Metal Nanoparticle-Functionalized DNA Tweezers: From Mechanically

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Metal Nanoparticle-Functionalized DNA Tweezers: From Mechanically Programmed Nanostructures to Switchable Fluorescence Properties Simcha Shimron, Alessandro Cecconello, Chun-Hua Lu, and Itamar Willner Nano Lett., Just Accepted Manuscript • DOI: 10.1021/nl4017539 • Publication Date (Web): 01 Jul 2013 Downloaded from http://pubs.acs.org on July 2, 2013

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Metal Nanoparticle-Functionalized DNA Tweezers: From Mechanically Programmed Nanostructures to Switchable Fluorescence Properties

Simcha Shimron‡, Alessandro Cecconello‡, Chunhua Lu and Itamar Willner* The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel ‡These authors contributed equally to this work. *All correspondence should be addressed to e-mail: [email protected]

E-mail: [email protected]; Fax: (+972) 2-652-7715 Tel: (+972) 2-658527 2

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Introduction DNA nanotechnology1-5 is a rapidly developing research field that implements the information encoded in the nucleic acid-base sequence to develop nanostructured sensor systems,6 one-, two- and three-dimensional nanostructures,7-22 DNA machines,23-27 and functional DNA computing nanostructures.28-30 Among the different DNA machines, the mechanical, fuelled, activation of “tweezers”,31,32 “walkers”,4,27,33-36 a “crane”,37 and other molecular devices23-26,38,39 were reported. Specifically, the opening and closure of DNA tweezers nanostructures were demonstrated by using: nucleic acid strands as fuels/anti-fuels, metal-ions as fuels and ligands as anti-fuels, DNAzymes, pH-signals, and photonic stimuli as the activators of the tweezers devices.31,32,40 The opening and closure of tweezers were applied to develop logic gates41-45 and to construct finite-state logic machines.46

The

programmed assembly of DNA-aided metal nanoparticle nanostructures in quasi-crystalline arrangements47

and

one-dimensional,48,49

two-dimensional50,51

or

three-dimensional

structures,52-55 was also accomplished. Here, we report on the functionalization of DNA tweezers with Au NPs and we present the switchable and programmed control of the Au NP nanostructures upon opening or closure of the tweezers. We further construct a set of hybrid tweezers consisting of a single Au NP and a single fluorophore, linked to spatially dictated positions. We demonstrate the reversible and cyclic fluorescence quenching or fluorescence enhancement phenomenon upon the dynamic opening / closure of the different tweezers.

Results Figure 1(A) depicts the Au NP-functionalized closed “tweezers”. 10 nm Au NPs each functionalized with single-stranded nucleic acids (1) or (2), are used as arms (for the detailed synthetic protocol and for the purification and assembly of the DNA/Au NP hybrid constructs, see Figure S1 and Methods in the Supporting Information). They are bridged by

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the nucleic acid (3), which is conjugated as a single strand to the 5 nm Au NPs. The tweezers are further bridged by the nucleic acid (4) to yield the closed configuration of the tweezers. Figure 1(B) shows representative STEM images. Figures S2-S4, Supporting Information, show three different representative large areas of STEM images of the closed tweezers. From these images we estimate the yield of the complete three nanoparticle structures to be 60% and the yield of the closed Au NP-functionalized tweezers to be 80%. The 20% of the open Au NP structures may be attributed to structures that are not bridged by (4) or to structures that are distorted on the grid support and therefore a confident definition of the structures, as closed configuration, is prevented. Treatment of the closed tweezers with the anti-fuel (5), which is complementary to (4), results in the strand displacement of (4) and the opening of the tweezers, Figure 1(C). The STEM images of representative Au NP structures, generated by the open tweezers, are presented in Figure 1(D). The distance separating the two 10 nm Au NPs, in the open configuration, is in the range of 3 nm to 15 nm, consistent with the flexible structure of the tweezers template. Figures S5 and S6 depict a series of large areas of STEM imaged structures of the open tweezers system. The yield of the complete three-NP tweezers-templated structures is estimated to be 64%, and the yield of three Au NPs associated with the open tweezers template is ca. 80%.

The structure of the Au NPs

associated with the tweezers could be reversibly switched between the closed state tweezers and the open state tweezers by the addition of the fuel strand (4) or the anti-fuel strand (5), respectively. We find, however, that the yield of the respective Au NP structures drops by ca. 5% to 10% upon each cycle. Fluorophores associated with metal (plasmonic) NPs exhibit interesting and unique photophysical properties. While intimate contact between the fluorophore and the metal NPs results in effective quenching of the fluorophore, short-distances between the fluorophore and the NPs surface, where the fluorophore is positioned in the plasmon field of the NP, result in


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fluorescence enhancement of the fluorophore.

The specific distance at which surface

enhanced fluorescence occurs is controlled by several parameters, including the size of the NPs, the fluorescence quantum yield of the fluorophore, the refractive index of the medium, the prolate aspect ratio and the distance between the fluorophore and the Au NPs.56 The binding of a fluorophore to the tweezers, modified with a single Au NP, could probe the “mechanical” control of the distances separating the fluorophore and the metal NP and provide a means to modulate the fluorescence properties of the system upon opening and closure of the tweezers structure. Furthermore, by changing the position of the fluorophore on the tweezers template, different separating distances between the fluorophore and the Au NP surface in the closed and open tweezers configurations are generated. Thus, one might anticipate that in the different tweezers structures, control over the fluorescence properties of the systems will be achieved, and eventually, the mechanically induced generation of enhanced fluorescence may be detected in one (or more) of the systems. The theoretical simulations of the distance dependent fluorescence yields of the fluorophore-functionalized tweezers, modified with a single 10 nm Au NP, is described in detail in the Supporting Information. It should be noted that the fluorescence quantum yields of the fluorophore Cy3, used in the present study, are sensitive to the buffer composition and its anchoring site to the DNA structure. The respective fluorescence quantum yields are discussed in the supporting material. Figure 2(AI) depicts a tweezers configuration, (T1), where the ends of the arms (1) and (2a) are labeled with the Au NP and fluorophore (Cy3), respectively. The tweezers are switched between the closed state and the open state by applying the respective fuel or antifuel strands (4) or (5); dc and do define the estimated range of distances between the fluorophore Cy3 and the Au NP surface in the respective states. Figure 2(BI) shows the switchable fluorescence intensities of Cy3 (at λ = 564nm) upon cycling the system between the two states. The experiment is initiated with the open tweezers. At the time marked with


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(a), the fuel strand (4) is added to the system, resulting in quenching of the fluorescence. At point (b), the anti-fuel strand (5) is added to the system, restoring the initial, less quenched, fluorescence of the fluorophore. By the cyclic addition of the fuel-strand and anti-fuel strand the fluorescence of the system is cycled between low and high fluorescence intensity values. The estimated distances separating the fluorophore and the Au NP in the closed and open configurations are shown in Table 1. The second tweezers configuration (T2) is depicted in Figure 2(AII) where the characteristic distance intervals between the fluorophore and the Au NP, in the open and closed states, are marked do and dc, respectively. The fluorophore is positioned in the middle of arm (2b), (11 bases from the 3’ end), while the Au NP is linked to the 5’-end of arm (1). The experiment is initiated with the open configuration of the tweezers and at the time marked with (a), the fuelstrand is added to the system. In contrast to the previous system, the closure of the tweezers results in a ca. 12-18% enhancement in the fluorescence of the fluorophore. At point (b) the anti-fuel strand (5) is added to the system, leading to the opening of the tweezers and the regeneration of the lower fluorescence intensity of the system, Figure 2(BII).

By the

reversible addition of the fuel and anti-fuel strands, the tweezers are cycled between closed and open states, leading to switchable low (open) and enhanced (closed, 12-18% increase) fluorescence responses of the system, Figure 2(BII). The estimated distances separating the fluorophore and the Au NP in the different states of the system are summerized in Table 1. Finally, the third tweezers system, (T3), was constructed, Figure 2(AIII). In this system the fluorophore was linked to the 3’-end of the bridging arm (3b), and the 10 nm Au NP was positioned, as previously described, on the 5’-end of arm (1). In these tweezers the distance ranges separating Cy3 and the Au NP surface, dc and do, in the respective closed and open states, are determined, mainly, by the rigidity of the nucleic acid connecting them. When the tweezers are in the open state, the nucleic acid linker is single-stranded, thus allowing a


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higher degree of freedom to that part of the structure, due to a lower rigidity and, as a consequence, leading to a shortening of the average fluorophore-Au NP separating distance. When the tweezers are in the closed state, the double-stranded arm is more rigid and the fluorophore-Au NP separating distance is longer. The switchable fluorescence features of this system are shown in Figure 2(BIII). While the open tweezers system reveals low fluorescence, the fueled closure of the tweezers reveals an increased fluorescence (ca. 30%). The estimated distances separating the fluorophore and the Au NP are given in Table 1. The expected distance-dependent fluorescence of the fluorophore, (Cy3), in the presence of the 10 nm Au NP was then theoretically calculated,56 Figure 2(C). The reference fluorescence quantum yield in the “tweezers” structures T1 and T3 (in the absence of the Au NPs) are identical (ca. 1%), and, hence, the theoretical distance-dependent fluorescence quantum yields in the Cy3/Au NP (10nm) “tweezers” structures T1 and T3 are identical. In turn, the quantum yield of the Cy3, internally modified in the tweezers structure T2, is only 0.6% to 0.5%,

57

and thus, a shift in the distance-dependent fluorescence quantum yields in the

Cy3/Au NPs (10nm), T2, is theoretically predicted. (For the details of the calculations see Supporting Information). Table 1 summarizes the estimated geometric distances separating the fluorophore (Cy3) from the 10 nm Au NPs in the open (dO) and closed (dC) states of the tweezers T1, T2 and T3. For “tweezer” T1, in the closed state, the distance separating the fluorophore from the Au NP is ca. 2 nm, a distance that, theoretically, predicts quenching of the fluorophore. In contrast, in the open tweezers, the distance separating the fluorophore from the Au NP is ca. 15 nm, implying no quenching. Thus, the experimental results are consistent

with

the

theoretically-calculated

fluorescence

quantum

yields

of

the

fluorophore/Au NP at the respective geometrically estimated distances, Figure 2(CI). For tweezers T2, the theoretical prediction for the open tweezers is that at a separation-distance of ca. 11 nm there is almost no effect on the fluorescence quantum yield as compared to the


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reference quantum yield of the fluorophore. For the closed tweezers configuration an enhanced fluorescence quantum yield should be observed, where a separation distance between the fluorophore and the Au NP surface of ca. 4 nm exists. Indeed, the experimental results are consistent with these theoretical predictions. For the tweezers T3, the open and closed configurations of the tweezers lead to separation distances of ൏2.4 nm and 2.4 nm between the fluorophore and the Au NP surface, respectively. These distances are both in the fluorescence quenching domain, but the theoretical prediction suggests that the closed state should reveal a lower degree of quenching, consistent with the experimental results. It should be noted that the distance separating the fluorophore and the Au NP in the open tweezers T1 and T2 is sufficiently large to yield distance independent fluorescence values, as compared to the reference fluorescence, while the lower fluorescence seen in the open state of T3, can be attributed to a shorter average distance between the fluorophore and the Au-NP due to a higher degree of flexibility of the single stranded region between the fluorophore and the AuNP.

By applying a bifunctional 10 nm Au NP, modified with two nucleic acids (1), a double tweezers, consisting of 2 fluorophores and 1 Au NP, was constructed. Figure 3(A) shows the double tweezers structure consisting of two T1-type tweezers. By switching the molecular DNA template between the open and closed states, the fluorophore undergoes cyclic transitions between the distance independent fluorescence (open state) and quenched fluorescence (closed state), respectively, similar to the single T1 tweezers system (Figure 3(B). For the double-tweezers system consisting of T3-type tweezers see Supporting Information, Figure S7). Furthermore, one may implement Au NPs functionalized with two nucleic acids and, particularly, two different sized Au NPs modified each with two nucleic acids, as bridging


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arms for the self-assembly of oligomeric or polymeric tweezers that could be reversibly cycled between the open and closed configurations, Figure S8(A). Figure S8(B) shows an image of the open configuration of a four-tweezers oligomer combining 10 nm and 5 nm NPs. Figure S8(C) shows an example of the closed configuration of an eleven-tweezers oligomers. Although the results demonstrate that by using bifunctional nucleic acid modified Au NPs, the synthesis of tweezers structures of enhanced complexity is feasible, one should realize the future challenges in this area of DNA nanotechnology. The diversity of the oligomer structures and the difficulties to separate sufficient quantities of pure and defined structures is, at present, a fundamental obstacle.

Conclusions To conclude, the present study has introduced the DNA tweezers as a functional machine for the switchable “mechanical” programming of Au NP structures. Furthermore, through the positioning of a fluorophore/Au NP pair on the DNA tweezers, the “mechanical” and switchable control, over the fluorophore quenching or surface enhanced fluorescence, was demonstrated by the dynamic opening or closure for the respective structures of the tweezers. The experimental results were consistent with the theoretically predicted distances separating the fluorophore and the Au NP surfaces in the different structures.

The extent of the

fluorescence enhancement is relatively small (10% to 20%), depending on the tweezers structure. The relatively small fluorescence enhancement value is mainly attributed to the size of the Au NPs and the use of larger NPs would enhance the effects. Nonetheless, the difficulties in synthesizing and purifying single nucleic acid modified Au NPs, larger than 10 nm, limit, at the present time, the performance of such experiments. It should be noted that the enhanced fluorescence might also be affected by excitation enhancement or scattering


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phenomena. However, since we use 10 nm sized NPs, the contributions of these two effects should be small.58,59

Acknowledgement: This study is supported by the European Research Council (ERC).

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Figure captions Figure 1. Mechanical control of the three-Au NP nanostructure by means of opening and closure of the DNA tweezers using fuel/antifuel strands; (A) Scheme of the three Au NP/DNA closed tweezers; (B) representative STEM images of the three Au NPs associated with the closed state of the tweezers; (C) Scheme of the three Au NP/DNA open tweezers; (D) representative STEM images of the three Au NPs associated with the open state of the tweezers.

Figure 2. (A) Mechanical control of the fluorescence properties of different fluorophore/Au NP functionalized tweezers by the cyclic opening and closure of the tweezers by means of fuel/antifuel DNA strands. (I) The Au NP (10 nm) and the fluorophore are positioned at the ends of strands (1) and (2a), respectively. (II) The Au NP is positioned at the 5’ end of (1), the fluorophore is positioned internally in strand (2b). (III) The Au NP is positioned at the 5’ end of strand (1), the fluorophore is positioned at the 3’ end of strand (3b). do and dc correspond to the distances separating the fluorophore and the Au NP in the open and closed states, respectively. The distances are estimated by geometrical considerations, see table 1. (B) Time-dependent cyclic fluorescence spectra occurring upon closure and opening of the respective tweezers: (I) open tweezers reveals high fluorescence, closed tweezers reveals low fluorescence; (II) open configuration shows low fluorescence, closed configuration shows enhanced fluorescence; (III) open configuration shows low fluorescence, closed configuration shows high fluorescence. For all systems (a) corresponds to the triggering of the closed state of the tweezers and (b) to the triggering of the open state of the tweezers. The lines (a) and (b) indicate the starting points of the time intervals where the fuel (4) or the antifuel (5) were added, respectively. The mechanically driven reversible transitions of the tweezers are always initiated in the open state with no fuel (4) added. (C) Correlation of the fluorescence patterns observed upon opening and closing of the tweezers, with the 13 Environment ACS Paragon Plus

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theoretically predicted fluorescence/fluorophore-Au NP separating distances in the three different tweezers configurations.

Figure 3. (A) Schematic opening and closure of a double tweezers comprising a Au NP and two fluorophore units using fuel/antifuel DNA strands. (B) Time dependent fluorescence changes corresponding to the cyclic closure and opening of the tweezers structure: (a) low fluorescence, closed configuration; (b) high fluorescence, open configuration.

TOC text: DNA tweezers lead to programmed arrangements of metal nanoparticles and to switchable fluorescence properties.


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Figure 1


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Figure 2


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Figure 3


Nano Letters

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TOC


Page 18 of 19

Page 19 of 19

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

Nano Letters

T1

T2

T3

Open state (dO)

10-18 nm

9-14 nm

൏ 2.4 nm

Closed state (dC)

1-2 nm

3.8-4 nm

2.4 nm

Table 1

Table 1: Estimated geometrical distances separating the fluorophore (Cy3) and Au NP surface in the different configurations of tweezers T1, T2 and T3.


Metal Nanoparticle-Functionalized DNA Tweezers: From Mechanically

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