DNA Origami - and Applications of Smart and

ABSTRACT

4. DNA Origami

The term “DNA origami” was proposed by Paul Rothemund in 2006 to describe his invention of a new type of DNA nanomaterial (Rothemund 2006). In that revolutionary work, he showed the ability of controlled folding of a long, single-stranded scaffold DNA, with the help of hundreds of short staple strands, into exquisite nanopatterns. After his invention, this technique has been a constant focus in the fi eld of DNA nanotechnology for the past few years. Great efforts have been made to build new 2D and 3D DNA origami structures, improve assembly strategy, study inherent properties, and develop new applications.

4.1 Invention and Structural Evolution

In 2006, the invention of DNA origami by Rothemund greatly increased the complexity and size of man-made DNA nanostructures, as well as largely simplifi ed the design and preparation processes. Inspired from the same name Japanese paper-folding art, Rothemund used term “origami”

to describe this new milestone strategy. In brief, DNA origami involves raster-fi lling the desired shape with a long single-stranded scaffold with the help of hundreds of short oligonucleotides, called staple strands, to hold the scaffold in place (Fig. 4a) (Sanderson 2010). Rothemund chose the genomic DNA from the virus M13 mp18 with more than 7000 bases as the scaffold. More than 200 staple strands were used to help folding, and different shapes were assembled from different sets of staple strands, such as square, triangle, star, disk, and so on (Fig. 4b). The resulting DNA structures all conform well to the design and have a diameter of roughly 100 nm and a spatial resolution of 6 nm. DNA origami is considered as a breakthrough in structural DNA nanotechnology, which has produced two main achievements. The fi rst is the amazing nanoarchitecture it has made possible. The second achievement is experiment simplifi cation. Since DNA origami has so many advantages, several studies have undertaken the construction of a number of 2D (Fig. 4c) (Qian et al. 2006, Andersen et al.

2008a) and 3D (Andersen et al. 2009, Kuzuya and Komiyama 2009) intricate and creative architectures.

The above DNA origami nanostructures were all constructed by folding planar sheets. This design principle is simple and straightforward but since planar DNA origami has intrinsic fl exibility, it would be diffi cult to build rigid and various 3D nano-objects. The next breakthrough in this fi eld was reported by Shih’s group (Douglas et al. 2009). They used a different strategy to achieve the building of custom 3D shapes (Fig. 4d). The key in their design principle is that the 3D shapes are composed of honeycomb lattice. This design could be conceptualized as stacking corrugated sheets of antiparallel helices. The resulting structures resemble bundles of double helices constrained to a honeycomb lattice. The shape and size could be adjusted by changing the number, arrangement and lengths of the helices in the lattice. In addition, hierarchical assembly of structures can be achieved by programming staple strands to link separate scaffold strands. Based on this design, they also engineered complex 3D shapes with controlled twist and curvature at the nanoscale, by targeted insertions and deletions of base pairs (Dietz et al. 2009). Later on, Shih’s group collaborated with Yan’s group to achieve a more compact design which used square lattice instead of honeycomb lattice (Ke et al. 2009).

Following the effort to increase the complexity of DNA origami shapes, Yan’s group reported the fi rst topological DNA origami architecture—a

Figure 4. Structural evolution of DNA origami technique. (a) Folding principle of 2D DNA origami. Reprinted with permission from ref. (Sanderson 2010). Copyright 2010 Nature Publishing Group. (b) 2D DNA origami patterns created by Rothemund. Reprinted with permission from ref. (Rothemund 2006). Copyright 2006 Nature Publishing Group. (c) A 2D DNA origami mimicking the shape of China map. Reprinted with permission from ref. (Qian et al. 2006). Copyright 2006 Springer Science + Business Media. (d) 3D objects created by Shih’s group. Reprinted with permission from ref. (Douglas et al. 2009). Copyright 2009 Nature Publishing Group. (e) A Möbius strip. Reprinted with permission from ref. (Han et al. 2010).

Möbius strip (Fig. 4e) (Han et al. 2010). It is a topological ribbon-like structure that has only one side. Recently, in an escape from the rigid lattice model used for conventional DNA origami nanostructures, they also reported a new strategy for the building of 3D DNA origami with complex curvatures (Han et al. 2011). Following this design principle, a series of 2D and 3D DNA nanostructures with high curvature, such as concentric rings, spherical shells, ellipsoidal shells, and a nanofl ask were assembled successfully. To engineer wireframe architectures and scaffolds of increasing complexity, they presented a design strategy to create gridiron-like DNA structures (Han et al. 2013). A series of four-arm junctions were used as vertices within a network of double-helical DNA fragments. The new milestone in this fi eld was created by Yin’s group (Wei et al. 2012). They used a conceptually new technique which was based on the assembly of

“single-stranded tiles” (SST) (Fig. 4f). It is proved that this approach can be used to build 3D DNA objects with defi ned geometry while it has more advantages (Wei et al. 2013, Ke et al. 2014, Wei et al. 2014).

While building new complex DNA origami structures is the prominent goal in the fi eld, efforts towards optimizing and developing assembly methods have also gained more and more attentions. Distinct from the conventional annealing methods, isothermal assembly technique (Jungmann et al. 2008), room temperature assembly technique (Zhang et al. 2013), and magnesium-free technique (Martin and Dietz 2012) have been proposed. Furthermore, Fu et al. have proved that the assembly could be fi nished in as short as 10 min (Fu et al. 2013). Double-stranded DNA scaffolds have also been shown able to prepare two distinct DNA origami shapes in a one-pot reaction (Hogberg et al. 2009). New purifi cation methods for DNA origami were reported by Shih’s group based on a modifi ed DNA electroelution (Bellot et al. 2011), while Dietz’s group described a method based on poly (ethylene glycol)-induced depletion of species with high molecular weight (Stahl et al. 2014).

Although DNA origami technique shows superior ability in preparing arbitrary nanostructures with high complexity, the size of DNA origami is strictly dependent on the length of long scaffold strand. In most reported cases, ~7 kb M13 strand was used and therefore for 2D DNA origami, its size should be ~7000 nm³ which is still too small for possible practical applications. One simple way to solve this problem is using longer scaffold strand. Fan’s group prepared a 26 kilobase single strand DNA fragment, which was obtained from long-range PCR amplifi cation and subsequent enzymatic digestion, for folding large DNA origami (Zhang et al. 2012b).

The results showed that this strand could fold into a super-sized DNA with a theoretical size of 238 × 108 nm². Yan’s group reported a more complex design by using a double-stranded scaffold to fabricate integrated DNA origami structures that incorporate both of the constituent ssDNA molecules

(Yang et al. 2012). In a recent publication by LaBean’s group, they described two methods that overcome some of the major challenges for future progress of the DNA origami fi eld (Marchi et al. 2014).

Different from the long scaffold strategy, a more effi cient and practical strategy is the higher-order assembly of individual DNA origami units into large arrays. This idea was fi rst proposed by Rothemund in his pioneer work, in which he designed extended staples on DNA triangle edges to induce the assembly of six triangles into a big hexagon (Rothemund 2006). This principle was then followed by other researchers. Endo and Sugiyama proposed a programmed-assembly system using DNA jigsaw pieces where each jigsaw piece contains sequence-programmed connection sites, a convex connector, and a corresponding concavity (Endo et al. 2010).

Another strategy for scaling up was invented by Yan’s group. In that design (Zhao et al. 2010), they suggested that instead of ssDNA staples used in DNA origami, an origami itself may also mimic the function of a staple if single-stranded overhangs are extended at the four corners. By introducing bridge strands, each origami-based “staple tile” could hybridize with the scaffold and form large structures that contain several small staple tiles.

On another hand Simmel’s group demonstrated that by electrostatically controlling the adhesion and mobility of DNA origami structures on mica surfaces, by the simple addition of monovalent cations, large ordered 2D arrays of origami tiles can be generated (Aghebat Rafat et al. 2014).

Rothemund recently also reported the self-assembly of DNA origami rectangles into two-dimensional lattices based on the stepwise control of surface diffusion, implemented by changing the concentrations of cations on the surface (Woo and Rothemund 2014).

4.2 As Templates for Nanoparticles Self-Assembly

DNA nanostructures, especially DNA origami, receive close interest because of the programmable control over their shape and size, precise spatial addressability, easy and high-yield preparation, mechanical fl exibility and biocompatibility. Therefore, DNA origami structures have been widely used as templates for precise geometrical control over the positioning of nanoscale objects.

Metal nanoparticles, including Au and Ag nanoparticles, have been successfully positioned on DNA origami by many groups. The fi rst work is the assembly of lipoic acid-modifi ed DNA-AuNPs conjugates onto a rectangular DNA origami template (Sharma et al. 2008). Later on, DNA origami has been demonstrated to organize different-sized Au nanoparticles to form a linear structure with well-controlled orientation and < 10 nm spacing (Ding et al. 2010). This structure could be used to generate extremely high fi eld enhancement and thus work as a nanolens. Discrete and well-

ordered AgNPs nanoarchitectures on DNA origami structures of triangular shape, by using AgNPs conjugated with chimeric phosphorothioated DNA (ps-po DNA) as building blocks, have been achieved (Pal et al. 2010).

Discrete monomeric, dimeric, and trimeric AgNP structures and an AgNP–

AuNP hybrid structure could be constructed reliably in high yield. Besides, Yan’s group achieved programmable positioning of one-dimensional (1D) gold nanorods (AuNRs) by DNA directed self-assembly (Pal et al. 2011).

AuNR dimer structures with various predetermined inter-rod angles and relative distances were constructed with high effi ciency. Recently, Fan’s group reported a jigsaw-puzzle-like assembly strategy mediated by gold nanoparticles (AuNPs) to break the size limitation of DNA origami (Yao et al. 2015a). They demonstrated that oligonucleotide-functionalized AuNPs function as universal joint units for the one-pot assembly of parent DNA origami of triangular shape to form sub-microscale super-origami nanostructures. AuNPs anchored at predefi ned positions of the super- origami exhibited strong interparticle plasmonic coupling.

Fluorescent semiconductor quantum dots are another kind of NPs.

Bui et al. fi rst reported assembly of streptavidin functionalized QDs on DNA origami tube at predetermined locations with full control over the number of QDs on each origami and the separating distance between them (Bui et al. 2010). Ko et al. investigated the binding kinetics of these QDs to DNA origami quantitatively and established some thumb rules that affect binding effi ciency (Ko et al. 2012). Wind and co-workers organized disparate functional nanomaterials, namely, semiconducting QDs and metallic nanoparticles, on a single DNA origami template for the fi rst time (Wang et al. 2012). Liedl’s group used rigid DNA origami scaffolds to assemble metal nanoparticles, quantum dots and organic dyes into hierarchical nanoclusters that have a planet–satellite-type structure (Schreiber et al. 2014). The nanoclusters have a tunable stoichiometry, defi ned distances of 5–200 nm between components and controllable overall sizes of up to 500 nm.

Besides inorganic nanoparticles, biological particles and carbon nanotubes have also been positioned on DNA origami templates in recent years. Kuzyk et al. explored two general approaches to the utilization of DNA origami structures for the assembly of streptavidin-binding pattern (Kuzyk et al. 2009). Kuzuya et al. designed a punched DNA origami assembly that can selectively capture exactly one streptavidin tetramer each of any of its predetermined wells and stably accommodate them (Kuzuya et al. 2009). On the basis of biotin–streptavidin (STV) interactions, Niemeyer’s group demonstrated that DNA nanostructures can be site- specifi cally decorated with several different proteins by using coupling systems orthogonal to the biotin–STV system (Saccá et al. 2010).

Another way to assemble biological materials on origami is DNA hybridization. Yan and co-workers used peptides immobilized on the surface of a DNA nanotube to template-direct the in situ nucleation and growth of gold nanoparticles from soluble chemical precursors. The prepared peptide–DNA conjugate was hybridized to complementary DNA capture probes present on the surface of preformed DNA nanotubes (Stearns et al. 2009). Besides, Francis and co-workers adopted the same method to immobilize virus capsids on DNA origami with nanoscale precision (Stephanopoulos et al. 2010). Other techniques, including nitrilotriacetic acid (NTA) and Histidine-tag metal linked interaction (Shen et al. 2009) and Zinc-Finger proteins for site-specific protein positioning on DNA origami structures (Nakata et al. 2012), were also reported.

Single-walled carbon nanotubes were assembled on DNA origami templates through streptavidin-biotin interaction. Furthermore, this method is a general method for arranging single-walled carbon nanotubes in two dimensions (Maune et al. 2010). Yan’s group reported a convenient, versatile method to organize discrete length single-walled carbon nanotubes (SWNT) into complex geometries using 2D DNA origami structures (Zhao et al. 2013).

4.3 Applications in Plasmonics

The fast-growing fi eld of plasmonics, which study the abilities of metal nanostructures to localize, guide, and manipulate electromagnetic waves beyond the diffraction limit, down to the nanometer-length scale, is an emerging research area (Gramotnev and Bozhevolnyi 2010). Morphological parameters for metal nanostructures such as size, shape, geometry, and interparticle distance could substantially infl uence the plasmonic coupling and the subsequent optical and electrical properties (Rycenga et al. 2011).

With the help of DNA origami techniques, it is possible to render more exquisite control for nanopatterning, since DNA origami techniques can meet the critical demands of both structural robustness and nanoscale addressability in 1D–3D. Yan’s group, as mentioned above, contributed signifi cantly in this direction by establishing some reliable metal nanoparticle immobilization techniques on DNA origami. They then reported the fi rst DNA origami-based plasmonic nanostructure by arranging gold nanorods dimer with variable orientations and observed plasmonic coupling induced band shifts in UV-vis spectra (Pal et al. 2011). They also studied the distance dependent local electric fi eld enhancement of both monomeric and dimeric AuNPs structures and their effects on the photophysics of the fl uorophores in close proximity to the AuNPs (Pal et al. 2013).

Some other groups were focusing on the circular dichroism effect originated from chiral geometry of gold nanoparticles arrays. Liedl and

co-workers showed that DNA origami-based gold nanoparticles’ nano- helices exhibited defi ned circular dichroism (CD) and optical rotatory dispersion effects at visible wavelengths (Fig. 5a) (Kuzyk et al. 2012). Ding et al. (Shen et al. 2012, Shen et al. 2013) and Wang et al. (Lan et al. 2013) observed pronounced circular dichroism from chiral gold nanoparticles and nanorod arrays assembled on planar rectangular DNA origami templates, respectively. The Liedl group reported switchable CD responses by toggling the orientation of the same construct, as shown in their previous paper, with respect to incident light (Schreiber et al. 2013). Most recently two groups, in collaboration, fabricated a reconfi gurable plasmonic nanostructure with AuNRs placed onto two, interlinked DNA origami bundles at specifi c angles (Kuzyk et al. 2014). This smartly designed dynamic system is capable of switching between two conformations to tune the angle between the two bundles by DNA strand displacement, which was refl ected in distinctive

Figure 5. Applications of DNA origami in plasmonics. (a) Directed assembly of gold nanoparticle arrays with defi ned chiral geometry. Reprinted with permission from ref. (Kuzyk et al. 2012). Copyright 2012 Nature Publishing Group. (b) Characterization and SERS spectra of individual origami-AuNP dimmers. Reprinted with permission from ref. (Kühler et al.

alteration in the CD spectra. They envisioned this to be an in situ probe for monitoring dynamic biological process.

Another important progress in this direction is the regulation of fl uorescence effi ciency by plasmonic arrays on DNA origami. Tinnefeld et al. prepared nanoantennas by attaching one or two gold nanoparticles to a DNA origami pillar structure (Acuna et al. 2012), which also incorporated docking sites for a single fl uorescent dye next to one nanoparticle, or in the gap between two nanoparticles. They studied the dependence of the fl uorescence enhancement on nanoparticle size and number and obtained a maximum of 117-fold fl uorescence enhancement. Liu et al. studied a similar fl uorescence enhancement effect by using a simple DNA origami triangle as the template (Pal et al. 2013). Recently, Kuang et al. extended the application of this technique to waveguides based on linear gold nanoparticle arrays assembled on a multiscaffold DNA origami ribbon (Klein et al. 2013). This showed the great potential of this technique for building more functional devices.

Another major application of plasmonic NPs is in enhancing resonance Raman signal. It was discovered decades ago that a rough surface of silver or gold can induce signifi cant enhancement of Raman signal, a phenomenon called surface enhanced Raman scattering (SERS). With the unique addressability of DNA origami, two or more large Au/AgNPs placed in close proximity behaved as a nanoantenna, creating a plasmonic hot spot with an intense local electric fi eld at their junction. Three recently published papers used DNA templated assembly to place Raman molecules (RhodamineSYBR-Gold or 4-aminebenzenethiol) in between two or more AuNPs and showed a several magnitude fold enhancement of the SERS signal (Thacker et al. 2014, Pilo-Pais et al. 2014, Kühler et al. 2014).

Feldmann’s group characterized SERS spectra from individual origami- AuNP dimers (Fig. 5b).

4.4 Applications in Nano-Reactors

In living cells, metabolism is spatially regulated through the site-specifi c compartmentalization of multi-enzymatic cascades in subcellular organelles (Agapakis et al. 2012). The high level of spatial organization and integration make metabolism an optimized network of interconnected biological reactions, guiding the production, transportation and consumption of nutrients, and allowing the maintenance, growth and reproduction of life.

Inspired by nature, synthetic biologists are aiming at building biomimetic nano-/micro-factories for positional immobilization of multi-enzymatic cascades with nanoscale precision (Lee et al. 2012a, Schoffelen and van Hest 2013, Chen and Silver 2012). These artifi cial systems are expected to regulate reaction pathways in high effi ciency, and hold great promise in producing

expensive medicines and materials that are diffi cult for common synthetic chemistry, as well as generating cheap renewable fuels.

Towards this goal, Gothelf’s group carried out the fi rst DNA origami- templated chemical reaction for the addressable coupling and cleavage of some chemical bonds (Voigt et al. 2010). Then, Liu et al. conducted the directed polymerization of macromolecular patterns (Liu et al. 2010). In this design, dendrimers were used as model molecules and assembled on a rectangular DNA origami template. Then, through covalently coupling between adjacent dendrimers, a polymerized macromolecular pattern can be obtained (Fig. 6a). DNA origami nanostructures have also been proved

Figure 6. Applications of DNA origami as nano-reactors. (a) Directed coupling of dendrimers into polymerized patterns. Reprinted with permission from ref. (Liu et al. 2010). Copyright 2010 American Chemical Society. (b) Regulating GOx-HRP bienzyme cascade. Reprinted with permission from ref. (Fu et al. 2012). Copyright 2012 American Chemical Society.

Dalam dokumen and Applications of Smart and (Halaman 34-45)