NN1: DNA Self-Assembly
Chair: Michael Mertig
- Tuesday AM, April 10, 2012
- Marriott, Yerba Buena, Nob Hill A
8:30 AM - *NN1.1
Structural DNA Nanotechnology
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.
9:30 AM - *NN1.2
Controllable Thin Films of Nanoparticle Superlattices through DNA Interactions
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€œbottom-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.
10:00 AM -
10:30 AM - *NN1.3
DNA Programmed Assembly of Molecules
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 and position dendrimers. We have used DNA origami to assemble organic molecules, study chemical reactions with single molecule resolution . We have also formed 3D DNA structures such a DNA origami box and our current progress in this area will be presented. We have developed a DNA actuator that can be shifted between 11 discrete positions . The motion was followed by FRET and by performing chemical reactions that are only geometrically possible in certain states of the actuator. References  RavnsbÃ¦k; J. B et al. Angew. Chem. Int. Ed. DOI: 10.1002/anie.201105095  Liu, H. et al. J. Am. Chem. Soc. 2010, 132, 18054-18056.  Voigt, N. V. et al. Nature Nanotech. 2010, 5, 200.  Andersen, E. S. et al. Nature 2009, 459, 73.  Zhang, Z. et al. Angew. Chem. Int. Ed. 2011, 50, 3983â€“3987.
11:00 AM - NN1.4
Exploring Strand Paths through Holiday Triangles: What are the Paths, and Why Do They Matter?
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€™s 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.
11:15 AM - *NN1.5
Watching DNA Tile Nanotube Nucleation and Polymerization in Real Time
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.
NN1.6 Transferred to RR1.8Show Abstract
NN2: Integration of DNA Nanostructures
Chair: Clemens Richert
- Tuesday PM, April 10, 2012
- Marriott, Yerba Buena, Nob Hill A
2:15 PM - *NN2.1
Placement and Orientation of DNA Origami Shapes on Lithographic Substrates
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.
2:45 PM - NN2.2
Molecular Lithography Using DNA- and Peptide-nanostructures
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.
3:00 PM -
NN3: Sensing Devices
Chair: Clemens Richert
- Tuesday PM, April 10, 2012
- Marriott, Yerba Buena, Nob Hill A
3:15 PM - *NN3.1
DNA Origami Nanopores
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.
3:45 PM - NN3.2
Lining Bioconjugated Quantum Dots over a Single-molecule DNA Nanowire to Prepare a One-dimensional Bionanosensor for Enhancing Target-molecule Probing and Detection
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.
4:00 PM - NN3.3
Ordering of DNA and Visualisation It by the Nonlinear Optics Methods
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) . Interpretation of the results is performed using a theoretical model developed for PSTPM investigation of isolated nanoparticles . 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€œWelcomeâ€ program. References  Leforestier A and Livolant F, Biophys. J. 65, 56 (1993).  Livolant F, Levelut A M, Doucet J and Benoit J P, Nature 339, 724 (1989).  Mojzisova H., Olesiak J, Zielinski M, Matczyszyn K, Chauvat D and Zyss J, Biophys. J. 97, 2348 (2009).  Olesiak J, Matczyszyn K, Mojzisova H, Zielinski M, Chauvat D and Zyss J, Mat.Sci.-Poland 27, 813 (2009).  Olesiak-Banska J, Mojzisova H, Chauvat D, Zielinski M, Matczyszyn K, Tauc P, Zyss J, Biopolymers 95, 365 (2011).  Cherstvy A. G., J. Phys. Chem. B 112, 12585 (2008).  Zielinski M., Winter S., Kolkowski R., Nogues C., Oron D., Zyss J., Chauvat D. Optics Express 19: 6657 (2011)
4:15 PM - NN3.4
Size-dependent Electrophoretic Behavior of Long DNA Molecules under Pressure Gradient in Nanoslit
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 Î»-DNA (48.5 kbp) and T4-DNA (166kbp) were used as the standard of long DNA molecules.
4:30 PM - NN3.5
Optical Nanosystems for DNA Engineering
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.