Bulletin of the American Physical Society
APS March Meeting 2010
Volume 55, Number 2
Monday–Friday, March 15–19, 2010; Portland, Oregon
Session Q18: Focus Session: Biological-Synthetic Hybrid Materials II |
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Sponsoring Units: DBP DPOLY Chair: Oleg Gang, Brookhaven National Laboratory Room: B117 |
Wednesday, March 17, 2010 11:15AM - 11:27AM |
Q18.00001: Particle Assembly with Double-Helix DNA Dazhi Peter Sun, Andrea Stadler, Daniel van der Lelie, Oleg Gang The use of DNA-functionalized particles and DNA motifs for programmable assembly has been extensively studied in the past decade. However, the majority of the previous successful efforts have been based on a paradigm in which a hybridization of single-stranded DNA(ssDNA)-functionalized particles is utilized to group particles into clusters or large scale assemblies. Here, we report a novel strategy that allows for controllable and programmable assembly of double-stranded DNA (dsDNA)-modified nanoparticles using molecular intercalators. Transmission electron microscopy (TEM), Atomic Force Microscopy (AFM) and dynamic light scattering (DLS), applied to assembled structures, confirm successful assembly of designed clusters using this approach. The efficiency of assembly and thermodynamic properties of formed structures have been also studied. The presented approach is broadly applicable to varieties of existing DNA-based nano-architectures and might provide a platform for development of novel assembly motifs. The potential utility of our approach for a fabrication of complex structures will be also discussed. [Preview Abstract] |
Wednesday, March 17, 2010 11:27AM - 11:39AM |
Q18.00002: Flying Colloidal Carpets Erika Eiser, Sabrina Jahn, Nienke Geerts DNA plays a special role in polymer science not just because of the highly selective recognition of complementary single DNA strands but also because natural DNA chains can be made very long, yet perfectly monodisperse. Solutions of such long DNA chains are widely used as model systems in polymer science. Here, we present our recent results on the unusual self-assembly that takes place in systems of colloids coated with very long double-stranded DNA. We find that colloids coated with such long DNA can assemble into unique ``floating'' crystalline monolayers that are suspended at a distance of several colloidal diameters above a weakly adsorbing substrate. The formation of these 2dCrystals does not depend on DNA hybridization. These crystals can be lifted and do stay stable in the bulk. Hence they have potentially interesting applications as such ordered structures can be assembled in one location and then deposited somewhere else. This would open the way to the assembly of multi-component, layered colloidal crystals. [Preview Abstract] |
Wednesday, March 17, 2010 11:39AM - 11:51AM |
Q18.00003: Energy Landscapes of Small, Fixed Numbers of DNA-coated Colloids Jesse Collins, Vinothan Manoharan We experimentally investigate clustering of small numbers of colloidal spheres with short-range attraction via surface-grafted DNA-DNA molecular recognition. We coat 1 micron diameter spheres with 20nm long DNA strands; particles with different surface-bound DNA sequences represent different particle ``types.'' Pairwise interactions between some types are attractive but interactions between other types are purely repulsive. In a typical experiment, 6 total particles of 3 different types explore a volume less than 100 picoliters and assemble into equilibrium clusters. We optically characterize the structures and compare ensemble averages with statistical mechanical predictions. [Preview Abstract] |
Wednesday, March 17, 2010 11:51AM - 12:03PM |
Q18.00004: Structure of DNA-Carbon Nanotube Hybrids Suresh Manohar, Anand Jagota, Xiaomin Tu, Ming Zheng Hybrids of single-stranded DNA (ssDNA) and carbon nanotubes (CNT) render the latter water-dispersable and have allowed their separation by chirality. ssDNA adsorbs on the CNT through $\pi $ stacking while the negatively charged DNA backbone stabilizes the hybrid in solution. DNA-CNT hybrids have many potential applications in medicine and materials science. These include their use for imaging and as probes inside the cell, for thermal ablation to destroy cancer cells, and the sorting and patterned placement of CNTs. We have recently reported that sorting of CNTs occurs by recognition of individual chirality semiconducting CNTs by special ssDNA sequences. As the basis of this recognition we have proposed a novel ordered form for DNA analogous to the protein \textit{$\beta $}-sheet and \textit{$\beta $}-barrel structures. Using molecular dynamics simulations, we show that this structure is stabilized by interactions with the CNT substrate. We present experimental evidence supporting the existence of hydrogen-bond based ordering in special sequences, and discuss the structure and topology of these new secondary structures. [Preview Abstract] |
Wednesday, March 17, 2010 12:03PM - 12:15PM |
Q18.00005: Low temperature study of DNA-encapsulated silver clusters as optical emitters Sumant Oemrawsingh, Patrick O'Neill, Rick Leijssen, Elizabeth Gwinn, Deborah Kuchnir Fygenson, Dirk Bouwmeester Recently, it has been found that small clusters of silver atoms can be encapsulated by single-stranded DNA (Ag:DNA) and will absorb and emit at visible wavelengths. Unlike more conventional optical labels, such as colloidal quantum dots, the host DNA strand determines the size and optical properties of the emitters. We are currently performing spectroscopic studies of several species of Ag:DNA emitters at helium temperatures, in order to investigate their feasibility as well-defined single-photon sources that can interact coherently. If this proves successful, self-assembly of Ag:DNA emitters onto DNA scaffolded arrays with nanometer accuracy has potential applications in superfluorescence studies and quantum information processes. [Preview Abstract] |
Wednesday, March 17, 2010 12:15PM - 12:27PM |
Q18.00006: Yield, Purity and Mobility of a Silver-DNA Fluorophore in Solution Patrick O'Neill, Lourdes Velazquez, Peter Goodwin, Til Driehorst, Sumita Pennathur, Deborah Fygenson Chemical reduction of DNA oligonucleotide:Ag+ mixtures leads to the formation of fluorescent few-atom Ag clusters stabilized by the DNA. This reaction typically produces many species, some of which are fluorescent, with emission wavelengths and stabilities that vary widely with DNA sequence. While most DNA sequences studied produce many different Ag:DNA products, we identify a specific DNA sequence that strongly favors the formation of a green 11Ag cluster, stable for months under ambient conditions. We generate pure solutions of this emitter by synthesizing in the presence of excess silver and then removing free silver from solution. We report on results enabled by the purity of these samples, including determination of the extinction coefficient (using FCS), diffusion coefficient (using microfluidics) and bulk chemical yield of this fluorophore, and comment on the challenges that remain on the path to production of sufficient quantity and purity for high-resolution structure determination. [Preview Abstract] |
Wednesday, March 17, 2010 12:27PM - 12:39PM |
Q18.00007: Sensitivity of Ag:DNA fluorescence to single base mutations of hairpin strands Elisabeth Gwinn, Rameen Hassanzadeh, Patrick O'Neill, Deborah Fygenson DNA strands can stabilize fluorescent silver clusters composed of just a few atoms [1]. The small size of these photon emitters and their formation in single-stranded DNA [2] give Ag:DNA emitters promise for use in optically-active, self-assembled DNA nanostructures. Exploiting this promise requires an understanding of how fluorophore color relates to the sequence and conformation of the host DNA strand. Here we examine the optical properties of Ag:DNA solutions for a family of DNA hairpins that differ by single base mutations in the hairpin loop. Specific mutations result in spectral redistribution of the fluorescence and large changes in brightness, pointing to geometric control as a means to select specific emitter species.\\[4pt] [1] J.T. Petty, J. Zheng, N.V. Hud and R.M. Dickson, ``DNA-templated Ag nanocluster formation,'' J. Am. Chem. Soc, 126, 5207 (2004).\\[0pt] [2] E.G. Gwinn, P. O'Neill, A. Guerrero, D. Bouwmeester and D.K. Fygenson, ``Sequence-dependent fluorescence from DNA-hosted silver nanoclusters,'' Advanced Materials 20, 279 (2008). [Preview Abstract] |
Wednesday, March 17, 2010 12:39PM - 12:51PM |
Q18.00008: Can protein-imprinted polymers be used as selective binding assays? Simcha Srebnik, Liora Levi We developed a computer simulation to study synthetic materials capable of specific and selective recognition of proteins via molecular imprinting. Polymer-based protein recognition systems are believed to have enormous potential within the clinical and diagnostic fields due to their reusability, biocompatibility, ease of manufacturing, and potential specificity. The imprinting mechanism involves the creation of cavities of complementary shape, size, and functionality to the original template molecule. While imprinting of small molecular templates has met with considerable success, experiments with protein-imprinted polymers (PIPs) have so far resulted in materials with limited selectivity. Several factors contribute to poor recognition, including limited synthesis conditions and the need for porous and flexible gels necessary for diffusion of the protein into imprinted sites binding. We investigated some factors that contribute to poor imprinting of proteins using a coarse-grained lattice model. Our studies indicate that while gel properties may be tuned to increase selectivity, protein surface properties play a decisive role in recognition. [Preview Abstract] |
Wednesday, March 17, 2010 12:51PM - 1:03PM |
Q18.00009: Viscoelastic and not Viscous Glue Drops Produced by Orb-Weaving Spiders Sahni Vasav, Todd Blackledge, Ali Dhinojwala Spiders use highly extensible and adhesive silk threads (capture silk) to capture prey. The capture silk, in addition to sticking to rough surfaces like insect setae, also adheres to smooth surfaces like glass. Here, we have studied the capture silk of modern orb weaving spiders that use viscous glue drops to capture prey. To understand the adhesion mechanism of this viscous glue has been challenging because the adhesive forces measured at pull-off depends on the mechanics of highly extensible axial silk and the adhesive glue drops. Here, we have developed an energy model to separate the adhesion energy required to peel the viscous glue droplets from the mechanics of the axial silk thread. Using this model and single glue drop experiments, we find that the glue is highly \textit{viscoelastic} and is strongly affected by humidity and the rate of peeling. Knowledge of the adhesion and the mechanics of the glue will aid in developing bioinspired adhesives in the future. [Preview Abstract] |
Wednesday, March 17, 2010 1:03PM - 1:39PM |
Q18.00010: DNA: Not Merely the Secret of Life Invited Speaker: DNA is well-known as the genetic material of living organisms. Its most prominent feature is that it contains information that enables it to replicate itself. This information is contained in the well-known Watson-Crick base pairing interactions, adenine with thymine and guanine with cytosine. The double helical structure that results from this complementarity has become a cultural icon of our era. To produce species more diverse than the DNA double helix, we use the notion of reciprocal exchange, which leads to branched molecules. The topologies of these species are readily programmed through sequence design; it is also possible to program 3D structures. Branched species can be connected to one another using the same interactions that genetic engineers use to produce their constructs, cohesion by molecules tailed in complementary single-stranded overhangs, known as ``sticky ends.'' Such sticky-ended cohesion is used to produce N-connected objects and lattices, as well as nanomechanical devices. We have used this system to self-assemble macroscopic 3D crystals whose structures have been determined by X-ray crystallography. We have also combined 2-state nanomechanical DNA devices with a DNA walker on a DNA origami surface to produce a programmable DNA assembly line. [Preview Abstract] |
Wednesday, March 17, 2010 1:39PM - 1:51PM |
Q18.00011: Designing autonomously motile gels that follow complex paths Pratyush Dayal, Olga Kuksenok, Anna C. Balazs Using theory and simulation, we determine the effect of light on the motion of polymer gels undergoing the Belousov-Zhabotinsky (BZ) reaction. The BZ gels undergo rhythmic mechanical oscillations in response to the periodic reduction and oxidation of ruthenium catalyst that is grafted to the polymer network. The Ru-catalyzed BZ reaction is photosensitive, with light of a certain wavelength suppressing the oscillations within the gel. We exploit this property to control the self-sustained motion of millimeter-sized BZ gel ``worms''. By tailoring the arrangement of illuminated and non-illuminated regions, we direct the movement of these worms along complex paths, guiding them to bend, reorient and turn. In particular, these gels can make both 90 degree and U-turns. Notably, the path and the direction of the gel's motion can be dynamically and remotely reconfigured. Hence, our findings can be utilized to design intelligent, autonomously moving biomimetic system that can be reprogrammed ``on demand'' to move to a specific target location and to remain at this location for a chosen period of time. We also determine the controlling parameters that govern their motion. Our findings establish necessary and sufficient conditions required for the movement of these active gels. [Preview Abstract] |
Wednesday, March 17, 2010 1:51PM - 2:03PM |
Q18.00012: Buckled Membranes in Mixed-Valence Ionic Amphiphile Vesicles Analyzed by X-Ray Scattering Michael Bedzyk, Cheuk Leung, Megan Greenfield, Liam Palmer, Graziano Vernizzi, Monica Olvera de la Cruz, Samuel Stupp We demonstrate that charged amphiphilic molecules, including molecules with biological motifs, organize into non-spherical shapes expected for elastic membranes. Specifically, we demonstrate that anionic (-1) water insoluble amphiphiles and cationic amphiphiles (+3) (which form micelles in water), can co- assemble into small buckled vesicles ( J. Am. Chem. Soc., 131, 2030-12031 (2009) ). The strong electrostatic interaction between the +3 and -1 head groups increases the cohesion energy of the amphiphiles and favors the formation of two-dimensional, flat ionic domains on the vesicle surface, resulting in edges and a buckled shape. WAXS measurements confirm the presence of crystalline domains induced by these ionic correlations. [Preview Abstract] |
Wednesday, March 17, 2010 2:03PM - 2:15PM |
Q18.00013: Hybrid static/fluidic synthetic substrates to interface living and nonliving Theobald Lohmueller, Jay T. Groves The goal of our project is the development of novel nano-patterned synthetic materials to establish functional interfaces between living cells and nonliving devices. In particular, we focus on spatial and mechanical aspects of how cells interact with specific signaling molecules. Quasi-hexagonal arrays of gold nanoparticles serve as static anchor points for proteins. The particle size can be adjusted in the range of 2-50 nm to match the structural dimensions of cell membrane receptors. The deposition of a lipid bilayer between the particles results in a system where certain molecules are tethered at the interface with nanoscopic precision, while membrane bound molecules are able to diffuse freely on the surface. By mimicking biological interfaces with defined chemical composition and physical properties, we aim to characterize the coupling mechanisms that link cytoskeletal dynamics to chemical signaling pathways inside living cells. [Preview Abstract] |
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