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Tunable fluorescence of a semiconducting polythiophene positioned on DNA origami Johanna Zessin, Franziska Fischer, Andreas Heerwig, Alfred Kick, Susanne Boye, Manfred Stamm, Anton Kiriy, and Michael Mertig Nano Lett., Just Accepted Manuscript • DOI: 10.1021/acs.nanolett.7b02623 • Publication Date (Web): 26 Jul 2017 Downloaded from http://pubs.acs.org on July 27, 2017

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Tunable fluorescence of a semiconducting polythiophene positioned on DNA origami Johanna Zessin1,2, Franziska Fischer1,2, Andreas Heerwig2,3, Alfred Kick3, Susanne Boye1, Manfred Stamm1, Anton Kiriy1, Michael Mertig2,3,* 1

Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany

2

Physikalische Chemie, Mess- und Sensortechnik, Technische Universität Dresden, 01062

Dresden, Germany 3

Kurt-Schwabe Institut für Mess- und Sensortechnik e.V. Meinsberg, 04736 Waldheim, Germany

*

Corresponding author:

Email: [email protected] Phone/Fax: +49 351 479 40 294/299

1 ACS Paragon Plus Environment

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Abstract. A novel approach for the integration of π-conjugated polymers (CPs) into DNA-based nanostructures is presented. Using the controlled Kumada catalyst-transfer polycondensation, well-defined thiophene-based polymers with controllable molecular weight, specific end groups and water-soluble oligoethylene glycol-based side chains were synthesized. The end groups were used for the easy but highly efficient click chemistry-based attachment of end-functionalized oligodeoxynucleotides (ODNs) with predesigned sequences. As demonstrated by surface plasmon resonance spectroscopy, the prepared block copolymers (BCPs), P3(EO)3T-b-ODN, comprising different ODN lengths and specific or repetitive sequences, undergo specific hybridization with complementary, thiol-functionalized ODNs immobilized on a gold surface. Furthermore, the site-specific attachment of the BCPs to DNA origami structures is studied. We demonstrate that a nanoscale object, i.e., a single BCP with a single ODN handle, can be directed and bound to the DNA origami with reasonable yield, site-specificity and high spatial density. Based on these results, we are able to demonstrate for the first time that optical properties of CP molecules densely immobilized on DNA origami can be locally fine-tuned by controlling the attractive π- π-stacking interactions between the CPs. In particular, we show that the fluorescence of the immobilized CP molecules can be significantly enhanced by surfactant-induced break-up of π-π-stacking interactions between the CP’s backbones. Such molecular control over the emission intensity of the CPs can be valuable for the construction of sophisticated switchable nanophotonic devices and nanoscale biosensors.

Key words: conjugated polymers, block copolymers, DNA nanotechnology, high-resolution atomic force microscopy, surface plasmon resonance spectroscopy, π-π stacking


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Because of the unique recognition properties of DNA, DNA-based self-assembled structures have a great potential to act as molecular “breadboards” for the arrangement of functional nanoscale objects. In particular, DNA origami-based methods1 provide a promising toolbox due to their robustness, highly parallel fabrication and large structural diversity of the constructed breadboards. DNA origami structures have been used as submicrometer-sized templates for the site-specific decoration with different types of nano-scaled objects such as metallic or inorganic semiconducting nanoparticles2,3, fluorescent dyes4, proteins5 or CNTs6. Usually, a site-specificity of about 2 nm is obtained7. Discussed potential applications of these functionalized DNA origami hybrid structures are nanophotonics, nanoelectronics and biosensing. For instance, DNA origami can be used as template for plasmonic waveguides8–10, plasmonic nanoantennas11–13 or nanoscale field-effect transistors6. The integration of new types of functional elements, such as πconjugated polymers (CPs) into DNA origami will further increase the scope of potential applications. In contrast to the majority of polymers, CPs can act as semiconductors or even possess near-metallic conductivity in a doped state due to the extended π-system along their polymer backbone. Because of these outstanding properties, CPs have already found numerous applications in macroscopic (opto-)electronic devices such as organic field effect transistors14,15, organic light emitting diodes16, organic solar cells17, light harvesting18 and sensing systems19–21. At the same time, examples of the incorporation of CPs into nanoscale DNA origami-based structures remain scarce in the literature22–24. To the best of our knowledge, there are only three reports in the literature that describe a site-specific positioning of CPs onto DNA origami. The first method of Wang et al. involves a polymerization of aniline into polyaniline (PANI) catalyzed by hydrogen peroxide that is produced by enzymes pre-positioned in desired locations on the DNA origami22. Although PANI is an excellent conductor, its use as an active material in semiconducting devices is not favorable because of its spontaneous oxidation into a permanently conductive state. In addition, the method of Wang et al. is restricted to polymers obtainable by poorly controllable oxidative polymerization. However, most of the high-performance semiconducting polymers are produced by more advanced methods, such as metal-catalyzed cross-coupling polycondensations. In two other recent reports, Knudsen et al. and Krissanaprasit et al. reported the synthesis of a “bottle-brush type” polyparaphenylene vinylene (PPV) comprising oligodeoxynucleotide side chains23,24. With this method, very long PPV molecules can be synthesized and positioned at DNA origami templates. The preparation of the bottle brushes involves a solid-state DNA synthesis which can be considered as a drawback that limits 3 ACS Paragon Plus Environment

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the scalability of the method. Furthermore, although PPV was the very first benchmark polymer for photovoltaic devices25–27, its suitability for the build-up of electronic devices such as transistors has never been demonstrated, to the best of our knowledge. In addition, both of the discussed approaches regarding the synthesis of DNA-CP hybrid structures use step-growth polymerization for the preparation of CPs that suffers from a poor control over the molecular weight (MW) and the degree of polymerization of the resulting polymers. Herein, we describe a different approach for the synthesis of CPs and their site-specific positioning on DNA origami templates. For that purpose, we synthesized block copolymers each comprising of an ODN and a water-soluble semiconducting polymer. The semiconducting polymer

of

choice

is

a

regioregular

head-to-tail

polythiophene

poly(3-tri(ethylene

glycol)thiophene), P3(EO)3T. These P3RT types of polythiophenes are well-known for their excellent optoelectronic properties which - to a large extent - are provided by their structural regularity, controlled MW and controllable end group composition. Furthermore, the potential of P3(EO)3T as p-type semiconductor in organic field-effect transistors was already reported by Shao et al.28. These useful features originate from the chain-growth, “quasi-living” character of the Kumada catalyst-transfer polycondensation (KCTP) method used in the synthesis of this type of polythiophene. Here we use the advantages of this “quasi-living” polymerization method and prepare a regioregular P3(EO)3T with a protected aromatic amine as a specific starting group. The starting group was used in the following BCP preparation to attach one specifically designed ODN via click chemistry to each polymer. The resulting P3(EO)3T-b-ODN block copolymer molecules were site-specifically positioned on a two-dimensional (2D) DNA origami structure through hybridization of the ODN block to complementary single-stranded handles protruding from the DNA origami at well-defined positions. The results of our investigations indicate that by designing dense BCP patterns on the DNA template one can court π-π-stacking of the backbones of the immobilized polythiophene molecules. The strong optical response of the immobilized P3RT-type polythiophenes to such interchain stacking allows us to tune their fluorescence properties. We demonstrate this “switching” effect by a stepwise break-up of the interchain stacking by a surfactant resulting in a bathochromic shift and a significantly enhanced intensity of the fluorescence signal.


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We synthesized three BCPs that differ in the sequences and lengths of the ODNs. The first ODN is 20 bases long and has a specific sequence (5’-CTTTGGTGGTCGGCTTTGTC-3’ = 20N), whereas the second and the third ODNs possess poly(dT) sequences of different lengths (5’-T10-3’ = 10T as well as 5’-T18-3’ = 18T). Binding of the BCP with the 20N ODN to its complementary handle (5’-GACAAAGCCGACCACCAAAG-3’ = 20N’) will result in exactly one double-stranded product that fixes the BCP firmly to the DNA origami structure. The hybridization of a poly(dT) ODN with its complementary poly(dA) handle, however, allows sliding29 of the two single strands along each other. We investigated whether these ODN-related properties affect the hybridization kinetics and have an impact on the yield and positioning specificity in the BCP-DNA origami hybrid formation. A series of amino end-functionalized P3(EO)3T polymers was synthesized via the ex-situ initiated KCTP, as originally developed by Senkovskyy et al.30 (Scheme 1). Triethylene glycol groups were introduced as side chains into the monomer 4 to ensure the water-solubility of the resulting polymer, as described previously by Adachi et al.31. The amino function was incorporated as the starting group in the polymer 3 by transfer from the respective functional initiator. To facilitate the conjugation of P3(EO)3T with the end-capped ODNs, a small-molecule linker containing an azide end group (NHS-activated azidoacetic acid) was attached to the amino end group of the polymer 3 yielding the polymer 2. The azide group allows Huisgen-type click reactions32–34. Here, we used the especially efficient strain-promoted alkyne-azide cycloaddition (SPAAC) which does not require any catalysts and results in high product yields without side reactions35,36. The azide-functionalized P3(EO)3T 2 was conjugated to a dibenzocyclooctyne-endcapped ODN bearing different sequences. The reaction was performed in aqueous solution yielding the P3(EO)3T-b-ODN BCP 1. The synthesis route is presented in detail in the Supporting Information (SI) in Figure SI. The crude BCP was purified with HPLC to remove impurities of the ODN and the excess of P3(EO)3T (SI, Fig. S2). In contrast to other approaches targeting synthetic polymer-DNA BCPs23,37,which involve DNA solid-state synthesis, here an easy and scalable method is presented, which can be applied to many other functional end-capped, watersoluble polymers.


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Scheme 1. Synthesis route towards BCP P3(EO)3T-b-ODN 1. DBCO is dibenzocyclooctyne. Three different BCPs were synthesized that differ in the ODN’s length and sequence: the first ODN is 20 bases long and has a specific sequence (5’-CTTTGGTGGTCGGCTTTGTC-3’ = 20N), the second and the third ODNs possess poly(dT) sequences of different lengths (5’-T10-3’ = 10T as well as 5’-T18-3’ = 18T). The P3(EO)3T and the P3(EO)3T-b-ODN samples were characterized by gel permeation chromatography (GPC), nuclear magnetic resonance spectroscopy (NMR), UV/Vis spectroscopy, dynamic light scattering (DLS) and asymmetric flow field-flow fractionation (AF4). The results are presented in detail in the SI (Figs. S3-S6 and Tabs. S1-S3). The polymer MW could be well adjusted by the ratio of monomer to initiator in a range from 2400 to 9200 g/mol corresponding to a degree of polymerization from 9 to 35, respectively, with narrow dispersities between 1.1 to 1.3 (SI, Tab. S1). The polymer with a MW of 4900 g/mol (SI, Tab. S1: P3) was used for the 6 ACS Paragon Plus Environment

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attachment experiments to DNA origami structures. The degree of functionalization (DF) was calculated from the 1H-NMR spectra by the ratio of the integrated signals of the protons of the methyl group of the ex-situ initiator to the protons of an opposite end group of the polymer (SI, Fig. S3 and Tab. 2). For the different polymer batches, we obtained DFs in the range of 38 71 %. Although the DF value in some cases is only moderate, the non-functionalized polymer chains do not participate in further transformations (such as, click reaction and ODN hybridization experiments), so their presence does not affect the experiments of interest of this work. The conjugated polymer has a characteristic absorption band in its UV/Vis spectrum at 410 nm in aqueous solution. In thin films this band is red-shifted to 450 nm suggesting some aggregation in solid state (SI, Fig. S4a). The corresponding optical bandgap of the polymer film is estimated to be 2.1 eV, which is consistent with typical bandgaps for semiconductors. It should be stressed that a good solubility of P3(EO)3T in water solutions, desirably down to a molecular level, is essential for the purpose of this work because the chain aggregation may prohibit preparation of block copolymers and their hybridization with complimentary ODNs. To study the aggregation behavior of the P3(EO)3T, DLS measurements were done. The results of these experiments (SI, Fig. S5) reveal a narrow, monomodal size-distribution of the polythiophene samples in aqueous solution (1xTris·HCl buffer) at room temperature. Depending on the MW, the hydrodynamic diameters of the polymer particles are in a range from 3 to 6 nm, which corroborates with the molecular coil dimensions. A more detailed insight of the size-distribution of the starting compound P3(EO)3T (Tab. S1, P4) and the corresponding BCP P3(EO)3T-b-20N formed after the clicking of P3(EO)3T with the 20N ODN was obtained by AF4 measurements (SI, Fig. S6 and Tab. S3). These measurements, performed in aqueous solutions (1x PBS buffer), again confirmed the absence of severe aggregation in the samples of interest and reveal a successful coupling of P3(EO)3T and the corresponding end-modified ODN to form the desirable BCP. Particularly, the MW analysis of the expected coupling product between P3(EO)3T and ODN 20N revealed a MW of 24950 g/mol which correlates well with the calculated one for P3(EO)3T-b-20N of 22000 g/mol. Furthermore, the narrow dispersity of 1.1 inherent for the P3(EO)3T block is maintained for the BCP, confirming the well-defined molecular structure of the latter.


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The ability of P3(EO)3T-b-ODN to undergo hybridization with their complementary singlestranded counterparts was investigated by surface plasmon resonance (SPR) spectroscopy. Due to its high sensitivity, SPR proved to be a powerful tool to monitor biomolecular binding processes, as e.g. DNA hybridization processes38,39. In particular, thiol-functionalized ODN probes (SH20N’ and SH-18A, see SI for the precise chemical structure) were immobilized on the gold surface of the SPR chip under a constant flow using a microfluidic system. The procedure was adapted from Kick et al.40 with few adjustments. The hybridization of the target structures to the immobilized ODN probes was detected by monitoring the shift of the SPR minimum (Fig. 1a).

Figure 1. (a) Schematic representation of the SPR setup for measuring the hybridization performance of the ODNs and the BCP: the respective thiol-functionalized ODN probes (SH-20N’ or SH-18A) are immobilized on a gold surface and used for binding of either the bare ODN or the BCP. (b) SPR signals of the hybridization kinetics of the bare ODN 20N (black line) and the BCP P3(EO)3T-b-20N (red line) on a chip surface with complementary SH-20N’ probes. (c) SPR signals of the hybridization kinetics of the P3(EO)3T-b-18T on a chip surface with complementary SH-18A probes.


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First, the hybridization capability of the SH-20N’ ODN probes was studied with the bare 20N ODN (positive test). A rate constant for the hybridization of 2.32·104 M-1·s-1 was calculated from the data shown in Fig. 1b (black curve). As a negative test, a non-complementary 20N’ ODN sample was used. Accordingly, no shift in the signal was measured, confirming both, the reliability of the experiment and the specificity of the 20N sequence. Then the hybridization constant of the P3(EO)3T-b-20N to the SH-20N’ probes was determined. It was found to be 1.26·104 M-1·s-1 (Fig. 1b, red curve), which is 1.8 times smaller than for the bare 20N ODN. This meets satisfactorily our expectation, as the MW of the BCP is 1.6 times higher compared to the bare ODN so that a larger diffusion barrier, and hence, slower reaction kinetics can be expected. The reaction constant of the P3(EO)3T-b-18T was also measured using a chip surface with SH-18A ODN probes immobilized via a thiol linker. Compared to P3(EO)3T-b-20N, here the hybridization process (Fig. 1c, blue curve) has a slightly larger reaction constant of 1.44·104 M-1·s-1. The slightly faster hybridization kinetics of the mononucleotide sequence ODN 18T can be explained by a higher binding flexibility/probability due to a possible sliding motion of the complementary strands along each other29,41. Although results obtained by SPR measurements cannot be directly transferred to the case of the DNA origami system, they confirm a general accessibility of the ODNs in the BCP molecules for hybridization. In the next step, we have studied the site-specific attachment of the P3(EO)3T-b-ODNs to a twistcorrected, rectangular 2D DNA origami structure further referred to as pad (Fig. 2a-c). The size of the pad is 150 nm x 50 nm. It is made of 16 parallel oriented, cross-linked DNA double helices. The origami is prepared from a single-stranded M13mp18 virus DNA scaffold and 210 custom-designed staples. Details of the pad design generated by CaDNAno42 and the pad synthesis are described in the SI (Figs. S7-S10). The pad has three chiral characteristics: an unpaired scaffold loop, a truncated corner and single-stranded DNA handles for the BCP attachment configured to protrude to one side of the pad. In contrast to other nanoscale objects like metallic nanoparticles2,43 or quantum dots3,44 that usually are functionalized with multiple ODNs for the attachment to DNA origami, each BCP carries solely one ODN. To study the binding of the different BCPs, pads with three types of handle patterns were designed (Fig. 2a; for further details see SI, Figs. S7-S8). Pad type I carries a “vertical” double line of 14 handles in the middle each having the 20N’ sequence. Type II possesses three “vertical” single lines, about 50 nm apart from each other. Each line consists of seven 15A handles. Type III is equipped with 9 ACS Paragon Plus Environment

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a handle array, 103 nm x 16 nm in size, of four “horizontal lines” with ten handles each. These handles have an 8A sequence. For all three pad types, the distances between next neighbor handles are given in detail in the SI (Fig. S8).

Figure 2. (a) Schematic representations of the bare DNA origami pads; the different handle patterns are referred to as type I, type II and type III. (b) AFM topography image of a bare pad type II with dsDNA handles, obtained by hybridization of 15T ODNs to the 15A handles, to visualize the attachment lines. (c) AFM phase image of a bare pad type III, with protruding ssDNA handles, scale bars: 50 nm. (d - f) AFM topography images of the three types P3(EO)3T@pad hybrid structures: (d) type I, scale bar: 100 nm, (e) type II, scale bar: 50 nm, (f) type III, scale bar: 200 nm. (g) Height distribution of the P3(EO)3T-b-10T objects on the pad type III, with its mean at 5.3 ± 0.8 nm. (h - i) Schematic and AFM topography images of a type III pad in the (h) preferred (69 %) face-up (P3(EO)3T to tip) and (i) less preferred (31 %) face-down orientation (P3(EO)3T to substrate) on mica substrates, scale bars: 50 and 20 nm. For the BCP attachment to the origami pads, the P3(EO)3T-b-ODNs and the pads with complementary handles were mixed with a 20-fold BCP excess per handle and held in a thermomixer at 15 °C for at least 24 h. The attachment protocol resulted in the successful positioning of all BCP species at the respective pads. This was verified by AFM, where globular objects were found along the handle line patterns of the imaged pads (Fig. 2d-f). For P3(EO)3T-b10 ACS Paragon Plus Environment

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18T and P3(EO)3T-b-10T, nearly 100 % of the pads showed at least one attached globular object. For P3(EO)3T-b-20N, the corresponding yield was 93 %. For the characterization of the number and heights of these objects, the AFM images of P3(EO)3T@pad hybrid structures were analyzed with a semiautomatic, custom-made image analysis routine based on the “FindFoci” algorithm of the “ImageJ” software45,46. Furthermore, the objects’ locations on the pads were determined as explicitly described in the SI (Fig. S11a-b). For all three pad types, monomodal height distributions were found for the attached objects. Exemplarily, the height distribution of P3(EO)3T-b-10T attached to type III is given in Fig. 2g. The mean height for 97 analyzed objects was 5.3 ± 0.8 nm. A similar value of 5.2 ± 0.7 nm was found for 183 P3(EO)3T-b-18T objects on pad type III. The height values of the objects attached to the other pad types were similar as well. Analyzing 133 P3(EO)3T-b-18T objects on type II yielded a height of 5.1 ± 0.9 nm and 46 P3(EO)3T-b-20N objects on type I yielded a height of 4.9 ± 0.8 nm. Hence, the measured heights of the attached objects correlate well with the hydrodynamic radius of the P3(EO)3T particles obtained by DLS measurements (SI, Fig. S5). Next, the dependence of the obtained attachment patterns and yields on the handle sequence and the pad type was studied. First, we analyzed the attachment of P3(EO)3T-b-20N at type I (cf. Fig. 2a, d). The handles are placed in an array with 6 nm spacing (SI, Fig. S8). Virtually all hybrids display at least one attached object. On average, four objects are found per pad. In many cases the BCPs seem to cluster adjacently on the pads. As every pad contains 14 handles, the occupation probability per handle is 0.29. Secondly, we studied the binding ability of P3(EO)3T-b-18T to the type II pads containing three lines with seven 15A handles each (cf. Fig. 2a, e). In contrast to the BCP with the specific sequence that does not tolerate hybridization mismatches during the binding process, the P3(EO)3T-b-18T allows sliding of the ODN and handle against each other29,41. Therefore, more than one hybridization configuration provides reasonable binding, which, even if not perfect, can further maximize binding energy by base-pair sliding without dissociation of the P3(EO)3T-b-18T from the pad. Regardless of the possible sliding mechanism, it was found that the occupation probability is only slightly higher in the second case. On average, seven objects were found per pad, corresponding to an occupation probability of 0.33. As in the case for the type II pad, the BCPs are bound to the type III pad via sliding-allowing ODNs (cf. Fig. 2a, f). However, instead of 15A handles, 2.8 nm long 8A handles were used, to 11 ACS Paragon Plus Environment

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which P3(EO)3T-b-10T or P3(EO)3T-b-18T were hybridized. For both BCPs, ten objects were averagely found per pad having 40 handles corresponding to an occupation probability per handle of 0.25. This value is smaller than that for the sliding 15A handle sequence on the pad type II. We hypothesize that this is caused by the lower melting temperature of the shorter handle. If we compare the occupation probabilities obtained for the different linkers and pads with occupation probabilities reported for metal nanoparticles on origami structures10,47,48, than the polymer occupation seems to be much smaller. However, usually at least three linkers per particle are used for metal particles. And, even more importantly, the distance between individual attachment sites is usually larger because of the metal particle size. To the best of our knowledge, metal particle attachment with a center-to-center distance of 6 nm has never been reported so far. In our case, the occupation density corresponds to nearly 7000 objects per µm2.

Figure 3. Quantifying the occupation of the different binding sites with P3(EO)3T-b-10T on a type III pad with AFM images. (a) Height image of one pad that was analyzed, scale bar: 20 nm. (b) Enlarged section of this pad. The grid on the AFM image represents the double-helix pattern of the underlying origami (lines) and the handle sites (circles). The P3(EO)3T objects were assigned to four defined positions a, b, c and d that are exemplarily shown on the first part of the 12 ACS Paragon Plus Environment

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grid. (c) Distribution of the relative occupation of the P3(EO)3T objects regarding these four positions of nine analyzed pads (97 objects in total). (d) The relative distribution of the P3(EO)3T objects on the four lanes. A favored allocation of the BCPs on the inner lanes L2 and L3 is observed. In the next step, we investigated the fidelity of the positioning by analyzing how many objects are placed directly at the sites, where the handles stick out from the pad, and how many are positioned in-between two handles. In other words, we compared the object positions to the designed handle positions. The analysis was done for the type III pad because they show the highest number of attached objects. For well-populated hybrids, continuous “lines” of objects along the entire length of the handle pattern of 103 nm are observed (Figs. 2h and 3a as well as SI Fig. S12). Fig. 3b exemplarily shows a zoom-in into the BCP binding area of one pad. The handle positions a are indicated as circles and the underlying DNA helices lattice as crossing lines. The radius of the circles is related to the handle length. The positioning of the circles and the lattice lines on a pad is described in detail in the SI (Fig. S11a-d). The four lanes of 10 protruding handles each are indicated as lanes L1-4. The analyses presented in Figs. 3c, d (P3(EO)3T-b-10T) and in SI, Figs. S13c, d (P3(EO)3T-b-18T), show that only about 30 % of the identified objects are positioned on a where the handles are protruding out from the pad. The remaining objects are found to be located in areas in-between the designed handle positions, classified as b, c and d (Figs. 3b, c). Most objects (about 70 %) are located on the positions b and c with a closer proximity to the neighboring handle, and hardly at d. The position d is typically occupied with < 2 % of all attached objects. Additionally, we found that most of the attached objects are located on the two inner lanes L2 and L3. Both P3(EO)3T-b-10T and P3(EO)3T-b-18T occur about three to four times more frequently on L2 and L3 than on L1 and L4, as depicted in Fig. 3d and SI, Fig. S13d, respectively. Because the handles on all four lanes are equivalent, the P3(EO)3T objects apparently favor a close packing. We hypothesize that metallic nanoparticles would behave in the opposite manner. As their charged surfaces repel each other, they would most likely bind on sites that have a maximum distance in between, and thus, should attach on the lanes L1 and L4 rather than forming aligned particle lines on the inner lanes. The particular behavior of the BCPs hints to an attractive interaction between adjacent polymer objects. Probably, the extended π-system along the polythiophene backbone plays a key role here. It is 13 ACS Paragon Plus Environment

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known that such polymers tend to interchain aggregation due to π-π-stacking interactions. This kind of “stacking-assembly” would favor the formation of continuous, linear paths of CPs on the DNA template, and thus, possibly allow charge carrier movement. It is notable that the DNA origami can serve as a scaffold for such a phenomenon. Anyhow, currently it is challenging to directly proof the existence of stacking polymer units by measuring charge transport along the polymer chains immobilized on DNA pads. However, π-π-stacking interactions can effectively be suppressed by treating CPs with appropriate surfactants as reported for bulk measurements on water-soluble, aggregated πconjugated polymers including polythiophenes49–52. In particular, suppression of π-π-stacking causes a significant increase of the fluorescence efficiency. Consequently, conducting an experiment, where the P3(EO)3T@pad solutions are thoroughly purified to remove any unbound BCPs from the solution before the optical investigation should provide validation of our hypothesis that the observed attractive interaction between origami-immobilized BCPs is indeed caused by π-π-stacking. To this aim, the fluorescence of the P3(EO)3T@pad hybrid structure in the presence of the zwitterionic surfactant N,N-dimethyldodecylamine N-oxide (DDAO) was studied (Fig. 4). As already mentioned, before the optical investigations, the P3(EO)3T@pad solutions were purified to remove any unbound BCPs. The resulting fluorescence emission spectra of the P3(EO)3T@pad hybrid structure at different DDAO concentrations are shown in Fig. 4b. Without any surfactant, the emission of the P3(EO)3T@pad solution has its maximum at 605 nm. By increasing the DDAO concentration up to 0.3 wt.-%, two effects emerge. First, the emission maximum is blue-shifted down to 560 nm, and second, the intensity of the maximum of emission increases by a factor of 16 (Fig. 4c). The shift of the emission maximum to a lower wavelength is most likely caused by a decreasing polarity of the surrounding of the polythiophene chains. The less polar surfactant molecules cover the polymer chains against the highly polar aqueous surrounding, and thus, prevent solvent relaxation processes50. Moreover, the observed blue-shift of the emission might also originate from a partial twisting of the polymer backbone (i.e., monomer units with respect to each other) due to attachment of (rather bulky) surfactant molecules. This twisting effect reduces effective conjugation length which results in the emission blue-shift. The break-up of the stacked polythiophene chains would also explain the second observed effect, i.e., the strong increase of the emission intensity. Fluorescence selfquenching of CPs is known in many emissive systems to occur upon the transition from solution 14 ACS Paragon Plus Environment

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to films. It is caused by interchain quenching of the stacked polymer chains in the solid state53,54. Taking this into account, the observed increase in the emission intensity can be seen as a strong indication that the polythiophene chains are stacked on the DNA origami pad, which would be crucial for any electric functionality.

Figure 4. (a) Scheme of the surfactant induced break-up of the stacked polythiophene backbones on an ideally occupied type III P3(EO)3T@pad sample. (b) Fluorescence spectra of a P3(EO)3T@pad sample at different DDAO concentrations (0.0, 0.003, 0.03 and 0.3 wt.-%). (c) Wavelength (blue dashed curve), at which the maximum of emission occurs, and the corresponding intensity (black solid curve) plotted against DDAO concentration of the P3(EO)3T@pad sample. Ergo, considering these investigations and the observed dense packing of the BCPs in the highresolution AFM images, we see strong evidence that the BCPs, which are site-specifically attached to the DNA origami pad, consist of stacked polythiophene units. On the one hand, this feature is useful in the context of a possible achievement of DNA origami templated, chargeconducting structures. On the other hand, the above-described AFM investigations are limited to resolve whether the observed polymer objects consist of one, two or three BCPs, because of the tip broadening. Conversely, this means that the above determined occupation probabilities are actually higher when expressed in BCPs per handle and not in objects per handle. 15 ACS Paragon Plus Environment

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Finally, a difference in the adsorption behavior of bare DNA origami pads (SI, Fig. S9) versus P3(EO)3T@pad hybrids onto the mica surface (Fig. 3) was evaluated. Interestingly, the adsorption of bare pads on both sides does not occur with the same probability. A statistical analysis over about 500 pads yielded that 56 % of the pads are facing up, i.e., with the protruding handles pointing away from the mica surface. However, the P3(EO)3T@pad hybrids adsorb with a probability of 69 % with the BCPs up, whereas only 31 % are placed with the BCPs towards the surface. These results are based on the easy identifiable chirality elements of the pad structures. The lower preference to adsorb with the polymer carrying side can be attributed to a more efficient binding of the flat DNA origami site with the positively functionalized mica surface due to electrostatic interactions55–58. To prove this hypothesis for the pads, 23T ODNs were hybridized to the handles of the type II and III pads. The formed double strands on the pad were found to be bulky enough to induce the same change in the deposition behavior. Here, the ratio was 32:68. In summary, we have synthesized a block copolymer with tailored structural, chemical and physical properties, and demonstrated its site-specific attachment to a DNA origami-based, 2D nanostructure. The block copolymer comprised of a thiophene-based, π-conjugated polymer and an oligodeoxynucleotide used for the sequence-specific attachment to the origami pad. The water-soluble P3(EO)3T polymer was synthesized using the state-of-the-art Kumada catalysttransfer polycondensation method which allows to control the degree of polymerization, and thus, the molecular weight of the regioregular head-to-tail polythiophene. A rigorous characterization of the synthesis products revealed a narrow mass dispersity of 1.1. The ODNs were bound to the end-functionalized polythiophene by means of highly efficient and easily scalable click chemistry. Specific binding of the block copolymers to complementary linker strands was demonstrated by SPR spectroscopy and by high-resolution AFM measurements of block copolymers which were bound to DNA origami in a site-specific manner. The statistical analysis of a larger number of polymer-DNA hybrid structures revealed that the block-copolymers could be attached with a reasonable yield and a high spatial density. The DNA-origami template enabled directing the polymers to assemble into linear structures, and furthermore, apparently those structures favoring a close packing of polymers. We hypothesized the latter to π-π-stacking between the attached polythiophenes. In order to substantiate this hypothesis, experiments were carried out where stacking was gradually reduced by employing surfactants configured to break 16 ACS Paragon Plus Environment

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up such stacked CP backbones. Depending on the concentration of the surfactant, a strong optical response of the attached P3(EO)3T was observed. These experiments demonstrated that CP molecules, which are densely immobilized on a DNA origami template, exhibit optical properties that can be manipulated on the molecular level. This feature broadens the application scope of such DNA-polymer hybrid structures as they can also be utilized in optical nanodevices and sensors where a highly efficient, yet switchable fluorescence signal is crucial. The obtained results will significantly contribute to the extension of DNA nanotechnology-based assembly strategies to a new class of materials – namely bottom-up fabricated functional polymers. DNA-polymer hybrids with well-defined structure and tailored properties will certainly enhance the diversity and complexity with which functional elements can be assembled in a parallel manner. In particular, taking the intriguing properties of π-conjugated polymers into account, the approach described herein could pave the way for future design and synthesis of sophisticated photonic and electronic nanodevices.


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ASSOCIATED CONTENT Supporting Information Materials and methods, details of the block copolymer’s synthesis and characterization, the DNA origami and hybrid structure’s design, synthesis and structural analysis and the oligonucleotide sequences of the pad are given in the Supporting Information. This material is available free of charge at the Internet at http://pubs.acs.org. AUTHOR INFORMATION Corresponding Author E-mail: [email protected] Author Contributions The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript. Notes The authors declare no competing financial interest. ACKNOWLEDGMENTS The authors gratefully acknowledge financial support by German Excellence Initiative via the DFG Cluster of Excellence EXC “Center for Advancing Electronics Dresden” (cfAED, EXC1056/1) and the ESF project MindNano (100226937). We thank Hartmut Komber for the 1

H-NMR measurements.


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