Triggered Reversible Reconfiguration of G-Quadruplex-Bridged

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Triggered Reversible Reconfiguration of G-Quadruplex-Bridged “Domino”Type Origami Dimers: Application of the Systems for Programmed Catalysis Jianbang Wang, Liang Yue, Shan Wang, and Itamar Willner ACS Nano, Just Accepted Manuscript • DOI: 10.1021/acsnano.8b06191 • Publication Date (Web): 14 Nov 2018 Downloaded from http://pubs.acs.org on November 15, 2018

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Triggered Reversible Reconfiguration of G-Quadruplex-Bridged “Domino”-Type Origami Dimers: Application of the Systems for Programmed Catalysis Jianbang Wang, Liang Yue, Shan Wang and Itamar Willner* Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel *E-mail: [email protected]; phone: +972-2-6585272; fax: +972-2-6527715 KEYWORDS: DNA; switch; nanotechnology; DNAzyme; machine

ABSTRACT: The reversible and switchable reconfiguration of the two origami dimers mixture AB+CD into the dimers mixture DA+BC and back, using the triggered

formation

of

K+-ion-stabilized

G-quadruplexes

and

subsequent

treatment with 18-crown-6-ether is presented. The reconfiguration processes are followed by AFM imaging of the dimers structures that include tiles marked with 0, 1, 2 and 3 4× hairpin labels. By the functionalization of AB and CD dimers 1 ACS Paragon Plus Environment

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with the Mg2+-ion-dependent DNAzyme subunits, the AB+CD mixture leads to the cleavage of the fluorophore/quencher-modified substrate of the DNAzyme and

to

the

activation

of

the

fluorescence

of

the

fluorophore

(fluorescein)-modified fragment product. The K+-ion-induced isomerization of the mixture AB+CD into the mixture DA+BC separates the Mg2+-ion-dependent DNAzyme

subunits

and

concomitantly

reconfigures

the

K+-ion-stabilized

G-quadruplex associated with the two dimers. After the binding of hemin to the G-quadruplexes, the hemin/G-quadruplex DNAzyme is generated, leading to the catalyzed oxidation of Amplex Red by H2O2 to yield the fluorescent Resorufin product. By the cyclic treatment of the AB+CD mixture with K+ ions to yield the DA+BC mixture, and the subsequent recovery of the AB+CD mixture by subjecting the DA+BC mixture to 18-crown-6-ether, the fluorescence output signals of the system are switched “ON” and “OFF” between the fluorescence of fluorescein and Resorufin, respectively.

The base sequences composing nucleic acid encode structural and functional information into the biopolymer.1 Different nucleic acid nanostructures such as the formation of DNA tetrahedra,2 interlocked DNA structures,3 and DNA machines,4 such as tweezers,5 walker6,7 and reconfigurable DNA switches8 were 2 ACS Paragon Plus Environment

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reported. These nanostructures were used as functional assemblies for the organization of nanoparticles9 and chiroplasmonic nanoparticle assemblies,10 for controlling biocatalytic cascades11 and for the bottom-up construction of metallic nanowires.12,13 Specifically, two-dimensional (2D) and three-dimensional (3D) origami structures attract growing interest as building blocks for the construction of

nanostructures

and

particularly

functional

nanostructures.14−19

Besides

ingenious 2D and 3D shapes that can be generated by the dictated folding of the

long-chain

secondary

M13

phage

assembly

of

DNA

2D

by

appropriate

origami

structures

“staple” into

3D

units,

and

the

structures,20−26

self-assembled origami “tiles” or “frames” provide versatile “playgrounds” for the construction

of

programmed

nanostructures

of

enhanced

complexity.27−29

Specifically, the easy assembly of origami tiles or origami frames with dictated protruding tethers provides means to construct scaffolds for the organization of molecular,30,31 macromolecular32,33 and nanoparticle structures,34,35 and to study chemical transformations at the single-molecule level.30 For example, the programmed

assembly

of

nanoparticles

on

geometrically-defined

origami

scaffolds,36−39 the ordered assembly of enzymes on origami tiles at pre-designed distances and the activation of biocatalytic cascades,40 were reported. Also, the assembly of DNA machines, e.g. walkers on pre-design paths on origami tiles 3 ACS Paragon Plus Environment

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and the imaging of machine functions of the systems at the single molecule level,

were

demonstrated.6,41

Similarly,

chemical

transformations

at

the

single-molecule level were followed in origami frames using fast AFM imaging methods.42,43 In addition, 3D origami structures were reported as scaffolds for the organization of nanostructures that exhibit unique functions. For example, 3D origami structures were used as templates for the assembly of plasmonic antennas,44

chiroplasmonic

gold

nanoparticles,10,45−49

and

chiroplasmonic

machines.50,51 Also, different applications of 3D origami structures for the controlled release of payloads were suggested.52,53 Recently, our laboratory has introduced the concept of “origami chemistry”, in which stimuli-responsive bridges interconnecting dimer or trimer origami tiles were used as functional structures for programmed dissociation or switchable dissociation/reformation of the structures. Cofactor-dependent DNAzymes54 or aptamer-ligand complexes55 were

used

for

the

dictated

cleavage

of

trimer

origami

tiles,

and

the

programmed pH-stimulated reversible dissociation and reformation of trimer origami tiles, using pH-responsive i-motif or triplex interconnecting bridges,56 were demonstrated. In addition, we reported the triggered interconversion and reconfiguration

of

origami

dimers

as

a

principle

to

control

the

intercommunication between origami structures and as a means to enhance the 4 ACS Paragon Plus Environment

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complexity of interlinked origami networks.57 This system was based, however, on the interconversion between origami dimers by applying the fuel/anti-fuel strand displacement processes. This required, however, the use of a large number, and extensive contents, of the fuel/anti-fuel strands to induce the reconfiguration processes, and had difficulties that result from inter-nucleic acid crosstalks, low yields to recycle the systems and serious limitations to enhance the complexity of the dynamic reconfigurations of the origami networks. Recent

studies

reported

on

the

structural

reversible

reconfiguration

of

G-quadruplexes.8,58 While guanine-rich strands assemble, in the presence of K+ ions, into K+-ion-stabilized G-quadruplexes, they are dissociated, in the presence of crown ethers, into the random coil configuration through extraction of the K+ ions.

The

cyclic

and

reversible

self-assembly

of

the

K+-ion-stabilized

G-quadruplex and their separation in the presence of crown-ether or cryptates, were used to develop DNA-based hydrogels with controlled stiffness,59,60 to develop signal-triggered drug carriers61,62 and to assemble DNA machines, e.g., tweezers63 or walkers.64 In the present study, we report the cyclic and reversible reconfiguration (isomerization) of two origami dimers, using K+ ions and crown ethers as functional triggers that control the dynamic reconfiguration of

the

dimers

network.

We

demonstrate

that

the

reversible,

triggered 5

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reconfiguration of the system leads to programmed switchable catalytic functions of the network.

RESULTS AND DISCUSSION

Figure 1. (A) Schematic cyclic reconfiguration of the origami dimers mixture AB+CD into DA+BC using K+ ions and 18-crown-6-ether as triggers. (B) Cyclic dissociation/assembly

of

origami

dimers

in

the

presence

of

K+

ions/18-crown-6-ether: (1) Separation of AB dimer and its reassembly. (2)

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Separation of CD dimer and its reassembly. (3) Assembly of DA dimer and its separation. (4) Assembly of BC dimer and its separation.

Figure 1 presents schematically the goal of the present study. The system includes two dimers AB and CD. In the presence of K+ ions, the bridges of the two

dimers

are

dissociated

through

the

formation

of

K+-ion-stabilized

G-quadruplexes, leading to the formation of the individual origami tiles A, B, C and D. The presence of K+ ions in the solution stimulates, however, the recombination of the tiles to yield the reconfigured dimers DA and BC crosslinked by energetically favored G-quadruplexes. Similarly, the treatment of the

dimers

mixture

DA

and

BC

with

18-crown-6-ether

separates

all

G-quadruplexes associated with the different origami tiles, leading to the formation of the monomer mixture A, B, C and D that self-organizes into the AB and CD dimers mixture, in the absence of K+ ions. To realize such reconfiguration processes, the individual dimers AB, CD, DA and BC should


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follow

the

triggered

transformations

outlined

Page 8 of 55

in

eq.

1

–

eq.

4.

Accordingly, in order to demonstrate the overall reversible isomerization of the tiles AB+CD to DA+BC, we had to demonstrate the feasibility to induce the stepwise transitions corresponding to the separation and reformation of the respective dimers.


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Figure 2. (A) Reversible and switchable dissociation and reassembly of the origami dimer AB (marked with (0, 2) labels) in the presence of K+ ions and 18-crown-6-ether. (B) AFM images corresponding to: (I) AB dimer. (II) The mixture of the separated origami tiles A (0 label) and B (two 4× hairpin labels), 9 ACS Paragon Plus Environment

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generated by the treatment of dimer AB with K+ ions. (III) The reassembled AB dimer by the treatment of the mixture of monomer tiles of A and B with 18-crown-6-ether. (C) Cross-section analysis corresponding to: (I) the circled AB dimer. (II) The two circled monomer tiles A and B. (III) The circled AB dimer generated by the treatment of the monomer tiles with 18-crown-6-ether. (D) Statistical analysis of the origami constituents: (I) As prepared origami dimer AB. (II) The K+-ion-induced separation of the dimer AB into the monomer tiles A and B. (III) The reassembled AB dimers generated by the treatment of the origami monomer mixture of A and B with 18-crown-6-ether. Error bars were derived from the statistical evaluation of the dimer structures on three to five 5 μm × 5 μm scanned imaged areas for each of the dimer mixtures systems.

Figure 2(A) presents the principle to control the reversible and switchable reconfiguration of the origami dimer AB (marked with (0, 2) labels) using K+ ions and 18-crown-6-ether as triggers (Cf. Figure 1, eq. 1). The tiles comprising the dimer are labeled for identification, in which tile A is not labeled and tile B is marked with two hairpin labels (each of the labels including 4× hairpins). Dimer AB is interlinked by 3× pairs of bridges, in which tile A is modified on its edge with 3× tethers L1 and L3 and tile B is functionalized on its edge with 10 ACS Paragon Plus Environment

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3× tethers L2 and L4. The tethers L1/L2 and L3/L4 reveal partial base-pair complementarity (a/a’ and b/b’) that allows the bridging of the tiles with duplexes generated between L1/L2 and L3/L4. The nucleic acids L2 and L4 include single strand tethers g1 that are G-rich. Part of the duplex domains a/a’ and b/b’ includes, however, the domains a’ and b’ caged G-sequences. The caged G-sequences in domains a’ and b’ of L2 and L4 together with g1 tethers can

reconfigure,

in

the

presence

of

K+

ions,

into

the

K+-ion-stabilized

G-quadruplexes. Accordingly, subjecting the interconnected dimer AB to K+ ions results in its separation, due to the reconfiguration of the 3× L2 and 3× L4 into K+-ion-stabilized G-quadruplexes. The subsequent treatment of the monomer mixture of A and B with the crown ether dissociates the G-quadruplexes, due to the elimination of the K+ ions by the crown ether receptor units, leading to the reassembly of the origami AB dimer, Cf. Figure 2(A). That is, by the cyclic treatment of AB dimer with K+ ions and then with 18-crown-6-ether, the dimers AB are dissociated into monomer tiles A and B, and then are recovered into the AB dimer structures. Figure 2(B) presents the AFM images of AB dimers before the treatment with K+ ions, state I, the mixture of the separated origami tiles generated after the treatment of dimer AB with K+ ions, state II, and the reassembled dimer AB after the treatment of monomers A and B with 11 ACS Paragon Plus Environment

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18-crown-6-ether, state III. While in state I, most of the structures are dimer AB with (0, 2) marks, the system in state II consists of monomer tiles that are marked with 0 or 2 labels. The treatment of the mixture of single tiles with 18-crown-6-ether regenerates the (0, 2) dimer structure AB, state III. Each of the AFM images in state I, II and III shows enlarged structures (upper right) of the respective (0, 2) origami dimer AB, states I and III, and the separated 0 and 2 labeled tiles, state II. Figure 2(C) shows the cross-section analysis of dimer AB and of the separated tiles A and B. Evidently, the monomer tiles show two ca. 100 nm long tiles (one without label and a second tile with one spike, ca. 1 nm height above the base origami tile of ca. 2 nm height, corresponding to the 4× hairpin label), whereas in state I and state III, ca. 200 nm long tiles that include a single spike (ca. 1 nm height), consistent with the dimer (0, 2), are observed. Figure 2(D) presents the yields of dimer AB in states I and III and the yields of the monomer tiles A and B evaluated by the statistical analysis of several large area images of the respective states. (For the details of the statistical analysis, see Figure S1 and accompanying Table S1). The yields of the dimer structures in states I and III are ca. 75%, whereas the yields of the separated monomers, A and B, in state II, are almost 100%. It should be noted that the origami tiles A and B are further modified on the 12 ACS Paragon Plus Environment

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edges opposite to the interlinking bridges by tethers L10, L12 and L13, L15, respectively. These tethers do not participate in the triggered separation of dimer AB or the recombination of the separated tiles A and B. Nonetheless, these tethers will play a key function in the triggered transition between AB+CD and DA+BC, vide infra. Further support for the yields of reconfiguration of the dimer

AB

to

the

separated

monomer

tiles

and

back

was

obtained

by

quantitative agarose gel electrophoretic separation of the respective tiles, see Figure S1(C).


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Figure 3. (A) Reversible and switchable separation of dimer CD (marked with (1, 3) labels) into the monomer origami tiles C (marked with one 4× hairpin label) and D (marked with three 4× hairpin labels), in the presence of K+ ions, and the reverse dimerization of the tiles, in the presence of 18-crown-6-ether. 14 ACS Paragon Plus Environment

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(B) AFM images corresponding to dimer CD, panel I, after the treatment of the dimer with K+ ions and the generation of the separated tiles, panel II, and after subjecting the separated tiles to 18-crown-6-ether, panel III. (C) Cross-section analysis of the marked origami structures in the different states. (D) Statistical analysis of the origami constituents in state I (dimer CD), state II (separated monomer mixture composed of C and D) and state III (dimer CD). Error bars were derived from the statistical evaluation of the dimer structures on three to five 5 μm × 5 μm scanned imaged areas for each of the dimer mixtures systems.

Figure 3(A) shows the cyclic separation of dimer CD (marked with (1, 3) labels) to the individual tiles C and D and their reversible reassembly into dimer CD in the presence of K+ ions and 18-crown-6-ether (Cf. Figure 1, eq. 2). The monomer C is marked with one hairpin label (each label composed of 4× hairpins), whereas monomer D is marked with three labels (each label composed of 4× hairpins). The monomer origami C is functionalized on one edge with 3× tethers L5 and L7, which include domains c and d, respectively, and the monomer origami D is functionalized on one edge with 3× tethers L6 and L8 that include domains c’ and d’, respectively. The complementarity of the 15 ACS Paragon Plus Environment

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domains c/c’ (in L5/L6) and d/d’ (in L7/L8) leads to the crosslinking of the tiles to yield dimer CD. Note that the free tethers g1 are extended by respective protruding strands that are a part of the sequences c’ and d’, and include caged G-units. In the presence of K+ ions, the G-rich tethers g1, together with the caged G domains in c’ and d’, self-assemble into the K+-ion-stabilized G-quadruplexes, associated with origami monomer D. The process leads to the separation of dimer CD to monomer tiles C and D. In the presence of 18-crown-6-ether,

the

G-quadruplexes

are

dissociated

resulting

in

the

reassembly of the dimer (1, 3). Note that the edges opposite to the dimer inter-bridging sites associated with tiles C and D are functionalized with additional tethers. Tile C is modified with 3× tethers L14 and L16, and tile D is modified with 3× tethers L9 and L11. These tethers do not participate in the triggered separation of dimer CD (in the presence of K+ ions) or in the reassembly of the monomers to the dimer. Nonetheless, these tethers play a key function in the reconfiguration of the mixture AB+CD into DA+BC mixture. Figure 3(B) shows the AFM images of CD dimers before the treatment with K+ ions, state I, monomer tiles C and D after the treatment of dimer CD with K+ ions, state II, and the reassembled dimer CD by subjecting monomers C and D to 18-crown-6-ether, state III. In state I, most of the structures are dimers (1, 16 ACS Paragon Plus Environment

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3), and in state II, the system consists of the monomer tiles mixture of C and D.

The

treatment

18-crown-6-ether

of

the

mixture

regenerates

of

the

the (1, 3)

separated

monomer

dimer structures

(state

tiles

with

III).

The

enlarged insets (upper right) show the respective structures of the (1, 3) origami dimer CD (states I and III), and the separated monomer tiles C and D (state II). Figure 3(C) presents the cross-section analysis of the dimer (1, 3) and of the separated monomer tiles C and D. Evidently, in state II, the monomer tiles show two ca. 100 nm long tiles (tile C with one spike and tile D with two spikes corresponding to the 4× hairpin labels), whereas in state I and state III ca. 200 nm long tiles are observed, and they include three spikes, consistent with dimers CD. The heights of the spikes are ca. 1 nm above the base origami tiles (ca. 2 nm height). Figure 3(D) shows the yields of dimers CD in states I and III, and the yields of monomer tiles C and D in state II. (For the details of the statistical analysis, see Figure S2 and accompanying Table S2). The yields of the dimer structures in states I and III are ca. 75%, whereas the yields of the separated monomers, C and D, are almost 100% in state II. Further support for the yields of reconfiguration of the dimer CD to the separated

monomer

tiles

and

back

was

obtained

by

quantitative

gel

electrophoretic separation of the respective tiles, see Figure S2(C). 17 ACS Paragon Plus Environment

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Figure 4. (A) Reversible and switchable assembly and dissociation of the origami dimer DA (with (3, 0) labels), using K+ ions and 18-crown-6-ether as triggers. (B) AFM images corresponding to: (I) The mixture of the monomer origami tiles D (labeled with three 4× hairpin labels) and A (no label). (II) 18 ACS Paragon Plus Environment

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Dimer DA after the treatment of the monomer tiles mixture with K+ ions. (III) The separated monomer mixture of D and A after subjecting the (3, 0) origami dimer to 18-crown-6-ether. (C) Cross-section analysis of the respective origami structures: (I) Analysis of two monomer tiles D and A. (II) Analysis of the (3, 0)-labeled origami dimer, DA, generated by subjecting the monomer mixture to K+ ions. (III) Analysis of the monomer origami tiles mixture of D and A after the treatment of the (3, 0) dimer origami with 18-crown-6-ether. (D) Statistical analysis of the origami constituents in the different monomer/dimer states: (I) The monomer mixture composed of tiles D and A. (II) Dimer DA generated upon subjecting the monomer tile mixture to K+ ions. (III) The regenerated mixture of monomer tiles D and A upon the treatment of dimer DA with 18-crown-6-ether. Error bars were derived from the statistical evaluation of the dimer structures on three to five 5 μm × 5 μm scanned imaged areas for each of the dimer mixtures systems.

In the next step, we examined the K+-ion-induced dimerization of the monomer origami tile D (marked with three 4× hairpin labels) and tile A (no label),

and

the

reverse

separation

of

the

dimer

in

the

presence

of

18-crown-6-ether (Cf. Figure 1, eq. 3). In the dimerization process, we made 19 ACS Paragon Plus Environment

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use of 3× tethers L9 and L11, associated with tile D and 3× tethers L10 and L12, associated with tile A. Tethers L9 and L11 include the sequence domains e and f extended by a G-rich sequence g2. In addition, tethers L10 and L12, linked to tile A, include a G-rich sequence g2 extended by e’ and f’ (complementary

to

e

and

f

domains

in

L9

and

L11).

Despite

the

complementarity of the domains e/e’ and f/f’, the base-pairing is insufficient to stabilize the bridging of dimer DA (only six base-pairs in each of these duplexes). In the presence of K+ ions, dimer origami DA is formed by the crosslinking of the tiles by the cooperatively stabilized by the e/e’ and f/f’ duplexes and the G-quadruplex bridges between L9/L11 and L10/L12 strands. The subsequent addition of 18-crown-6-ether separates the G-quadruplex units associated with the cross-linkers L9/L10, L11/L12, resulting in the secondary separation of the weak duplexes e/e’ and f/f’, leading to the separation of dimer DA, Figure 4(A). Figure 4(B) shows the AFM images corresponding to the separated monomer tiles D and A marked with three or no labels, respectively, state I. The AFM image of the K+-ion-stimulated formation of DA dimer is displayed in state II, and the AFM image of the 18-crown-6-ether-induced separation of dimer DA to monomer tiles D and A is presented in state III. The enlarged insets (upper right in the three states) represent the respective marked 20 ACS Paragon Plus Environment

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constituents of the monomer tiles or dimer structures. Figure 4(C) depicts the cross-section analysis of the marked constituents in the different states. The separated tiles show two spikes structures (ca. 1 nm height) above the height of the base origami tiles (ca. 2 nm) for D (ca. 100 nm length), and no spike for tile A (ca. 100 nm length). Dimer DA reveals a length of ca. 200 nm and a height of ca. 2 nm, and includes two spikes (ca. 1 nm height) consistent with two linear positioned hairpin marks across the (3, 0) DA dimer structure. Figure 4(D) shows the statistical quantitative analysis of the constituents in the states I, II and III. (For detail of the analysis, see Figure S3 and Table S3, supporting information). In states I and III, the populations of monomer components D and A are ca. 100%, whereas in state II, the DA dimer population is ca. 75%. Further support for the yield of reconfiguration of the dimer DA was obtained by quantitative agarose gel electrophoretic separation of the respective tiles, see Figure S3(C).


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Figure 5. (A) Reversible and switchable assembly and dissociation of BC origami

dimer

18-crown-6-ether.

(with (B)

(2, AFM

1)

labels), images

in

the

presence

corresponding

to:

(I)

of

K+

The

ions mixture

and of

monomer origami tiles B and C labeled with two and one 4× hairpin labels, 22 ACS Paragon Plus Environment

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respectively. (II) Dimer BC after the treatment of the monomer tiles mixture with K+ ions. (III) The separated monomer mixture of B and C after subjecting the (2, 1) origami dimer to 18-crown-6-ether. (C) Cross-section analysis of the respective origami structures: (I) Analysis of two monomer tiles B and C. (II) Analysis of the (2, 1) origami dimer BC generated by subjecting the monomer mixture to K+ ions. (III) Analysis of B and C monomer origami tiles mixture after the treatment of dimer BC with 18-crown-6-ether. (D) Statistical analysis of the origami constituents in the different states: (I) The tiles B and C monomer mixture. (II) The dimer origami BC generated by subjecting the monomer tiles mixture to K+ ions. (III) The separated mixture of monomer tiles B and C formed upon the treatment of dimer origami BC with 18-crown-6-ether. Error bars were derived from the statistical evaluation of the dimer structures on three to five 5 μm × 5 μm scanned imaged areas for each of the dimer mixtures systems.

Figure 5(A) depicts the switchable assembly and separation of origami dimer BC, marked with two and one 4× hairpin labels for tiles B and C, respectively (Cf. Figure 1, eq. 4). The monomer tile B is functionalized on its edge with 3× tethers L13 and L15, including domains h and i that are conjugated to the 23 ACS Paragon Plus Environment

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G-rich domains g2. The monomer tile C is modified on its edge with 3× tethers L14 and L16 that include the sequence domains h’ and i’, respectively, which are extended with domain g2, while domains h’ and i’ in L14 and L16 are complementary to domains h and i, associated with L13 and L15. All of the domains

g2

represent

subunits

of

the

G-quadruplex.

Despite

the

base

complementarity of domains h/h’ and i/i’, the base-pairing is insufficient to stabilize the duplex bridging of dimer BC. In the presence of K+ ions, the cooperative stabilization of K+-ion-stabilized G-quadruplexes and duplex domains yield stable 3× h/h’-G-quadruplex and 3× i/i’-G-quadruple bridges between L13/L14 and L15/L16. These bridges lead to the stabilization of BC origami dimer identified with marks (2, 1). The treatment of the resulting BC dimer with 18-crown-6-ether dissociates the G-quadruplex subunits, and this results in the dissociation of BC origami dimer into the individual monomer tiles B and C. Figure 5(B) presents the AFM images corresponding to monomer tiles B and C (state I), BC dimer after the treatment of the monomer mixture with K+ ions (state II), and the separated monomers B and C formed by subjecting the dimers (2, 1) to 18-crown-6-ether (state III). The enlarged insets (upper right) represent the respective marked constituents of the monomer tiles or dimer structures in the different states. Figure 5(C) shows the cross-section analysis 24 ACS Paragon Plus Environment

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of the marked constituents in the different states. The separated tiles B and C show single spike structures (ca. 1 nm height) above the height of the base origami tiles (ca. 2 nm) and the lengths of ca. 100 nm. The dimer (2, 1) reveals a length of ca. 200 nm and a height of ca. 2 nm, and includes two spikes (ca. 1 nm height) consistent with two linear positioned hairpin marks across the dimer structure. Figure 5(D) presents the statistical analysis of the constituents of the monomer mixture or the dimer structures in states I, II and III. (For detail of the analysis, see Figure S4 and Table S4, supporting information). In states I and III, the populations of the monomer components B and C are ca. 100%, whereas in state II, the population of dimer BC is ca. 75%. Further support for the yield of reconfiguration of the dimer BC was obtained by quantitative agarose gel electrophoretic separation of the tiles, see Figure S4(C).


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Figure 6. (A) The switchable and reversible reconfiguration of the dimers mixture AB+CD into BC+DA, and back, using K+ ions and 18-crown-6-ether as triggers. (B) AFM images corresponding to: (I) The mixture of origami dimers AB+CD. (II) The reconfigured origami dimers mixture BC+DA generated by the


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treatment of the mixture AB+CD with K+ ions. (III) The dimers mixture AB+CD formed upon the reconfiguration of the dimers mixture BC+DA, in the presence of 18-crown-6-ether. (C) The triggered switchable yields of the origami dimers mixture AB+CD and of the BC+DA dimers mixture formed in the presence of K+ ions and 18-crown-6-ether. Error bars were derived from the statistical evaluation of the dimers structures on three to five 5 μm × 5 μm scanned imaged areas for each of the dimers mixtures systems.

In the next step, dimers AB and CD were mixed, and the switchable and reversible K+-ion/18-crown-6-ether interconversion of the AB+CD dimers mixture into the BC+DA dimers mixture and back were evaluated, Figure 6(A). In view of the pre-engineered sequences associated with tiles A, B, C and D, the K+-ion-induced separation of dimers AB and CD, and reconfiguration of the separated tiles A, B, C and D lead to a new mixture of dimers BC and DA. That is, the addition of K+ ions separates the L1/L2 and L3/L4 bridges of AB, through the formation of the respective K+-ion-stabilization of the G-quadruplex structures of g1 subunits. Similarly, the bridging strands L5/L6 and L7/L8 of dimer CD are separated, in the presence of the added K+ ions, through the stabilization

of

the

G-quadruplexes

of

the

respective

g1

subunits.

The 27


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separation of the two dimers, and the existence of the pre-engineered sequences L13, L15, L10, L12 and of L14, L16, and L9, L11, stimulate the reconfiguration of the system to a new dimers mixture consisting of BC and DA. Dimers BC are interlinked by the bridges composed of 3× L13/L14 and L15/L16 comprising the respective G-quadruplexes, generated by g2 subunits, which

are

cooperatively

stabilized

by

the

duplex

domains

h/h’

and

i/i’,

respectively. Similarly, dimer tiles DA are self-organized by the bridging units composed by 3× L9/L10 and L11/L12 bridges that are cooperatively stabilized by the K+-ion-stabilized G-quadruplexes of g2 subunits and the duplex domains e/e’ and f/f’. Note that, in addition to the K+-ion-stabilized G-quadruplex units of g2 domains that bridge the respective dimers, g1 tethers associated with strands L2/L4, L6/L8, also, form K+-ion-stabilized G-quadruplexes on the counter edges to the interlinking bridges of dimer BC and DA. For a detailed evaluation of the free energy changes associated with the conversion of the dimers mixture AB+CD into BC+DA, see supporting Figure S5 and accompanying discussion.

The

treatment

of

the

dimers

mixture

BC

and

DA

with

18-crown-6-ether results in the separation of the interlinking K+-ion-stabilized G-quadruplexes and of the K+-ion-stabilized G-quadruplexes comprising g1 subunits

on

the

counter

edges

to

the

interlinking

bridges.

The 28


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crown-ether-stimulated separation of the BC and DA mixture leads to the reconfiguration of the AB and CD dimers mixture. Figure 6(B) shows the AFM images

corresponding

to

the

dimers

mixture

AB+CD,

panel

I,

the

K+-ion-triggered formation of the BC+DA dimers mixture, panel II, and the reversible 18-crown-6-ether-induced reformation of the AB+CD dimers mixture, panel III. In the upper right, AFM images of the enlarged constituents of the respective mixtures are displayed. Panel I shows a rich population of the (0, 2) and (1, 3) dimers, whereas panel II reveals a high population of the (2, 1) and (3, 0) dimers, corresponding to the BC and DA dimers mixture. Panel III shows a rich population of the (0, 2) and (1, 3) dimers mixture, consistent with the recovery of the AB+CD dimers mixture. Figure 6(C) shows the switchable and reversible reconfiguration of the respective dimers. In the initial mixture, the dimers (0, 2) and (1, 3) are present at a yield of ca. 70% and the population of the (2, 1) and (3, 0) dimer constituents is basically zero. The treatment of the mixture with K+ ions yields the (2, 1) and (3, 0) dimers mixture with a yield of ca. 70%, while the yield of the (0, 2) and (1, 3) dimers drops to zero. The treatment of the latter mixture with 18-crown-6-ethers recovers the original high-yield mixture of (0, 2) and (1, 3) dimers, ca. 70%, and the yield of the (2, 1) and (3, 0) dimers drops to zero. It should be noted that the statistical 29 ACS Paragon Plus Environment

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analysis of the yields for interconversion of the mixture (AB+CD) to (BC+DA), and back, is based on the counting of the respective dimers on three to five 5 μm × 5 μm large imaged areas. (For a detailed statistical analysis of the compositions of the different dimers mixtures, see Figure S5 and Table S5, supporting information).


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Figure 7. (A) Controlling the switchable catalytic functions of reconfigurable origami dimers mixture, composed of the mixture AB+CD or the reconfigured 31 ACS Paragon Plus Environment

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dimers mixture BC+DA, using K+ ions or 18-crown-6-ether as triggers. The mixture AB+CD is engineered to reveal the Mg2+-ion-dependent DNAzyme functions that cleaves FAM/BHQ1-modified substrate leading to the catalyzed generation

of

the

FAM

fluorescence.

The

mixture

of

dimers

BC+DA

is

engineered to include the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme that catalyzes the oxidation of Amplex Red by H2O2 to form the fluorescent Resorufin product. (B) Switchable fluorescence features of the reversibly reconfigured AB+CD  BC+DA dimers mixture. The mixture AB+CD leads to the switched-ON fluorescence of FAM and switched-OFF fluorescence of

Resorufin,

while

the

dimers

mixture

BC+DA

yields

the

switched-ON

fluorescence of Resorufin and the switched-OFF fluorescence of FAM. Error bars were derived from a set of three experiments.

In the next step, we attempted to introduce switchable catalytic (DNAzyme) functions into the “domino”-type K+-ion/crown ether reconfigurable mixture of dimers AB and CD. Towards this goal, we further engineered the bridging units linking dimers AB and CD as outlined in Figure 7(A). (For a further detailed explanation of the structural changes introduced into the AB and CD dimers to reach the switchable catalytic functions, see Figure S6 and accompanying 32 ACS Paragon Plus Environment

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discussion). In dimer AB, strands 3× L2 and 3× L4 are unchanged. The bridging units L1 and L3 of the original AB dimer are, however, substituted by bridges 3× L17 and 3× L18, in which each of tethers L17 and L18 includes the original sequences of L1 and L3, respectively, that are conjugated to tile A through spacer domain x. These features of tethers L17 and L18 ensure the bridging of the two tiles of AB with duplex units as described in Figure 2, in which each of the bridges includes a single strand domain (x in L17 and L18 and g1 tether linked to L2 and L4). The resulting dimer AB was, then, subjected to the helper strand T that exhibits a sequence-specific domain x’, complementary to x, and to two Mg2+-ion-dependent subunits I1 and I2 that include complementary domain for hybridization with the single stranded toehold domains associated with T (of L17 and L18) and g1 (of L2 and L4). (For the detailed schematic assembly of the Mg2+-ion-dependent DNAzymes on 3× L17/L2 and 3× L19/L4, see Figure S6, supporting information). Similarly, dimer CD is reengineered to allow the switchable catalytic functions of the AB+CD dimers mixture. In this case, the bridging tethers L6 and L8 associated with tile D are unchanged. The original bridging tethers L5 and L7 are, however, substituted by two new bridging tethers 3× L19 and 3× L20, in which each of tethers L19 and L20 includes the original sequences of L5 and L7, respectively, 33 ACS Paragon Plus Environment

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that are conjugated to the edge of tile C by the spacer domain x. The interaction of L19/L6 and L20/L8 bridged dimer CD with the helper sequence T, and the Mg2+-ion-dependent subunits I1 and I2, results in the assembly of the respective DNAzyme units on dimer CD. Subjecting of the resulting AB+CD dimers mixture, state I, to the FAM/BHQ1-functionalized DNAzyme substrate, leads to the cleavage of the substrate, and the resulting fluorescence of the FAM-modified fragmented product reflects the catalytic functions of the origami dimers mixture in state I. The treatment of the AB+CD mixture with K+ ions results in the reconfiguration of the AB+CD mixture into the BC+DA dimers mixture. Under these conditions and according to the rearrangement mechanism discussed in Figure 6(A), the new dimers mixture BC+DA is generated, in which all Mg2+-ion-dependent DNAzyme bridging units linking dimer AB and CD are separated, and new K+-ion-stabilized G-quadruplex dimers are formed. That is, the inter-bridging linkers of dimers BC and DA include the 3× G-quadruplex modified linkers of L13/L14 and L15/L16 (in dimer BC) and 3× L9/L10 and L11/L12 (in dimer DA). In addition, the edge of tile B opposite to the inter-bridges is functionalized by 3× L2/L4 K+-ion-stabilized tethers, and the edge of tile D, opposite to the interlinking bridging units of dimer DA, is functionalized with the K+-ion-stabilized G-quadruplexes of 3× L6/L8 tethers. The 34 ACS Paragon Plus Environment

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association

of

hemin

to

the

different

G-quadruplex

units

yields

the

functionalization of the respective dimers with the hemin/G-quadruplexes as catalytic DNAzyme functional units. That is, the hemin/G-quadruplex DNAzyme units catalyze the H2O2-induced oxidation of Amplex Red to the fluorescent Resorufin product, a process that reports the catalytic functions of the BC+DA dimers mixture, state II of the system. By subjecting the dimers mixture BC+DA to 18-crown-6-ether, the separation of the K+-ion-stabilized G-quadruplexes leads to the reconfiguration of state II to state I. By the cyclic treatment of the dimers mixtures AB+CD and BC+DA with K+ ions and 18-crown-6-ether, respectively, the dimers mixtures are cycled between states I and II exhibiting switchable

and

reversible

Mg2+-ion-dependent

DNAzyme

and

hemin/G-quadruplex DNAzyme catalytic functions. Figure 7(B) shows the cyclic catalytic

functions

of

the

DNAzymes

associated

with

the

triggered

reconfiguration of AB+CD  BC+DA. In state I, the dimers mixture AB+CD yields

the

fluorescence

of

FAM,

originating

from

the

Mg2+-ion-dependent

DNAzymes associated with the crosslinking bridges of dimers AB and CD, while no hemin/G-quadruplexes stimulated fluorescence is detected. In turn, in the presence of K+ ions, the fluorescence of Resorufin generated by the hemin/G-quadruplex units associated with dimers DA and BC is observed. 35 ACS Paragon Plus Environment

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Under these conditions, the Mg2+-ion-dependent DNAzyme bridging units, linking dimer AB and CD, are separated, leading to the blocking of the catalytic cleavage of the FAM/BHQ1 substrate. Note that the catalytic performances of the AB+CD dimers mixture to cleavage of the FAM/BHQ1 substrate are monitored after a time-interval of six hours, whereas the catalytic performances of the BC+DA system to catalyze the H2O2-induced oxidation of Amplex Red are monitored after a time-interval of ten minutes. These differences are due to the different activities of the respective DNAzymes and to the higher number of hemin/G-quandruplex catalytic unit in the BC+DA mixture. (The switchable fluorescence spectra of the FAM-modified product and the Resorufin product, stimulated by the cyclic reconfiguration of the AB+CD mixture into the DA+BC mixture and back are displayed in Figure S7, supporting information).

CONCLUSIONS The present study has demonstrated the significance of the origami edges as functional elements to control the reversible and switchable reconfiguration of origami dimer structures, and to dictate switchable and reversible catalytic functions of the systems. The “stapled” origami tiles allowed the precise positioning of hairpin tethers on the surface of the origami tiles and each set of 36 ACS Paragon Plus Environment

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four hairpin structures provided a “label” that could be imaged by AFM. Each of the four tiles, comprising the dimers, was functionalized with a different number of “readout labels”, thus allowing the precise identification of the labels and the imaging of the structural triggered reconfiguration of the dimers. Specifically, the tiles were labeled with 0, 1, 2 and 3 labels that generated the AB+CD dimers mixture and the reconfigured DA+BC dimers mixture. In addition, the edges of the origami tiles were modified with “sets” of functional tethers. One set of functional tethers was engineered to interlink the dimers and to allow the reversible and switchable reconfiguration of the AB+CD mixture into the DA+BC mixture, and back, using K+ ions and 18-crown-6-ether as triggers, respectively. The second set of tethers included functional units that provided anchoring sites for bridging of the Mg2+-ion-dependent DNAzyme subunits and permanent tethers that can assemble into the hemin/G-quadruplex DNAzyme units. The reversible reconfiguration of the AB+CD dimers mixture into the DA+BC dimers mixture in the presence of K+ ions and 18-crown-6-ether enabled the switching of the catalytic functions of the different dimers mixture. The principles developed in the present study will provide means to design origami tile structures of enhanced complexity and triggered functions. Note that two edges of each tile are still “bare” and lack functional tethers. By the engineering of 37 ACS Paragon Plus Environment

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additional tethers on these edges and increasing the number of tiles in each tile origami oligomer (e.g., three tiles in each origami oligomer), the triggered reversible reconfigurations of origami oligomers may be envisaged. In addition, the engineering of additional triggered functions on the vacant edges of the structures is anticipated to increase the complexity of emerging catalytic functions of these systems.

MATERIALS AND METHODS Preparation of DNA origami tiles. The DNA origami tiles were assembled in 1× TAE-Mg2+ buffer (Tris, 20 mM; Acetic acid, 20 mM; EDTA, 1 mM; and Magnesium acetate, 12.5 mM; pH 8.0). Single-stranded M13mp18 phage DNA (10 nM, New England Biolabs) and short staple strands (100 nM, unmodified staple strands, functional edge-specific staple strands and hairpin-staple strands) (Integrated DNA Technologies) were dissolved in the 1× TAE-Mg2+ buffer. The mixture was heated to 95 ℃ in a thermal cycler and then allowed to cool down to 20 ℃ at a rate of 0.1 ℃ every 10 seconds. The respective DNA origami tiles were purified using agarose electrophoresis (1%, 100 V, 1.5 h, at 0 ℃) to remove the excess staple strands and then using Freeze ´N Squeeze spin columns (BioRad) to extract the DNA origami tiles. 38 ACS Paragon Plus Environment

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Preparation of origami tile dimers. The single DNA origami tiles were mixed at a molar ratio of 1:1 to form AB dimer and CD dimer in 1× TAE buffer (Mg2+, 8 mM). The A/B and C/D mixtures were kept at room temperature overnight for the assembly of dimers AB and CD, respectively, and then purified using agarose electrophoresis. For the separation process, 1 μl of a 2 M potassium ion solution were added to 19 μl of the origami dimer solution to yield a final K+-ion concentration of 100 mM. The mixture was kept at room temperature for two hours to allow the separation of the dimers to the respective monomers. For the re-assembly process of the dimers, 180 μl of a 55 mM solution of 18-crown-6-ether (including Mg2+, 8 mM) were added to the 20 μl of the separated origami tiles (the concentration of K+ ion in the resulting mixture corresponded to 10 mM and the concentration of the crown ether corresponded to 50 mM). The resulting mixture was kept at room temperature overnight and the resulting origami dimer solution was purified by agarose electrophoretic separation of the origami structures. The D/A and B/C mixtures were kept at room temperature for 2 hours after mixing DNA origami monomer tiles D and A, B and C at a molar ratio of 1:1. For the assembly of DA and BC dimers, 1 μl of a 2 M potassium ion solution were added to 19 μl of the origami monomer solution (monomer tiles D/A, B/C) to yield a final K+ ion 39 ACS Paragon Plus Environment

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concentration of 100 mM. The mixture was kept at room temperature overnight to allow the formation of the dimers and then, obtained origami structures was purified using agarose electrophoresis. For the separation process of the dimers, 180 μl of a 55 mM solution of 18-crown-6-ether (including Mg2+, 8 mM) were added to the 20 μl of the origami dimers (the concentration of K+ ion in the resulting mixture corresponded to 10 mM and the concentration of the crown ether corresponded to 50 mM). The resulting mixture was kept at room temperature for two hours. It should be noted that the experimental details describing the reversible transitions of AB or CD dimers to the respective monomer tiles in the presence of K+ ions, and their reassembly into the original dimers in the presence of 18-crown-6-ether involve a dilution step where the K+-ion concentration is reduced to 10 mM and the crown ether concentration is maintained at 50 mM. Also, the reversible transitions of the monomer tiles D/A and B/C to the dimers DA and BC, in the presence of K+-ions and the reverse formation of the monomer tile requires similar steps. These dilution steps are essential since the origami tiles are unstable at crown ether concentration higher than 70 mM, and due to the fact that the competitive elimination of the K+ ions from the system require a ca. 5-fold higher concentration of the crown ether, compared to the concentration of K+-ions. That is, the dilution steps 40 ACS Paragon Plus Environment

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guided by the stability of the origami tiles and by the K+ ion/crown ether complex, prohibit the cycling of the systems in solution and the imaging of reliable statistical analysis of the resulting origami structures in the diluted systems. This is the reason of the electrophoretic separation of the tiles that allows the concentration of the origami structures in a small volume (~ 20 μl) for the reliable analysis of the respective origami structures. Furthermore, we note that the concentrations of K+-ions (100 mM) to simulate the separation of the AB and CD or to induce the formation of the DA and BC dimers from the D/A and B/C monomers as well as the concentration of 18-crown-6-ether (ca. 50 mM) to induce the respective dimerization/separation processes represent optimized value. A two-fold lowering of the concentration of K+ ions or crown ether results in a substantially lower yield of the respective transformations. For the reversible reconfiguration experiment of two dimers, the purified origami tiles of A, B, C and D were mixed at a molar ratio of 1:1:1:1 in 1× TAE buffer (Mg2+, 8 mM). The mixture was kept at room temperature overnight for the assembly of the two dimers of AB and CD and then purified using agarose electrophoresis. For the reconfiguration of the AB+CD dimers into DA+BC dimers, potassium ions (100 mM) were added to the mixture that was kept

at

room

temperature

overnight,

and

then

purified

using

agarose 41


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electrophoresis. For the reconfiguration of the DA+BC dimers into AB+CD dimers, a five-fold excess of 18-crown-6-ether (50 mM), as compared to potassium ions were added to the samples, and the mixture was kept at room temperature overnight, and subsequently purified using agarose electrophoresis. Electrophoretic experiments for purification of dimer tiles were performed with 1% agarose gel, at a constant voltage of 80 V at 25 ℃ for 2 hours (1× TAE buffer with 8 mM Mg2+) for the DNA origami dimers without G-quadruplex, or at a constant voltage of 35 V at 25 ℃ for 2 hours (1× TAE buffer with 8 mM Mg2+ and 100 mM K+) for the DNA origami dimers with G-Quadruplexes. Quantitative electrophoretic evaluation of monomer and dimer origami tiles separated on agarose gels was achieved by staining the separated bands with GelRed and quantitatively analysis the contents of the bands by comparing the intensities of the stained separated bands using the ImageJ analysis method. AFM imaging. For the AFM experiment, 2 µL of the respective origami tile samples was deposited on freshly peeled mica. After adsorbing for 5 minutes, the samples were imaged using the tapping mode in an aqueous buffer (Bruke, Multimode Nanoscope VIII) using SNL-10 probes. Characterization of the catalytic functions of origami tile dimers. For the switchable catalytic functions of the origami dimers mixtures, the mixture of 42 ACS Paragon Plus Environment

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dimers AB+CD was prepared as described above (300 µL). This volume was separated into three sub-volumes (100 µL): One sub-volume includes the AB+CD mixture. The second sub-volume was subjected to K+ ions to simulate the reconfiguration of AB+CD to DA+BC, as described above. The third sub-volume was subjected to two sequential treatment consisting of K+ ions and 18-crown-6-ether to induce the stepwise reconfiguration of AB+CD → DA+BC → AB+CD. To each of these sub-samples, a five-fold concentration of the helper strand T and a five-fold concentration of the Mg2+-ion-dependent DNAzyme subunits were added. The different sub-samples were purified as described above.

For

evaluating

the

catalytic

rates

of

the

different

samples,

the

concentrations of the respective origami dimers mixtures were adjusted to a fixed

concentration

of

4.5

nM.

To

each

of

these

samples,

the

fluorophore/quencher-modified DNAzyme substrate (3 µM), hemin (120 nM), Amplex Red (100 µM), and H2O2 (5 mM), were added. To probe the switchable catalytic functions of the systems, the fluorescence intensities of FAM (at 518 nm) and Resorufin (at 585 nm) in each of the samples were monitored for the Mg2+-ion-dependent DNAzyme after a time interval of six hours, and for the hemin/G-quarduplex generated Resorufin after a time interval of 10 minutes. The switchable catalytic functions were repeated three times. 43 ACS Paragon Plus Environment

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ASSOCIATED CONTENT Supporting Information. AFM images corresponding to the analysis of the triggered transitions of the different dimer origami structures and statistical analysis of the yields of the origami structures in the different systems, quantitative gel electrophoresis experiments of the origami structures in the different systems, and the detailed evaluation of the free energy changes associated with the conversion of the dimers mixture AB+CD into BC+DA are provided. Also, the detailed description of the assembly and operation of the programmed switchable catalytic functions driven by the interconversion of the origami dimer structures are included. In addition, the fluorescence spectra of the fluorescent products generated by the triggered interconverting origami dimer structure are shown. A detailed list of all sequences involved in the assembly of the different origami tiles, and the functional sequences tethered to the different tiles are provided. The authors declare no competing financial interests. AUTHOR INFORMATION Corresponding Author 44 ACS Paragon Plus Environment

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*E-mail: [email protected]; phone: +972-2-6585272; fax: +972-2-6527715. ACKNOWLEDGMENT Parts of this research are supported by the Volkswagen Foundation, Germany and by the Israel Science Foundation. REFERENCES (1) Wang, F.; Lu, C.-H.; Willner, I. From Cascaded Catalytic Nucleic Acids to Enzyme−DNA Nanostructures: Controlling Reactivity, Sensing, Logic Operations, and Assembly of Complex Structures. Chem. Rev. 2014, 114, 2881−2941. (2) Lin, M.; Wang, J.; Zhou, G.; Wang, J.; Wu, N.; Lu, J.; Gao, J.; Chen, X.; Shi, J.; Zuo, X.; Fan, C. Programmable Engineering of a Biosensing Interface with Tetrahedral DNA Nanostructures for Ultrasensitive DNA Detection. Angew.

Chem. Int. Ed. 2015, 54, 2151–2155. (3) Lu, C.-H.; Cecconello, A.; Qi, X.J.; Wu, N.; Jester, S.S.; Famulok, M.; Matthies,

M.;

Schmidt,

T.L.;

Willner,

I.

Switchable

Reconfiguration

of

a

Seven-Ring Interlocked DNA Catenane Nanostructure. Nano Lett. 2015, 15, 7133−7137. (4) Bath, J.; Turberfield, A. J. DNA Nanomachines. Nat. Nanotechnol. 2007, 2, 275−284.


ACS Nano 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 46 of 55

(5) Yurke, B.; Turberfield, A. J.; Jr, A. P. M.; Simmel, F. C.; Neumann, J. L. A DNA-Fuelled Molecular Machine Made of DNA. Nature 2000, 406, 605−608. (6) Omabegho, T.; Sha, R.; Seeman, N. C. A Bipedal DNA Brownian Motor with Coordinated Legs. Science 2009, 324, 67−71. (7) Wang, Z.-G.; Elbaz, J.; Willner, I. DNA Machines: Bipedal Walker and Stepper. Nano Lett. 2011, 11, 304–309. (8)

Wang,

F.;

Liu,

X.;

Willner,

I.

DNA

Switches:

From

Principles

to

Applications. Angew. Chem. Int. Ed. 2015, 54, 1098–1129. (9) Elbaz, J.; Cecconello, A.; Fan, Z.; Govorov, A. O.; Willner, I. Powering the Programmed Nanostructure and Function of Gold Nanoparticles with Catenated DNA Machines. Nat. Commun. 2013, 4, 2000. (10) Kuzyk, A.; Schreiber, R.; Fan, Z.; Pardatscher, G.; Roller, E. M.; Hӧgele, A.; Simmel, F. C.; Govorov, A. O.; Liedl, T. DNA-Based Self-Assembly of Chiral Plasmonic Nanostructures with Tailored Optical Response. Nature 2012, 483, 311−314. (11) Liu, M.; Fu, J.; Hejesen, C.; Yang, Y.; Woodbury, N. W.; Gothelf, K.; Liu, Y.; Yan, H. A DNA Tweezer-Actuated Enzyme Nanoreactor. Nat. Commun. 2013, 4, 2127.


Page 47 of 55 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Nano

(12) Braun, E.; Eichen, Y.; Sivan, U.; Ben-Yoseph, G. DNA-Templated Assembly and Electrode Attachment of a Conducting Silver Wire. Nature 1998,

391, 775−778. (13) Wilner, O. I.; Shimron, S.; Weizmann, Y.; Wang, Z.-G.; Willner, I. Self-Assembly

of

Enzymes

on

DNA

Scaffolds:

En

Route

to

Biocatalytic

Cascades and the Synthesis of Metallic Nanowires. Nano Lett. 2009, 9, 2040−2043. (14) Zhao, Z.; Liu, Y.; Yan, H. Organizing DNA Origami Tiles into Larger Structures Using Preformed Scaffold Frames. Nano Lett. 2011, 11, 2997−3002. (15) Saccà, B.; Niemeyer, C. M. DNA Origami: The Art of Folding DNA.

Angew. Chem. Int. Ed. 2012, 51, 58−66. (16) Endo, M.; Sugiyama, H. Single-Molecule Imaging of Dynamic Motions of Biomolecules in DNA Origami Nanostructures Using High-Speed Atomic Force Microscopy. Acc. Chem. Res. 2014, 47, 1645−1653. (17) Pfeifer, W.; Saccà, B. From Nano to Macro through Hierarchical Self-Assembly: The DNA Paradigm. ChemBioChem 2016, 17, 1063−1080. (18) Hong, F.; Zhang, F.; Liu, Y.; Yan, H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem. Rev. 2017, 117, 12584−12640.


ACS Nano 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 48 of 55

(19) Dai, Z.; Leung, H. M.; Lo, P. K. Stimuli-Responsive Self-Assembled DNA Nanomaterials for Biomedical Applications. Small 2017, 13, 1602881. (20) Rothemund, P. W. K. Folding DNA to Create Nanoscale Shapes and Patterns. Nature 2006, 440, 297−302. (21) Andersen, E. S.; Dong, M.; Nielsen, M. M.; Jahn, K.; Lind-Thomsen, A.; Mamdouh, W.; Gothelf, K. V.; Besenbacher, F.; Kjems, J. DNA Origami Design of

Dolphin-Shaped

Structures

with

Flexible

Tails.

ACS

Nano

2008,

2,

1213−1218. (22) Andersen, E. S.; Dong, M.; Nielsen, M. M.; Jahn, K.; Subramani, R.; Mamdouh, W.; Golas, M. M.; Sander, B.; Stark, H.; Oliveira, C. L. P.; Pedersen, J. S.; Birkedal, V.; Besenbacher, F.; Gothelf, K. V.; Kjems, J. Self-Assembly of a Nanoscale DNA Box with a Controllable Lid. Nature 2009,

459, 73−76. (23) Dietz, H.; Douglas, S. M.; Shih, W. M. Folding DNA into Twisted and Curved Nanoscale Shapes. Science 2009, 325, 725−730. (24) Douglas, S. M.; Dietz, H.; Liedl, T.; Högberg, B.; Graf, F.; Shih, W. M. Self-Assembly of DNA into Nanoscale Three-Dimensional Shapes. Nature 2009,

459, 414−418.


Page 49 of 55 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Nano

(25) Torring, T.; Voigt, N. V.; Nangreave, J.; Yan, H.; Gothelf, K. V. DNA Origami: A Quantum Leap for Self-Assembly of Complex Structures. Chem.

Soc. Rev. 2011, 40, 5636−5646. (26) Simmel, S. S.; Nickels, P. C.; Liedl, T. Wireframe and Tensegrity DNA Nanostructures. Acc. Chem. Res. 2014, 47, 1691−1699. (27) Rajendran, A.; Endo, M.; Katsuda, Y.; Hidaka, K.; Sugiyama, H. Programmed Two-Dimensional Self-Assembly of Multiple DNA Origami Jigsaw Pieces. ACS Nano 2011, 5, 665−671. (28) Yang, Y.; Endo, M.; Hidaka, K.; Sugiyama, H. Photo-Controllable DNA Origami Nanostructures Assembling into Predesigned Multiorientational Patterns.

J. Am. Chem. Soc. 2012, 134, 20645−20653. (29) He, X.; Sha, R.; Zhuo, R.; Mi, Y.; Chaikin, P. M.; Seeman, N. C. Exponential Growth and Selection in Self-Replicating Materials from DNA Origami Rafts. Nat. Mater. 2017, 16, 993−997. (30) Voigt, N. V.; Tørring, T.; Rotaru, A.; Jacobsen, M. F.; Ravnsbæk, J. B.; Subramani, R.; Mamdouh, W.; Kjems, J.; Mokhir, A.; Besenbacher, F.; Gothelf, K. V. Single-Molecule Chemical Reactions on DNA Origami. Nat. Nanotechnol. 2010, 5, 200−203.


ACS Nano 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 50 of 55

(31) Yoshidome, T.; Endo, M.; Kashiwazaki, G.; Hidaka, K.; Bando, T.; Sugiyama, H. Sequence-Selective Single-Molecule Alkylation with a Pyrrole– Imidazole Polyamide Visualized in a DNA Nanoscaffold. J. Am. Chem. Soc. 2012, 134, 4654−4660. (32) Udomprasert, A.; Bongiovanni, M. N.; Sha, R. J.; Sherman, W. B.; Wang, T.; Arora, P. S.; Canary, J. W.; Gras, S. L.; Seeman, N. C. Amyloid Fibrils Nucleated and Organized by DNA Origami Constructions. Nat. Nanotechnol. 2014, 9, 537−541. (33) Wang, Z.-G.; Liu, Q.; Ding, B. Shape-Controlled Nanofabrication of Conducting Polymer on Planar DNA Templates. Chem. Mater. 2014, 26, 3364−3367. (34) Ding, B.; Deng, Z.; Yan, H.; Cabrini, S.; Zuckermann, R. N.; Bokor, J. Gold Nanoparticle Self-Similar Chain Structure Organized by DNA Origami. J.

Am. Chem. Soc. 2010, 132, 3248−3249. (35) Wilner, O. I.; Willner, I. Functionalized DNA Nanostructures. Chem. Rev. 2012, 112, 2528−2556. (36) Liu, Y.; Lin, C.; Li, H.; Yan, H. Aptamer-Directed Self-Assembly of Protein Arrays on a DNA Nanostructure. Angew. Chem. Int. Ed. 2005, 44, 4333−4338. 50 ACS Paragon Plus Environment

Page 51 of 55 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Nano

(37) Zheng, J.; Constantinou, P. E.; Micheel, C.; Alivisatos, A. P.; Kiehl, R. A.;

Seeman,

N.

C.

Two-Dimensional

Nanoparticle

Arrays

Show

the

Organizational Power of Robust DNA Motifs. Nano Lett. 2006, 6, 1502−1504. (38) Kuzuya, A.; Numajiri, K.; Komiyama, M. Accommodation of a Single Protein Guest in Nanometer-Scale Wells Embedded in a “DNA Nanotape”.

Angew. Chem. Int. Ed. 2008, 47, 3400−3402. (39) Sharma, J.; Chhabra, R.; Cheng, A.; Brownell, J.; Liu, Y.; Yan, H. Control

of

Self-Assembly

of

DNA

Tubules

Through

Integration

of

Gold

Nanoparticles. Science 2009, 323, 112−116. (40) Fu, J.; Liu, M.; Liu, Y.; Woodbury, N. W.; Yan, H. Interenzyme Substrate Diffusion for an Enzyme Cascade Organized on Spatially Addressable DNA Nanostructures. J. Am. Chem. Soc. 2012, 134, 5516−5519. (41) Gu, H.; Chao, J.; Xiao, S.-J.; Seeman, N. C. A Proximity-Based Programmable DNA Nanoscale Assembly Line. Nature 2010, 465, 202−205. (42) Rajendran, A.; Endo, M.; Sugiyama, H. Single-Molecule Analysis Using DNA Origami. Angew. Chem. Int. Ed. 2012, 51, 874−890. (43) Endo, M.; Takeuchi, Y.; Suzuki, Y.; Emura, T.; Hidaka, K.; Wang, F.; Willner, I.; Sugiyama, H. Single-Molecule Visualization of the Activity of a Zn2+-Dependent DNAzyme. Angew. Chem. Int. Ed. 2015, 54, 10550−10554. 51 ACS Paragon Plus Environment

ACS Nano 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 52 of 55

(44) Acuna, G. P.; Möller, F. M.; Holzmeister, P.; Beater, S.; Lalkens, B.; Tinnefeld, P. Fluorescence Enhancement at Docking Sites of DNA-Directed Self-Assembled Nanoantennas. Science 2012, 338, 506−510. (45) Xu, L.; Ma, W.; Wang, L.; Xu, C.; Kuang, H.; Kotov, N. A. Nanoparticle Assemblies:

Dimensional

Transformation

of

Nanomaterials

and

Scalability.

Chem. Soc. Rev. 2013, 42, 3114−3126. (46) Lan, X.; Chen, Z.; Dai, G.; Lu, X.; Ni, W.; Wang, Q. Bifacial DNA Origami-Directed

Discrete,

Three-Dimensional,

Anisotropic

Plasmonic

Nanoarchitectures with Tailored Optical Chirality. J. Am. Chem. Soc. 2013, 135, 11441−11444. (47) Shen, X.; Zhan, P.; Kuzyk, A.; Liu, Q.; Asenjo-Garcia, A.; Zhang, H.; Garcia de Abajo, F. J.; Govorov, A.; Ding, B.; Liu, N. 3D Plasmonic Chiral Colloids. Nanoscale 2014, 6, 2077−2081. (48) Jiang, Q.; Liu, Q.; Shi, Y.; Wang, Z.-G.; Zhan, P.; Liu, J.; Liu, C.; Wang, H.; Shi, X.; Zhang, L.; Sun, J.; Ding, B.; Liu, M. Stimulus-Responsive Plasmonic Chiral Signals of Gold Nanorods Organized on DNA Origami. Nano

Lett. 2017, 17, 7125−7130. (49) Cecconello, A.; Besteiro, L. V.; Govorov, A. O.; Willner, I. Chiroplasmonic DNA-Based Nanostructures. Nat. Rev. Mater. 2017, 2, 17039. 52 ACS Paragon Plus Environment

Page 53 of 55 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Nano

(50) Kuzyk, A.; Schreiber, R.; Zhang, H.; Govorov, A. O.; Liedl, T.; Liu, N. Reconfigurable 3D Plasmonic Metamolecules. Nat. Mater. 2014, 13, 862−866. (51) Kuzyk, A.; Yang, Y.; Duan, X.; Stoll, S.; Govorov, A. O.; Sugiyama, H.; Endo, M.; Liu, N. A Light-Driven Three-Dimensional Plasmonic Nanosystem that Translates Molecular Motion into Reversible Chiroptical Function. Nat. Commun. 2016, 7, 10591. (52) Douglas, S. M.; Bachelet, I.; Church, G. M. A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads. Science 2012, 335, 831−834. (53) Takenaka, T.; Endo, M.; Suzuki, Y.; Yang, Y.; Emura, T.; Hidaka, K.; Kato,

T.;

Miyata,

T.;

Namba,

K.;

Sugiyama,

H.

Photoresponsive

DNA

Nanocapsule Having an Open/Close System for Capture and Release of Nanomaterials. Chem. - Eur. J. 2014, 20, 14951−14954. (54) Wu, N.; Willner, I. DNAzyme-Controlled Cleavage of Dimer and Trimer Origami Tiles. Nano Lett. 2016, 16, 2867−2872. (55) Wu, N.; Willner, I. Programmed Dissociation of Dimer and Trimer Origami Structures by Aptamer-Ligand Complexes. Nanoscale 2017, 9, 1416−1422. (56)

Wu,

N.;

Willner,

I.

pH-Stimulated

Reconfiguration

and

Structural

Isomerization of Origami Dimer and Trimer Systems. Nano Lett. 2016, 16, 6650−6655. 53 ACS Paragon Plus Environment

ACS Nano 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 54 of 55

(57) Wang, J.; Zhou, Z.; Yue, L.; Wang, S.; Willner, I. Switchable Triggered Interconversion and Reconfiguration of DNA Origami Dimers and Their Use for Programmed Catalysis. Nano Lett. 2018, 18, 2718−2724. (58)

Tam,

D.

Y.;

G-Quadruplex-Mediated

Leung,

H.

Molecular

M.;

Switching

Chan, of

M.

S.;

Lo,

Self-Assembled

P. 3D

K. DNA

Nanocages. ChemNanoMat 2017, 3, 750−754. (59) Lu, C.-H.; Qi, X.-J.; Orbach, R.; Yang, H.-H.; Mironi-Harpaz, I.; Seliktar, D.; Willner, I. Switchable Catalytic Acrylamide Hydrogels Cross-Linked by Hemin/G-Quadruplexes. Nano Lett. 2013, 13, 1298−1302. (60) Kahn, J. S.; Trifonov, A.; Cecconello, A.; Guo, W.; Fan, C.; Willner, I. Integration

of

Switchable

DNA-Based

Hydrogels

with

Surfaces

by

the

Hybridization Chain Reaction. Nano Lett. 2015, 15, 7773−7778. (61) Zhang, Z.; Wang, F.; Sohn, Y. S.; Nechushtai, R.; Willner, I. Gated Mesoporous

SiO2

Nanoparticles

Using

K+-Stabilized

G-Quadruplexes.

Adv.

Funct. Mater. 2014, 24, 5662−5670. (62) Ren, J.; Hu, Y.; Lu, C.-H.; Guo, W.; Aleman-Garcia, M. A.; Ricci, F.; Willner, I. pH-Responsive and Switchable Triplex-Based DNA Hydrogels. Chem.

Sci. 2015, 6, 4190−4195.


Page 55 of 55 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

ACS Nano

(63) Aleman-Garcia, M. A.; Orbach, R.; Willner, I. Ion-Responsive Hemin– G-Quadruplexes for Switchable DNAzyme and Enzyme Functions. Chem. - Eur.

J. 2014, 20, 5619−5624. (64) Liu, X.; Niazov-Elkan, A.; Wang, F.; Willner, I. Switching Photonic and Electrochemical Functions of a DNAzyme by DNA Machines. Nano Lett. 2013,

13, 219−225.

BRIEFS A mixture consisting of two origami dimers AB+CD is reversibly reconfigured into

the

dimers

mixture

DA+BC,

leading

to

the

programmed

switchable

activation of two different DNAzymes. TABLE OF CONTENTS GRAPHIC


Triggered Reversible Reconfiguration of G-Quadruplex-Bridged

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