Download Session Locator (.pdf)2012-04-11
Symposium NNShow All Abstracts
- Michael Mertig, Technische Universitaet Dresden
- Hao Yan, Arizona State University
- Itamar Willner, The Hebrew University of Jerusalem
- Hendrik Dietz, Technische Universitaet Muenchen
- Asylum Research
Atomic Force F&E GmbH
NN4: Chemical and Biological Synthesis
Chair: Hao Yan
- Wednesday AM, April 11, 2012
- Marriott, Yerba Buena, Nob Hill A
9:00 AM - *NN4.1
Building with DNA: New Approaches for One- and Three-dimensional Structures
Chemistry, University of Stuttgart, Stuttgart, Germany.Show Abstract
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 Â°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.
9:30 AM - NN4.2
DNA-Mediated Assembly of Photoactive Virus Capsids
Francis2 1, James
Molecular Foundry, Lawrence Berkeley National Lab, Berkeley, California, USA; 2,
Department of Chemistry, University of California, Berkeley, Berkeley, California, USA.Show Abstract
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 FÃ¶rster 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.
9:45 AM - NN4.3
DNA Origami as Nanoscale Precision Templates for Directed Organization of Optically-active Virus Capsids
Materials Sciences Division and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, USA; 2,
Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; 3,
Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA.Show Abstract
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.
10:00 AM -
NN5: DNA Mediated Assembly of Nanoparticles
Chair: Hao Yan
- Wednesday AM, April 11, 2012
- Marriott, Yerba Buena, Nob Hill A
10:30 AM - *NN5.1
Structures and Transformations of DNA-mediated Nanoparticle Assemblies
Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York, USA.Show Abstract
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.
11:00 AM - *NN5.2
Nanoparticle Superlittice Engineering with DNA
Senesi1 2, Byeongdu
Macfarlane1 2, Daniel
Eichelsdoerfer1 2, Matthew
Jones2 4, Chad
Mirkin1 2 4.
Department of Chemistry, Northwestern University, Evanston, Illinois, USA; 2,
International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, USA; 3,
X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA; 4,
Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois, USA.Show Abstract
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.
11:30 AM - NN5.3
Gold Nanoparticle Dimers Built on a Dynamic DNATtemplate: Step-by-Step Assembly and Optical Properties
Institut Langevin, ESPCI ParisTech, CNRS UMR 7587, INSERM U979, Paris, France; 2,
Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette, France; 3,
Center for Nanophotonics, FOM Institute AMOLF, Amsterdam, Netherlands.Show Abstract
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 . 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 . 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.  M. P. Busson et al, Nano Lett. (2011), DOI: 10.1021/nl2032052
NN6: DNA Metallization
Chair: Paul Rothemund
- Wednesday PM, April 11, 2012
- Marriott, Yerba Buena, Nob Hill A
2:00 PM - *NN6.1
Structural DNA Nanotechnology for Nanophotonic Applications
Department of Chemistry & Biochemistry and The Biodesign Institute, Arizona State University, Tempe, Arizona, USA.Show Abstract
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.
2:30 PM - NN6.2
Site-Specific Metallization and Electrical Characterization of Conductive Nanowires Templated on DNA Origami
, Brigham Young University, Provo, Utah, USA.Show Abstract
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€œscaffoldâ€ into a designed shape with the use of a large number of shorter â€œstapleâ€ 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€œsticky 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.
2:45 PM - NN6.3
Ultrahigh Mechanical Performance of Continuous DNA Nanofilaments
Mechanical and Materials Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.Show Abstract
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.
3:00 PM -
NN7: DNA Based Nanomachines
Chair: Paul Rothemund
- Wednesday PM, April 11, 2012
- Marriott, Yerba Buena, Nob Hill A
3:30 PM - *NN7.1
Direct Observation of Single Molecular Event in DNA Origami Frame
Department of Chemistry, Kyoto University, Kyoto, Japan; 2,
Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan.Show Abstract
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 â€DNA frameâ€ 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.
4:00 PM - *NN7.2
Controlling the Motion of DNA Nanodevices with an Artificial Transcriptional Clock
Physics Department, TU München, Garching, Germany.Show Abstract
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.
4:30 PM - NN7.3
Design and Construction of an Autonomous Protein-based Motor
Samii1 2, Gerhard
Blab1 3, Heiner
Zuckermann1 2, Nancy
Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada; 2,
IRMACS Centre, Simon Fraser Univeristy, Burnaby, British Columbia, Canada; 3,
Molecular Biophysics, Utrecht University, Ultrecht, Netherlands; 4,
The Nanometer Structure Consortium (nmC@LU), Lund University, Lund, Sweden; 5,
School of Physics, University of New South Wales, Sydney, New South Wales, Australia.Show Abstract
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€œlawnmower,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.
4:45 PM - NN7.4
Macroscopic Highly Ordered DNA Spokes Using Controlled Evaporative Self-assembly
, Georgia Institute of Technology, Atlanta, Georgia, USA.Show Abstract
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.