Structural DNA nanotechnology allows the programmed self-assembly of diverse forms, from crystalline nanotubes and two-dimensional lattices to roughly 100 nanometer arbitrary shapes and patterns. The latter structures, formed by a method called "scaffolded DNA origami" are of great interest as potential pattern-generators for nanolithography or templates for the organization of nanoelectronic devices. To fulfill this potential, a number of challenges must be overcome. For example, DNA nanostructures are typically made in solution and, when deposited on surfaces, they fall at random locations with random orientations. We will discuss methods for depositing DNA origami at defined positions on lithographic substrates, using e-beam fabricated "sticky-patches" having the shape of the DNA origami. Previous results in this direction, on silicon dioxide surfaces, have depended on the binding of DNA origami to the surface via magnesium ions: negatively charged (ionized) surface silanols bind magnesium, which in turn binds the negatively charged DNA backbone. A drawback of this approach is that it requires a high (in excess of 60 millimolar) concentration of magnesium ions, which has the effect of precipitating or aggregating many interesting particles which might be organized using surface-bound DNA origami. For example, large gold nanoparticles (~50 nanometers diameter) for plasmonic metamaterials, are particularly hard to stabilize in high magnesium. We will present new results on the placement and orientation of DNA origami in low-magnesium buffers on patterned, positively-charged silane monolayers.

We demonstrate a new approach to bottom-up nanofabrication using DNA and peptide templates. We show that DNA and peptide nanostructures modulate the HF etching of SiO2 at the single-molecule level, resulting in a pattern transfer to the SiO2 substrate with sub-10 nm resolution.

We demonstrate for the first time that DNA origami structures can be inserted into solid-state nanopores and be used for single-molecule sensing. Single origami nanopores are repeatedly inserted in and ejected from solid-state nanopores with diameters around 10 nm. We show that DNA origami nanopores can be used for the detection of DNA translocations. Our novel approach paves the way for future development of adaptable single-molecule nanopore sensors based on the combination of solid-state nanopores and DNA origami self-assembly.

Detection of biomolecules is essential to medical diagnosis, immunoassays, and disease monitoring, etc. However, such detection is often limited by miniscule amounts of samples as well as by inherent transport deficiency posed by molecular diffusion. In this work we develop a new strategy for enhancing detection efficiency by overcoming these problems. It combines molecular combing and fluorescence resonance energy transfer (FRET) in such a way the former is to capture more target molecules and the latter is to signify specific target-ligand interactions involved. Through lining functionalized quantum-dot nanoprobes along stretched single DNA molecules, we demonstrate an addressable one-dimensional FRET sensor capable of capturing and detecting target molecules efficiently. We show that not only can FRET signals be significantly amplified, but also the FRET efficiency can be boosted up due to the unique double excitation mechanism created by the one-dimensional geometry.

Self organization of DNA chains into liquid crystalline (LC) phases as a biomimetic model of DNA packing in the cell nuclei is of great interest [1, 2]. The investigation of the structure of DNA various LC phases by means of polarization optical microscopy (POM) and polarization sensitive two-photon microscopy (PSTPM)was performed. PSTPM was successfully introduced by our group to resolve the 3D structure of ordered DNA stained with fluorescent dyes as well as to establish the relative orientation of the dye transition dipole with respect to the long axis of the DNA helix [3, 4]. We are also exploring the doping of DNA in similar structures with luminescent plasmonic nanorods to trace their organization in the DNA matrix and to observe the mutual impact of the nanostructures on the LC phases of DNA and the LC structures onto ordering of the nanorods. The organization of liquid crystal phases formed in aqueous solutions of DNA depends on the properties of the solution (e.g. DNA concentration) and dopant molecules (i.e binding mode, charge) [5]. Interpretation of the results is performed using a theoretical model developed for PSTPM investigation of isolated nanoparticles [6]. We comment on the scope and limitations of the technique and on the optimization of measurement conditions towards specific DNA samples. Acknowledgement The authors acknowledge financial support from the Foundation for Polish Science â?oWelcomeâ? program. References [1] Leforestier A and Livolant F, Biophys. J. 65, 56 (1993). [2] Livolant F, Levelut A M, Doucet J and Benoit J P, Nature 339, 724 (1989). [3] Mojzisova H., Olesiak J, Zielinski M, Matczyszyn K, Chauvat D and Zyss J, Biophys. J. 97, 2348 (2009). [4] Olesiak J, Matczyszyn K, Mojzisova H, Zielinski M, Chauvat D and Zyss J, Mat.Sci.-Poland 27, 813 (2009). [5] Olesiak-Banska J, Mojzisova H, Chauvat D, Zielinski M, Matczyszyn K, Tauc P, Zyss J, Biopolymers 95, 365 (2011). [6] Cherstvy A. G., J. Phys. Chem. B 112, 12585 (2008). [7] Zielinski M., Winter S., Kolkowski R., Nogues C., Oron D., Zyss J., Chauvat D. Optics Express 19: 6657 (2011)

The uniformly charged polymer such as DNA molecule moves with length-independent mobility in the electric field because the friction force is proportional to DNA contour length as well as the electrostatic force. This size-independent migration prevents separation in free buffer solution, and thus the sieving matrix such as agarose gels should be used. However, the DNAs above a critical length (typically ~20,000 basepairs) show the length-independent electrophoretical mobility even in sieving matrix, because the long DNA molecule becomes highly-oriented along the direction of electric field in the gels. As a result, the pulsed field gel electrophoresis (PFGC) is generally used for the long DNA separation, which is typically one-day process. To achieve the size-dependent behavior of the long DNAs, a novel concept, the electrophoresis under pressure gradient, is proposed in this report. A fluidic device of nanoslit style is fabricated on silicon wafer with microfabrication technique. Then, the electrode for electrophoresis was patterned on the fluid access holes and the PEEK tubes for hydrodynamic pressure was installed and connected with a high performance liquid chromatography (HPLC) pump. The electric potential and the hydrodynamic pressure were applied simultaneously, but with opposite direction. As a result, the different two kinds of DNA show the length-dependent behavior, where YOYO-I stained λ-DNA (48.5 kbp) and T4-DNA (166kbp) were used as the standard of long DNA molecules.

We have designed optical nanomaterials with molecular recognition domain by functionalizing them with nucleic acids. With molecular recognition and self-assembly capabilities of the nucleic acids, we have studied target-receptor interactions at the nanoscale. Our system is a powerful and unique optical platform that allows one to probe and analyze biomolecular reaction both in ensemble and at single molecule level. A few examples of the model systems we studied will be presented.

We build branched DNA species that can be joined using sticky ends to produce N-connected objects and lattices. We have used ligation to construct DNA stick-polyhedra and topological targets, such as Borromean rings. Branched junctions with up to 12 arms have been produced. Nanorobotics is a key area of application. We have made robust 2-state and 3-state sequence-dependent devices that change states by varied hybridization topology. Bipedal walkers, both clocked and autonomous have been built. We have constructed a molecular assembly line by combining a DNA origami layer with three 2-state devices, so that there are eight different states represented by their arrangements. We have demonstrated that all eight products (including the null product) can be built from this system. A central goal of DNA nanotechnology is the self-assembly of periodic matter. We have constructed 2-dimensional DNA arrays with designed patterns from many different motifs. We have used DNA scaffolding to organize active DNA components. Active DNA components include DNAzymes and DNA nanomechanical devices; both are active when incorporated in 2D DNA lattices. We have used pairs of 2-state devices to capture a variety of different targets. Multi-tile DNA arrays have been used to organize gold nanoparticles in specific arrangements. One of the key aims of DNA-based materials research is to construct complex material patterns that can be reproduced. We have recently built such a system from bent TX molecules, which can reach 2 generations of replication. This system represents a first step in self-reproducing materials. Recently, we have self-assembled a 3D crystalline array and have solved its crystal structure to 4 Ã. resolution, using unbiased crystallographic methods, shown below. More than ten other crystals have been designed following the same principles of sticky-ended cohesion. We can use crystals with two molecules in the crystallographic repeat to control the color of the crystals. Thus, structural DNA nanotechnology has fulfilled its initial goal of controlling the structure of matter in three dimensions. A new era in nanoscale control awaits us. This research has been supported by the NIGMS, NSF, ARO, ONR and the W.M. Keck Foundation.

Despite the great potential of nanomaterials in electronic and photonic applications, their incorporation into functional devices will require the combination of top-down lithographic large-area patterning with the high resolution and chemical precision afforded by bottom-up self-assembly. To address some of the challenges, there have been significant efforts to use â?obottom-upâ? or self-assembly approaches for patterning or organizing nanoscale materials. This talk will highlight some of our recent work at using highly parallel arrays of meso- and macroscale DNA scaffolds and DNA oligonucleotides to generate hierarchical assemblies of inorganic metal and semiconductor nanoscale materials. DNA arrays have recently been used to generate highly ordered, near-perfect metal nanocrystal superlattices at specific sites on a substrate through simple adsorption and annealing procedures that also demonstrate either hexagonal or cubic packing. In addition to the use of DNA interactions, the talk will also highlight our research efforts in controlling interparticle associations by solvent, temperature and molecular interactions to generate large area platelets of semiconductor nanorods in solution that can easily be deposited as inks onto substrates to rapidly generate macroscopic arrays of normally oriented nanorods from the substrate.

The idea behind our research is to use DNA as a programmable tool for directing the self-assembly of molecules and materials. The unique specificity of DNA interactions, our ability to code specific DNA sequences and to chemically functionalize DNA, makes it the ideal material for controlling self-assembly of components attached to DNA sequences. We have developed some new approaches in this area such as the use of DNA for self-assembly of organic molecules[1] and position dendrimers[2]. We have used DNA origami to assemble organic molecules, study chemical reactions with single molecule resolution [3]. We have also formed 3D DNA structures such a DNA origami box[4] and our current progress in this area will be presented. We have developed a DNA actuator that can be shifted between 11 discrete positions [5]. The motion was followed by FRET and by performing chemical reactions that are only geometrically possible in certain states of the actuator. References [1] Ravnsbæk; J. B et al. Angew. Chem. Int. Ed. DOI: 10.1002/anie.201105095 [2] Liu, H. et al. J. Am. Chem. Soc. 2010, 132, 18054-18056. [3] Voigt, N. V. et al. Nature Nanotech. 2010, 5, 200. [4] Andersen, E. S. et al. Nature 2009, 459, 73. [5] Zhang, Z. et al. Angew. Chem. Int. Ed. 2011, 50, 3983â?"3987.

DNA nanostructures are most commonly held together using Holliday junctions â?" assemblies incorporating four DNA strand segments arranged into two double helices in such a manner that two of the strands cross over from one double-helix to the other. In 2004, Chengde Maoâ?Ts lab created the first equilateral Holliday triangles consisting of three DNA double helices held together by three Holliday junctions. One DNA strand went through all three Holliday junctions on its path around the inner portion of the triangle, and six other strands reinforced the corners and edges. I have recently developed software that identifies low-strain configurations of Holliday triangles (equilateral and others), and generated an extensive database of such structures. In addition to opening up possibilities for engineering Holliday junctions with a wide assortment of angles between DNA domains, the new set of structures also include 64 different paths the strands can take through the three Holliday junctions. I will discuss the different types of strand paths and show why different ones are better or worse for various purposes. In particular, I will demonstrate how only triangles with certain strand paths can be effectively incorporated into DNA origami assemblies, but those triangles allow bending the origami at a sharp angle, or introducing crossed structures with controlled angles. Other classes of triangles can serve as rotational couplers â?" screwing motion along one edge of the triangle can generate a screwing action along a different axis. In contrast, some triangles frustrate branch migration, and thus might be stable, even if all of the component Holliday junctions had symmetric base sequences that would normally be expected to destabilize them. Research carried out in whole at the Center for Functional Nanomaterials, Brookhaven National Laboratory, which is supported by the U.S. Department of Energy, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886.

When constructing new materials and structures using self-assembly, we can generally only characterize the final product of a self-assembly process; information about self-assembly dynamics is not available. The resulting inability to "debug" the dynamics of self-assembly makes the design of complex, hierarchical self-assembly reactions a challenge. We describe a method for following the self-assembly of DNA tile nanotubes from start to finish using precision time-lapse fluorescence microscopy and show how the resulting knowledge of the self-assembly dynamics can provide new insight into the self-assembly process. This new information can aid in the design of more complex self-assembly processes, such as those involving multiple nanostructures.

In structural DNA nanotechnology, DNA molecules are used to build novel nanoscale structures and devices. Taking advantage of the programmability of DNA based self-assembly, a diverse range of potential applications has emerged. We have used DNA nanostructures to spatially organize various photonic elements to achieve controlled energy transfer. We recently demonstrated DNA templated construction of a series of structurally well-defined light harvesting complexes, each with several different chromophores organized similar to natural light harvesting antenna. We also showed that quantum dots (QDs) with emissions spanning the entire UV-visible to near infrared spectrum can be precisely assembled on DNA nanostructures. Finally, through DNA templated assembly we showed that distance dependent plasmonic interactions between metal nanoparticles and fluorescent molecules can be systematically studied.

Self-assembly methods have shown promise for the fabrication of complex structures with extremely small feature sizes. DNA origami, in particular, provides a simple method for designing shapes in the sub-100-nm regime. The DNA origami technique can produce a wide variety of two-dimensional, as well as three-dimensional, structures by folding a long single-stranded DNA â?oscaffoldâ? into a designed shape with the use of a large number of shorter â?ostapleâ? DNA strands. A distinct advantage of DNA origami is that the staple strands can be adjusted to engineer site-specific attachment points throughout the structure by extending staple strands with additional nucleotides and hybridizing these â?osticky endsâ? with a complementary sequence containing the desired functionality. Here we have used the ability to modify specific locations on the DNA to develop a method of fabricating electrically conductive nanowires from DNA origami templates. We have accomplished this by extending staple strands on our DNA origami in regions where we would like metallization. DNA modified gold nanoparticles are combined with the origami to allow base-paired attachment of the nanoparticles to the extended staple strands. Subsequent electroless plating increases the particle size until the gaps between neighboring particles are filled and a continuous nanowire is formed. In our process we have improved upon previously reported DNA origami metallization methods in at least three ways. 1) Our branched DNA origami structure allows for considerably longer wires than previously reported; 2) we have achieved a high gold nanoparticle seed density (median particle to particle gap size of 4.1 nm), which permits the fabrication of continuous metal structures of very small size; and 3) we have used electrical measurements to verify the conductivity of the DNA origami nanowires following the metallization process.

One-dimensional DNA nanofibers can be used as building blocks in bionanotechnology devices. So far, such structures have been produced by bottom-up self-assembly methods in discontinuous format. Continuous 100% DNA nanofibers were produced in this work using top-down electrospinning method. Nanofiber diameters were varied in the range from 50-500 nanometers by changing process parameters. Individual nanofibers were mechanically tested through failure using specially developed testing protocol. Significant improvement of nanofiber strength was observed with the decrease of nanofiber diameter while strain at failure remained constant within the experimental error. Stress-strain curves of individual nanofibers exhibited inverse S-shape and the toughness of DNA nanofibers far exceeded the toughness of the best structural fibers such as carbon or Kevlar and approached the toughness of spider silks. In addition to the double stranded (ds) DNA, nanofibers from single stranded (ss) DNA solutions were also prepared by a modified process. Mechanical testing of the ssDNA nanofibers exhibited qualitatively different scaling. In particular, strain at failure of the ssDNA nanofilaments increased with the decrease of their diameter. The highest strength values were on the par with structural polymer fibers strengths while toughness far exceeded structural fiber performance. The measured nanofiber strength also exceeded the published single DNA molecule strength by 4.5 times. Short range structural studies confirmed the conformational differences between the dsDNA and ssDNA nanofibers and the source DNA. Raman spectra revealed shifts of sugar-phosphate backbone and basepair vibrations peaks indicating possible transformations from B to A and Z duplexes in the dsDNA and ssDNA nanofibers. The observed unusual high mechanical performance of DNA nanofilaments, coupled with the recently demonstrated possibility to precision-assembly nanofilaments into controlled 1D, 2D, and 3D constructs, open up new exciting opportunities in DNA nanotechnology.

DNA is one of the most promising molecules for the creation of various self-assembled components and scaffolds to prepare complicated patterns, and for selective placement of functional molecules and nanomaterials. The DNA origami method developed for the preparation of fully addressable two-dimensional (2-D) structures has been utilized for the selective positioning of the functional molecules and nanoparticles and for the design of various 3-D architectures. The method is valuable for the preparation of predesigned 2D DNA structures, which leads to the defined assembly of meso-scaled structures. Here we report the design of �DNA frame� using the DNA origami method to examine enzymatic action. We recently developed the tension-controlled dsDNA substrates in the DNA frame and showed the importance of DNA strand relaxation in allowing double helix bending during enzymatic reaction. In our DNA frame, tensed and relaxed dsDNA can be created by bridging the defined length of dsDNA in the DNA scaffold. The relaxed strand can accommodate the enzymes to bind and bend the target sequences. On the other hand, the tensed strand allows binding of these enzymes, while this strand is a poor substrate for bending, resulting in the lower reaction efficiency. In addition, the DNA frame is valuable for analyzing the motion of the enzyme because of the defined coordinated space. The exact location and displacement of the enzyme in the reaction on the dsDNA can be monitored and analyzed. Therefore, the time-resolved reaction coordination between the enzymes and substrate can be estimated at meso-scale spatial resolution. In this presentation direct observation of DNA modifying enzymes such as DNA methylase (M. EcoRI), 8-oxoguanine glycosylase (hOgg1), T4 pyrimidine dimer glycosylase (PDG), and recombinase (Cre recombinase) as well as DNA structural change will be discussed.

One of the goals of DNA nanotechnology is the generation of autonomous molecular devices - devices that operate without external guidance and control. As one step towards this goal, we will discuss how artificial RNA-based reaction networks can be utilized as control circuits for biomolecular nanodevices. Specifically, we will use an artificial transcriptional oscillator to control the motion of the well-known DNA tweezers system. An important problem for the generation of large molecular circuits composed of smaller modules are so-called "retro-activity" effects, which characterize the influence of a load process on the behavior of the driving circuit. This issue will be discussed in the context of the coupled oscillator/tweezers system.

Biological motors are involved in various cellular processes such as intracellular transport, DNA replication and cell motility. These examples involve multi-subunit proteins which transduce chemical energy into mechanical work. To better understand the underlying principles by which biological motors operate, it is instructive to study simpler motors which use Brownian diffusion coupled with asymmetry in the system to bias the direction of motion. Here, we describe the design and construction of a novel protein-based synthetic motor, the â?olawnmower,â? which uses a burnt-bridges mechanism to autonomously and diffusively move forward. The blades of the lawnmower are proteases covalently linked to a quantum dot hub that interact with a one dimensional peptide substrate track via binding to and cleavage of the substrates. The protease motor diffuses to the substrate track where productive binding between the protease and substrate facilitates proteolytic cleavage of the substrate. Once cleaved, the decreased binding affinity between the protease and resulting product allows the motor to diffuse along the track and form new interactions with uncleaved substrate molecules. Experimentally, a kinetic assay monitoring protease activity confirmed that our lawnmower is an active motor and that there are an average of 8 protease blades on each motor. To make a one dimensional track, we use DNA as a linear biological building block to align the substrate peptides in one dimension. Cleavage of the substrate by the protease releases a quencher molecule at one end of the peptide resulting in increased fluorescence of the DNA-bound product. Increased track fluorescence thus provides an indicator of the processivity of the lawnmower along the peptide track, which can be correlated to the motion of the lawnmower hub along the track. This correlation would be useful in assessing the directionality and processivity of our molecular motor and provide insight into its mechanochemical coupling.

The use of DNA molecules, well known as bottom-up nanomaterials, to construct DNA nanowires and electronic devices for technological applications is appealing. Highly ordered parallel DNA spokes on the mm2-scale were successfully fabricated by a combination of controlled evaporation self-assembly and molecular combing. DNA arrays were stretched and aligned on the PMMA/HMDS spin-coated Si substrate by a receding meniscus. Evaporation was precisely controlled with geometry confinement by eliminating the temperature gradient and the possible convective instabilities. The robust modified molecular combing method opens up a new avenue for creating millimeter scale DNA nanowires in a simple and cost-effective manner.

Oligonucleotides are attractive starting materials for the construction of nanostructures. They are readily accessible through automated synthesis, and assemble via predictable base pairing interactions, forming fascinating new structures. Functional structures are beginning to emerge, and so do assemblies that use the power of organic synthesis to build assemblies with increased reactivity or storage capacity. But, nucleic acids are also at the center of studies aimed at creating self-evolving systems that mimic putative early phases of life on planet Earth. Results from two projects will be presented. The first project employs branched oligonucleotides to assemble novel nanostructured materials. The branching points are rigid synthetic organic cores, decorated with short oligonucleotide chains that drive the assembly into lattices and crystallites. We have developed solution-phase syntheses of DNA hybrids with up to six CG zippers as sticky ends. These assemble into novel materials at temperatures as high as 90 °C. The second project studies the self-copying properties of oligonucleotides (both RNA and aminoterminal DNA). Enzyme-free versions of primer extension, the reaction underlying replication, will be presented that allow incorporation of any of the four nucleotides (A/C/G/T or U), as directed by the sequence of a template. Chemical primer extension has the potential to explore the sequence space of functional nucleic acids and to allow for the construction of new, encoded nanostructures.

Biological organisms use tunable, highly specific interactions to perform molecular recognition and organize macromolecules with defined spacing and geometry. Light harvesting complexes in photosynthetic bacteria offer a clear example and suggest that biomimetic approaches that can take advantage of both molecular-scale structure and long-range organization may be successful in achieving similar levels of function. For this work, we used DNA linkers to assemble photoactive virus capsids, then studied their light-harvesting activity in solution and on surfaces. We are taking advantage of the specific binding and distance control afforded by DNA-mediated interactions to investigate the dependence of FRET on fluorophore spacing and organization. When the MS2 coat protein is recombinantly expressed, 180 chemically identical copies self assemble into hollow, approximately spherical capsids, 27 nm in diameter. These capsids are isolated in high yield, and their protein sequences can be modified with genetic methods to incorporate chemically reactive natural or unnatural amino acid side chains. Using site-specific bioconjugation reactions, we modified MS2 capsids with interior organic fluorophores and exterior single-stranded DNA. We noncovalently attached capsids to each other or to DNA-labeled surfaces by performing DNA hybridization. By modifying DNA length, we varied the spacing between capsids labeled with donor and acceptor fluorophores, then monitored Förster Resonance Energy Transfer (FRET) between capsids with solution fluorometry. We found that FRET signal was negligible for longer DNA linker lengths but showed increased efficiency with linkers under ~10 bases. With the aid of microcontact printing, we patterned DNA monolayers onto gold surfaces, then monitored adsorption of capsids bearing complementary DNA using optical methods and atomic force microscopy (AFM). Furthermore, we assembled FRET-active capsid clusters onto surfaces and used confocal fluorescence microscopy to image and obtain emission spectra for individual particle clusters. By assembling photoactive capsids using DNA linkers, we hope to construct ordered biomaterials and gain insights into the dynamics and photophysics of capsid assemblies.

Due to the well-defined molecular structures and extremely narrow size distribution, virus capsids have been widely exploited as 3D scaffolds for high-level assembly of inorganic materials and functional molecules. Researchers have built a variety of functions into viruses to enable site-specific binding of inorganic material, drug delivery, light harvesting, and use of high-surface area electrodes. To take advantage of the power of viral scaffolds and direct their organization into more complex patterns to achieve higher functionalities, various techniques have been investigated for the patterning viruses over large length scales. However, very few are able to control the inter-virus spacing and to position individual viruses with nanoscale precision. On the other hand, use of DNA origami as templates has been recently reported for directed assembly of many nanoscale objects, such as gold and silver nanoparticles, RNA molecules, and carbon nanotubes with exquisite precision. In this work, we explored DNA origami as an orthogonal chemical template for tunable photoemission enhancement by selective immobilization of photo-active bacteriophage MS2 capsids and gold nanoparticles, serving as optical emitters and antennas, respectively. The virus capsids are modified on their interior surfaces to include Alexa Fluor 532 as light harvesting centers and on their exterior surfaces with single strand DNA as probe strands. These optically-active virus capsids are then precisely assembled on DNA origami tiles that bear the complementary probe strands for linkage and gold nanoparticles for photoemission enhancement. Since the precise control over the spatial proximity between photo-emitting viruses and nanoparticle antennas is crucial to achieve photoemission enhancement, we take advantage of DNA origami as programmable templates to control emitter-antenna separation from ~0 to 70 nm. By using a combined approach of correlation between atomic force microscopy and confocal fluorescence microscopy, we indeed observed separation dependence of enhanced photoemission of the emitter-antenna assemblies. Efforts are currently underway to optimize the origami template design for maximum enhancement of photoemission, as well as to organize the origami templates at the micrometer-scale using strand complements patterned via scanned probe lithography or micro-contact printing.

The structural plasticity and tunable interactions provided by selectively interacting DNA chains offer a broad range of possibilities to direct the organization of nanoscale objects into well defined systems, as well as to regulate the structural transformations on demand. We have studied the assembly of clusters and 3D architectures from nanoscale components of multiple types driven by DNA recognition. Our work explores how DNA-encoded interactions between inorganic nano-components can guide the formation of well-defined superlattices, how the morphology of self-organized structures can be regulated in-situ, and what molecular factors govern a phase behavior. The role of flexible chains, particle anisotropy, and external stimuli on a structure formation and its transformation will be discussed in details. Our recent progress on the assembly of particle arrays into designed symmetries, and realizations of switchable and tunable superlattices in 3D and 2D will be presented. Research is supported by the U.S. DOE Office of Science and Office of Basic Energy Sciences under contract No. DE-AC-02-98CH10886.

Many researchers are interested in developing methods for rationally assembling nanoparticle building blocks into periodic lattices. These high-order structures could, in principle, be used to create designer materials with unique properties, useful in material synthesis, optics, biomedicine, energy, and catalysis. For certain applications, it is necessary to control the orientation and placement of such assemblies on surfaces. Herein, we present a DNA-based strategy for achieving epitaxial growth of nanoparticle thin film superlattices. DNA is an ideal ligand for the programmable assembly of nanoparticles, as synthetically tunable variations in nucleotide structure allow for precise engineering of the nanoparticle hydrodynamic radius with nanometer scale precision in addition to the coordination environment. These factors, in turn, dictate the crystallographic structure, symmetry and lattice parameters of the assembly. By employing a DNA-functionalized surface, we show that thin film superlattices of DNA-functionalized nanoparticles can be grown in a layer-by-layer fashion, while maintaining registry with the underlying substrate. We describe DNA coordination environments that govern the crystallographic orientation of the superlattice with respect to the substrate and show fine control of the number of particle layers in the assembly (i.e., film thickness). We also present a theoretical understanding of the assembly process. Importantly, these nanoparticle superlattices can be patterned at arbitrary locations on a substrate using molecular printing techniques such as dip-pen nanolithography (DPN) and polymer pen lithography (PPL). The principles developed in this work represent a major advance in the bottom-up synthesis of nanomaterials and a major step towards the integration of nanoscale materials into functional device architectures.

The ability of noble metal nanostructures to translate local chemical information into a macroscopic optical signal has been used in numerous biosensing schemes: surface plasmon resonance (SPR) spectroscopy, colorimetric sensing or plasmon rulers. In order to design gold nanostructures with an optical response sensitive to one DNA strand, we assemble a particle dimer on a single dynamic DNA template exhibiting a specific recognition site. Electrophoretic purification allows us to observe the step-by-step assembly of the two-dimensional DNA scaffold on 8 nm diameter gold particles. The molecular template includes a stem-loop in order to switch its shape reversibly when binding to a target DNA strand. The two sides of the dimer are hybridized together before a second electrophoretic purification step which indicates that opening the stem-loop induces a clear increase of the dimer hydrodynamic volume. Inter-particle distances are estimated in cryo-electron microscopy in order to analyze the dimer topology without drying effects or particle-substrate interactions. In order to translate the dynamic shape switching of a single DNA scaffold in a measurable optical signal, we need to optimize the scattering cross-section and the plasmon coupling of the dimer by increasing the particle diameters. We recently demonstrated that polyethylene glycol stabilized gold particles with diameters of 27 or 36 nm that are conjugated to a single DNA strand as short as 10 nm can be purified by electrophoresis [1]. This result is obtained by effectively lengthening the DNA strand during the purification process with several 100 bases long molecules, hybridized to each other over 15 base pairs. Static dimers with substantial scattering cross-sections and plasmon coupling are then readily obtained after hybridization of complementary DNA strands. The optical properties of single groupings, inserted in microfluidic chambers, are studied by confocal scattering spectroscopy. Shortening the DNA linker induces a clear red shift of the plasmon resonance wavelength. A statistical analysis of scattering spectra is performed over dozens of dimers and correlated with cryo-electron microscopy images. This analysis indicates that the particle dimers are stretched by electrostatic interactions in buffer solutions with low ionic strengths [1]. Preliminary results on 36 nm gold particle dimers linked by a dynamic DNA strand demonstrate that opening and closing a 48 bases long stem-loop induces a reversible resonance wavelength shift of the order of 20 nm. These results open up numerous perspectives on the design of plasmon-based nanostructures with single molecule sensitivity. [1] M. P. Busson et al, Nano Lett. (2011), DOI: 10.1021/nl2032052

Since smSERS (single molecule Surface-Enhanced Raman Scattering) was independently reported by S. Nie group and K. Kneipp group in 1997 [1][2], tremendous amount of interest has been shown to this field because Raman spectroscopy can provide molecular fingerprint together with multiplexing capability in bioassay. Regarding to the origin of this smSERS phenomena, so called â?oSERS hot spotâ?, these two groups argued against each other for several years: Nie group argued sharp edge in nanostructure, such as corners of a silver nanorod or even of a single nanoparticle, can play as a hot spot of smSERS, while Kneipp group argued they could observe smSERS signal only from colloidal aggregation in solution. Later on, Brus group and others showed that SERS hot spots, formed at the junction of two nanoparticles, likely play a major role in smSERS [3][4]. Theoretical calculations also support that SERS electromagnetic enhancement factors (EEM) can approach up to ~10(exp11) when inter-particle spacing reaches down to a few nanometer or less at the junction between nanoparticle pair. However, formation of these smSERS-active nanostructures, mostly dimer or colloidal aggregation of Ag or Au nanoparticles adsorbed with Raman active molecules (e.g., Rhodamine 6G), is a random process driven by salt-induced non-specific aggregation. This fact has been a main hurdle for smSERS toward advanced applications. Based on the idea that controlling this nano-gap between two noble metal nanoparticles is the key to realize reliable smSERS, we have designed a gold-silver nano dumbbell (GSND) and Gold Nanobridged Nanogap Particles (Au-NNP). As for GSND, two gold nano particles with different sizes were linked to each other by double helix DNA (30mer), with a single Raman dye molecule at the center position, to fix the two at a known gap distance (~10 nm). Then we narrowed the gap down to1 nm by standard silver staining method to endow the GSND with single molecule sensitivity. We have successfully detected smSERS signals, as well as typical single molecular blinking and polarization behaviors, from each GSNDs by Nano Raman spectroscopy at the single particle level [5]. As for Au-NNP, hollow gap (~1 nm) between the gold core and gold shell can be precisely loaded with quantifiable amounts of Raman dyes labeled on DNA backbone which is anchored at the gold core and then covered by gold shell [6]. *References: [1] S. Nie and S.R. Emory, Science 275, 1102 (1997). [2] K. Kneipp, Y. Wang, H. Kneipp, L.T. Perelman, I. Itzkan, R.R. Dasari, and M.S. Feld, Phys. Rev. Lett. 78, 1667 (1997). [3] A.M. Michaels, M. Nirmal, and L.E. Brus, J. Am. Chem. Soc. 121, 9932 (1999). [4] Y.D. Suh, G.K. Schenter, L. Zhu, and H.P. Lu, Ultramicroscopy 97, 89 (2003). [5] D. Lim, K.-S. Jeon, H.M. Kim, J.-M. Nam, and Y.D. Suh, Nature Materials 9, 60 (2010) [6] D. Lim, K.-S. Jeon, J.H. Hwang, H.Y. Kim, S.H. Kwon, Y.D. Suh, and J.-M. Nam, Nature Nanotechnology 6, 452 (2011).

Ordered vertical silicon nanocones arrays coated with silver nanoparticles (AgNPs@SiNCs) are developed as surface-enhanced Raman scattering (SERS)-active substrate, which features good uniformity and reliable reproducibility of SERS signals. Label-free DNA at low concentrations (10^-8 M) could be quantitatively analyzed via SERS using the AgNPs@SiNCs. The Raman peak at 732 cm^-1 due to adenine breathing mode was selected as an endogenous Raman marker for quantitative detection of label-free DNA. The AgNPs@SiNCs as high-performance SERS-active substrates are attractive for surface enhancement mechanism investigation and biochemical sensing applications.

We will create a self-assembled surface enhanced raman spectroscopy (SERS) antenna with an integral analyte attachment site that can be programmed to tether a diverse variety of single analyte molecules. Each antenna will be able to greatly enhance the Raman crossection of its tethered analyte so that the Raman signal from a small number of analyte molecules could be monitored in real time. These molecules could have interesting behavior on their own, or serve as molecular probes that indicate changes in their chemical environment or the binding of target ligands via changes in their Raman spectra. To construct the sensor, we will first self-assemble custom designed DNA origami which will serve as a nanoscale construction platforms. These platform will have a patterns of surface morphological and chemical features that facilitate the sticking of two metal nanoparticles onto the surface of each platform in a predetermined geometry with better than 10 nm positional accuracy. This results in a strongly enhanced Raman signals for molecules placed at the analyte attachment site between the two nanoparticles. The DNA origami will tether DNA-conjugated analyte molecules to the attachment site by displaying DNA hooks that can form complementary base-pair with the analytesâ?T DNA labels. The limits of detection depends on a variety of factors including the shape of the nanoparticles, the geometry of their placement, the conformation of the analyte, the analyteâ?Ts intrinisic Raman crossection and the transfer of electrons between the nanoparticles and the analyte. However, experiments and simulations reported in the literature indicates that singal enhancement up to 1014 fold should be possible, making single molecule level detection possible. So far, we have successfully reproduced literature results for assembly of DNA origami constructs and synthesis of triangular gold nanoprisms and we are now refining designs for our customized origami platform.

Elucidation of the molecular-level mechanisms by which DNA units are self-assembled nanostructures might provide new informative tools in the engineering of novel biomaterials. Our studies examine the role of DNA sequences and the environmental conditions on the morphology and mechanical properties of DNA assemblies by performing molecular dynamics simulations. We use a newly-developed coarse-grained model that bridges the gap between detailed atomistic models and extremely simplified models by capturing geometric and energetic details yet it is sufficiently simple to allow simulations of the spontaneous self-assembly of many DNA units simultaneously. We first examine the dependence of persistence length and melting temperature of as a function of ionic strength, composition and chain length. Our results from single-molecule simulations agree qualitatively with experimental data. To examine the kinetic mechanisms involved in DNA self-assembly, we perform constant-temperature simulations to observe the whole process of DNA assembly starting from random configurations of relatively large DNA systems. We also perform replica-exchange simulations to delineate a phase diagram characterizing different types of structure exhibited for each sequence as a function of the condition being examined. The findings of this research will guide experimentalists to identify systems of novel biomaterials with advantageous morphological properties.

DNA is increasingly used as a material in the design and construction of elaborate structures with nanoscale precision and functionalities. Whether self-assembled from tiles of short, synthetic oligomers or woven from purified genomic strands, most DNA nanostructures are based on parallel arrays of double-stranded DNA (dsDNA) held together by Holliday junction-like cross-links. There is considerable evidence that the double-helices thus intertwined are largely B-form in structure, but the mechanical integrity of the resulting nanostructures has gone largely unexplored.

Here we present a systematic study of the stiffness of DNA nanotubes with a defined number of double-helices in circumference (Yin, et al., Science 321:824 (2008)). We find nanotube stiffness is not a simple function of the number of double-helices. We propose to explain the measurements in terms of a propensity for the double-helical lattice to adopt a supertwist. We test the resulting predictions by a combination of fluorescence polarization microscopy, to distinguish the orientation of the helix axis with respect to the tube axis, and altering the axial repeat length of the underlying tile set, to eliminate specific supertwist states. This combination of measurement and modeling results in an estimate of the effective Youngâ?Ts modulus for cross-linked double-stranded DNA, which can be used to guide the design of nanomechanical DNA devices.

Structural DNA technology provides an attractive approach for the self-assembly of nanostructures in which molecules and particles are to be positioned with nanoscopic precision. Of special interest are DNA origami which can act as nanosheet scaffolds for constructing â?oarbitraryâ? 2D assemblies. The standard approach for characterizing origami-based structures is AFM, conducted either in air or more often under aqueous conditions. However, because this technique necessarily involves surface-mounting, it will give incomplete and possibly even erroneous information about the 2D nanostructures in solution, which for many applications is the condition of most interest. In this contribution, we explore pair-wise fluorescence resonance energy transfer (FRET) as a route to detailed in-solution characterization of nanostructures formed on DNA origami scaffolds. In principle DNA origami are capable of organizing fluorescent dyes and other chromophores into arbitrary 2D patterns. Such structures may ultimately find application in sensing or light harvesting; more immediately they can serve as means for studying the kinematics of the origami platform itself in solution. By using FRET as a spectroscopic ruler, the distance between dye pairs can be measured accurately, and subsequently correlated with the expected distance. By accumulating such data from a number of FRET pairs situated at various locations on the DNA-organized nanosheet one can obtained a detailed quantitative characterization of its shape and deformability in solution. To test the FRET-based characterization approach, we have designed and assembled two different origami using Rothemundâ?Ts methods with selected portions of M13 DNA acting as the backbones. Both origami are rectangular in shape, one a 8x16nm rectangle having a center seam, and the other a 20x30nm rectangle without seams. For the FRET measurements we have selected various positional pairs arranged about the DNA structure with specific emphasis on investigating anisotropy in the origamiâ?Ts mechanical properties. The dyes used were Fam and Tamra, and these were positioned either aligned with or across the â?oweaveâ? pattern created by the origami backbone. In evaluating the experimental data it is important to note that in flexible structures FRET tends to favor configurations in which the dye pairs are at their closest approach. This means that the FRET signal probes not the equilibrium shape but rather the extremes, and so provides information about the flexibility/deformability of the structure. Our initial results indicate that there is a strong anisotropy in the origami bending stiffness, with the measured spacing across the weave deviating much more from expectation than the spacing aligned along the weave pattern. These and other FRET results will be discussed in detail, along with comparisons with AFM measurements on the same structures and with estimates obtained from simplified molecular dynamics simulations.

Discrete DNA nanostructures allow for simultaneous features not possible with traditional DNA forms: encapsulation of cargo, display of multiple ligands, and resistance to enzymatic digestion. This latter property arises from steric hindrance and the rigidity of DNA at nanometer length scales. Overall, these unique features of DNA nanostructures suggested their use as a delivery platform. We will show that DNA pyramids displaying antisense motifs can specifically degrade mRNA and inhibit protein expression in vitro, and show improved cell uptake and gene silencing when compared to linear DNA. Furthermore, the activity of these pyramids can be regulated by the introduction of an appropriate complementary strand. Ongoing work involves the incorporation of environmentally-sensitive DNA motifs into these structures, to obtain DNA-based delivery vehicles that release their cargo based on physiological or pathological cues.

DNA-origami is a recently developed method to construct DNA nanostructures of arbitrary shape and property. The understanding of the mechanical behavior of nanostructures assembled by this technique is crucial for their application as rigid mechanical mediators or force sensing elements. We used magnetic tweezers that support direct force and torque measurements to determine the bending and torsional rigidities of four- and six-helical bundles of defined length. The bending rigidity was found to increase about 15-fold and 38-fold for 4-helix bundles and 6-helix bundles compared to double-strand DNA, respectively. In contrast, the torsional rigidity increased only 4-fold and 5.5-fold for 4-helix bundles and 6-helix bundles. We present a mechanical model explicitly including the crossovers between the individual helices in the origami structure that can describe the difference between bending and twisting mechanics of 3D DNA origami. We also show how the multi-helical structures can be rigidly attached to surfaces, which is an important prerequisite to effectively use their rigid properties in future nanomechanical applications.

Because it can be created inexpensively with atomic precision, DNA is an ideal candidate for a metrology standard. The force necessary to overstretch a double-stranded DNA molecule has been measured in a fashion traceable to the International System of Units, and provides an absolute calibration reference for atomic and molecular-scale force measurements. Details of the calibration and uncertainty analysis will be discussed, as will strategies for its use for calibration of a variety of small force measurment platforms.

A strand displacement-based system has been developed that substitutes inosine for guanosine in DNA sequences called â?ozippersâ?. Each zipper sequence employs traditional adenosine-thymine bonding as well as non-traditional inosine-cytidine bonding. The I-C bond consists of only 2 hydrogen bonds as opposed to the typical 3 hydrogen bonds found in G-C bonds. A zipper helix consists of one strand with A and C and a second strand with complementary I and T nucleotides. The second strand is displaced by the introduction of a strand with G and T nucleotides complementary to the first strand. These zippers can be introduced as an active element in larger DNA devices and be designed to be used in different situations. The first example is of zippers incorporated into single and double â?ospringâ? systems. The springs incorporate in such a manner that allow them be repeatedly extended and reset. Multiple springs can be incorporated into larger 2D and 3D DNA structures, allowing them to change between conformations on demand. Zippers can also be incorporated into a gating system for ion channels such as hemolysin and DNA tethered to a larger nanoparticle and passing through the hemolysin channel. Zippers at the end of such a strand could lock the DNA strand in place, effectively allowing the nanoparticle to block the channel on the other side. Finally DNA zippers have not been properly characterized by quantitative measurements yet. AFM or optical trap studies can be performed to study the binding energy of a zipper sequence.

We report a DNA zipper based actuator device termed â?~DNA- springâ?T with tunable and repeated cycles of extension and contraction ability. DNA zipper is a double-stranded DNA system engineered to open upon its specific interaction with appropriately designed single strand DNA (ssDNA), opening of the zipper is driven by binding energy differences between the DNA strands. The zipper system is incorporated with defined modifications to function like a spring, capable of delivering ~9 pN force over a distance of ~13 nm, producing ~116 kJ/mol of work. Time-lapse fluorescence and fluorescent DNA gel electrophoresis analysis is utilized to evaluate and confirm the spring action. A second zipper incorporated into the spring provides the ability to couple/decouple to an object/substrate. Such devices would have wide application, including for conditionally triggered molecular delivery systems and as actuators in nano-devices.