for large-scale DNA logic circuits.

Data Availability

All data included in this study are available upon request bycontact with the corresponding author.

Conflicts of Interest

The authors declare that there is no conflict of interestregarding the publication of this paper.

Acknowledgments

TEM analysis was supported by the Beijing Key Labora-tory of New Technology in Agricultural Application. This

Reporter

B B

BAA⁎

BA A A

OR

ANDbst

bAu

(a)

Outputarea

ExcessAuNPs

1 2 3 40

0bstbAu

5 6 7 8

0A⁎

0

10

0

01

0

11

1

00

1

10

1

01

1

11

0 0 0 0 0 1 1 1

(b)

Figure 4: (a) Scheme of OR gate. (b) Gel electrophoresis analysis.

Table 4: Truth table of the composite gate.

Input 1 Input 2 Input 3 OutputA∗ bst bAu Au-free TL

0 0 0 0

0 0 1 0

0 1 0 0

0 1 1 0

1 0 0 0

1 0 1 1

1 1 0 1

1 1 1 1

7Journal of Nanomaterials

work was supported by the Joint Fund of the EquipmentPreresearch Ministry of Education (6141A02033607,6141A02033608), the National Key R&D Program ofChina (2017YFGH001465), the National Natural ScienceFoundation of China (61872002), Beijing Natural ScienceFoundation (4182027), and Fundamental Research Fundsfor the Central University (2019JG001).

Supplementary Materials

Materials, experimental methods, and additional experi-mental data are provided in the supplementary materials.Figure S1: the detailed sequences of connections betweenDNA origami and AnNPs. Figures S2 to S5: the gel imagesof the concentration gradients of the trigger strand. FigureS6: scaffold/staple layout of the two-layer rod origami (TL).Figure S7: TEM image of TL. Figures S8 to S11: representa-tional TEM images of various output structures. Table S1:the statistical results of TEM images. Table S2: the sequencesof TL’s staples. Table S3: other DNA sequences used in thiswork. Table S4: thermal annealing ramp for TL. Table S5:fitting parameters for the statistical histograms of variousoutput structures. (Supplementary Materials)

References

[1] X. Qi, F. Zhang, Z. Su et al., “Programming molecular topolo-gies from single-stranded nucleic acids,” Nature Communica-tions, vol. 9, no. 1, article 4579, 2018.

[2] W. Pfeifer, P. Lill, C. Gatsogiannis, and B. Saccà, “Hierarchicalassembly of DNA filaments with designer elastic properties,”ACS Nano, vol. 12, no. 1, pp. 44–55, 2018.

[3] Y. He, T. Ye, M. Su et al., “Hierarchical self-assembly of DNAinto symmetric supramolecular polyhedra,” Nature, vol. 452,no. 7184, pp. 198–201, 2008.

[4] M. Langecker, V. Arnaut, T. G. Martin et al., “Synthetic lipidmembrane channels formed by designed DNA nanostruc-tures,” Science, vol. 338, no. 6109, pp. 932–936, 2012.

[5] G. Tikhomirov, P. Petersen, and L. Qian, “Triangular DNAorigami tilings,” Journal of the American Chemical Society,vol. 140, no. 50, pp. 17361–17364, 2018.

[6] G. Tikhomirov, P. Petersen, and L. Qian, “Fractal assembly ofmicrometre-scale DNA origami arrays with arbitrary pat-terns,” Nature, vol. 552, no. 7683, pp. 67–71, 2017.

[7] L. L. Ong, N. Hanikel, O. K. Yaghi et al., “Programmable self-assembly of three-dimensional nanostructures from 10,000unique components,”Nature, vol. 552, no. 7683, pp. 72–77, 2017.

[8] T. Gerling, K. F. Wagenbauer, A. M. Neuner, and H. Dietz,“Dynamic DNA devices and assemblies formed by shape-com-plementary, non-base pairing 3D components,” vol. 347,no. 6229, pp. 1446–1452, 2015.

[9] M. Bathe and P. W. K. Rothemund, “DNA nanotechnology: afoundation for programmable nanoscale materials,”MRS Bul-letin, vol. 42, no. 12, pp. 882–888, 2017.

[10] S. Nummelin, J. Kommeri, M. A. Kostiainen, and V. Linko,“Evolution of structural DNA nanotechnology,” AdvancedMaterials, vol. 30, no. 24, article 1703721, 2018.

[11] A. J. Thubagere, W. Li, R. F. Johnson et al., “A cargo-sortingDNA robot,” Science, vol. 357, no. 6356, article eaan6558,2017.

[12] P. W. Rothemund, “Folding DNA to create nanoscaleshapes and patterns,” Nature, vol. 440, no. 7082, pp. 297–302, 2006.

[13] K. Matsuda, A. M. R. Kabir, N. Akamatsu et al., “Artificialsmooth muscle model composed of hierarchically orderedmicrotubule asters mediated by DNA origami nanostruc-tures,” Nano Letters, vol. 19, no. 6, pp. 3933–3938, 2019.

[14] H. Ijäs, I. Hakaste, B. Shen, M. A. Kostiainen, and V. Linko,“Reconfigurable DNA origami nanocapsule for ph-controlledencapsulation and display of cargo,” ACS Nano, vol. 13,no. 5, pp. 5959–5967, 2019.

[15] K. F. Wagenbauer, C. Sigl, and H. Dietz, “Gigadalton-scaleshape-programmable DNA assemblies,” Nature, vol. 552,no. 7683, pp. 78–83, 2017.

[16] P. Zhan, P. K. Dutta, P. Wang et al., “Reconfigurable three-dimensional gold nanorod plasmonic nanostructures orga-nized on DNA origami tripod,” ACS Nano, vol. 11, no. 2,pp. 1172–1179, 2017.

[17] X. Luo, P. Chidchob, J. F. Rahbani, and H. F. Sleiman, “Encap-sulation of gold nanoparticles into DNA minimal cages for3D-anisotropic functionalization and assembly,” Small,vol. 14, no. 5, article 1702660, 2017.

[18] C. Shen, X. Lan, X. Lu et al., “Site-specific surface functionali-zation of gold nanorods using DNA origami clamps,” Journalof the American Chemical Society, vol. 138, no. 6, pp. 1764–1767, 2016.

[19] T. G. W. Edwardson, K. L. Lau, D. Bousmail, C. J. Serpell, andH. F. Sleiman, “Transfer of molecular recognition informationfrom DNA nanostructures to gold nanoparticles,” NatureChemistry, vol. 8, no. 2, pp. 162–170, 2016.

[20] T. M. Nguyen, E. Nakata, M. Saimura, H. Dinh, and T. Morii,“Design of modular protein tags for orthogonal covalent bondformation at specific DNA sequences,” Journal of the Ameri-can Chemical Society, vol. 139, no. 25, pp. 8487–8496, 2017.

[21] K. Zhou, Y. Ke, and Q. Wang, “Selective in situ assembly ofviral protein onto DNA origami,” Journal of the AmericanChemical Society, vol. 140, no. 26, pp. 8074–8077, 2018.

[22] F. Praetorius and H. Dietz, “Self-assembly of geneticallyencoded DNA-protein hybrid nanoscale shapes,” Science,vol. 355, no. 6331, article eaam5488, 2017.

[23] J. Sharma, Y. Ke, C. Lin et al., “DNA‐Tile‐Directed Self‐Assembly of Quantum Dots into Two‐Dimensional Nanopat-terns,” Angewandte Chemie International Edition, vol. 47,no. 28, pp. 5157–5159, 2008.

[24] H. Bui, C. Onodera, C. Kidwell et al., “Programmable period-icity of quantum dot arrays with DNA origami nanotubes,”Nano Letters, vol. 10, no. 9, pp. 3367–3372, 2010.

[25] H. T. Maune, S. Han, R. D. Barish et al., “Self-assembly ofcarbon nanotubes into two-dimensional geometries usingDNA origami templates,” Nature Nanotechnology, vol. 5,no. 1, pp. 61–66, 2010.

[26] H. Atsumi and A. M. Belcher, “DNA origami and G-quadruplex hybrid complexes induce size control of single-walled carbon nanotubes via biological activation,” ACS Nano,vol. 12, no. 8, pp. 7986–7995, 2018.

[27] J. D. Le, Y. Pinto, N. C. Seeman, K. Musier-Forsyth, T. A.Taton, and R. A. Kiehl, “DNA-templated self-assembly ofmetallic nanocomponent arrays on a surface,” Nano Letters,vol. 4, no. 12, pp. 2343–2347, 2004.

[28] C. Hartl, K. Frank, H. Amenitsch, S. Fischer, T. Liedl, andB. Nickel, “Position accuracy of gold nanoparticles on DNA

8 Journal of Nanomaterials

origami structures studied with small-angle X-ray scattering,”Nano Letters, vol. 18, no. 4, pp. 2609–2615, 2018.

[29] J. Ye, S. Helmi, J. Teske, and R. Seidel, “Fabrication of metalnanostructures with programmable length and patternsusing a modular DNA platform,” Nano Letters, vol. 19,no. 4, pp. 2707–2714, 2019.

[30] M. J. Urban, S. Both, C. Zhou et al., “Gold nanocrystal-mediated sliding of doublet DNA origami filaments,” NatureCommunications, vol. 9, no. 1, p. 1454, 2018.

[31] C. Zhang, J. Ma, J. Yang, Y. Dong, and J. Xu, “Control of goldnanoparticles based on circular DNA strand displacement,”Journal of Colloid and Interface Science, vol. 418, pp. 31–36,2014.

[32] X. Yang, Y. Tang, S. D. Mason, J. Chen, and F. Li, “Enzyme-powered three-dimensional DNA nanomachine for DNAwalking, payload release, and biosensing,” ACS Nano, vol. 10,no. 2, pp. 2324–2330, 2016.

[33] Z. Zhao, E. L. Jacovetty, Y. Liu, and H. Yan, “Encapsulation ofgold nanoparticles in a DNA origami cage,” Angewandte Che-mie International Edition, vol. 50, no. 9, pp. 2041–2044, 2011.

[34] F. N. Gür, F. W. Schwarz, J. Ye, S. Diez, and T. L. Schmidt,“Toward self-assembled plasmonic devices: high-yieldarrangement of gold nanoparticles on DNA origami tem-plates,” ACS Nano, vol. 10, no. 5, pp. 5374–5382, 2016.

[35] C. Tian, M. A. L. Cordeiro, J. Lhermitte et al., “Supra-nanopar-ticle functional assemblies through programmable stacking,”ACS Nano, vol. 11, no. 7, pp. 7036–7048, 2017.

[36] G. Yao, J. Li, J. Chao et al., “Gold‐Nanoparticle‐Mediated Jig-saw‐Puzzle‐like Assembly of Supersized Plasmonic DNA Ori-gami,” Angewandte Chemie International Edition, vol. 54,no. 10, pp. 2966–2969, 2015.

[37] M. P. Busson, B. Rolly, B. Stout et al., “Optical and topologicalcharacterization of gold nanoparticle dimers linked by a singleDNA double strand,” Nano Letters, vol. 11, no. 11, pp. 5060–5065, 2011.

[38] F. Li, H. Zhang, C. Lai, X. F. Li, and X. C. le, “A MolecularTranslator that Acts by Binding‐Induced DNA Strand Dis-placement for a Homogeneous Protein Assay,” AngewandteChemie International Edition, vol. 51, no. 37, pp. 9317–9320,2012.

[39] J. Sharma, R. Chhabra, C. S. Andersen, K. V. Gothelf, H. Yan,and Y. Liu, “Toward reliable gold nanoparticle patterning onself-assembled DNA nanoscaffold,” Journal of the AmericanChemical Society, vol. 130, no. 25, pp. 7820-7821, 2008.

[40] X. Shen, A. Asenjo-Garcia, Q. Liu et al., “Three-dimensionalplasmonic chiral tetramers assembled by DNA origami,”NanoLetters, vol. 13, no. 5, pp. 2128–2133, 2013.

[41] J. Yang, Z. Song, S. Liu, Q. Zhang, and C. Zhang, “Dynamicallyarranging gold nanoparticles on DNA origami for molecularlogic gates,” ACS Applied Materials & Interfaces, vol. 8,no. 34, pp. 22451–22456, 2016.

[42] C. Zhou, X. Duan, and N. Liu, “A plasmonic nanorod thatwalks on DNA origami,” Nature Communications, vol. 6, arti-cle 8102, 2015.

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