Team: Indian Institute of Technology, Guwahati, Assam, India — DNA Maestros
Title: Small molecule triggered cargo release from a designer DNA polyhedron
Abstract: The unique properties of DNA such as its persistence length and specific associations enabled by Watson-Crick base pairing have helped it emerge as a powerful substrate for nanoconstruction. Three dimensional polyhedra based on DNA are emerging as strong candidates for display and delivery of small biomolecules in living systems. However, achieving controlled release of the encapsulated cargo with spatial and temporal control aided by molecular cues remains a challenge. Here, we show the controlled opening of a complex DNA polyhedron i.e the icosahedron, in response to an external trigger, namely cyclic-di-GMP (c-di-GMP). The icosahedron is engineered with aptamers for c-di-GMP which act as locks for the icosahedral cage. In the presence of c-di-GMP, these aptameric locks remodel due to formation of tertiary structure that results in the dissociation of the icosahedron into its two constituent halves due to strand displacement. This leads to release of encapsulated internal cargo, such as fluorescent Dextran. Using various fluorescence methods such as quenching and RET, we elucidate tight control over the opening of the DNA icosahedron. This suggests that cargo-loaded polyhedra can be integrated with naturally occuring pathways and their specific secreted molecular cues that in turn provide spatial and/or temporal control over cargo release in diverse contexts.
Team: Hong Kong Baptist University, Kowloon Tong, Hong Kong — BU Magician
Title: Self-assembly of Iron Nanoparticles under Magnetic Field for siRNA Delivery
Abstract: The project aimed at designing self-assembling magnetic iron particles under a magnetic field, including maghemite (Fe2O3) and magnetite (Fe3O4), for small interference RNA (siRNA) delivery then provided cell protection to neurons. Previous work has shown that magnetic iron nanoparticles are effective carriers for gene delivery in cells. We explored the possibility of using magnetic iron nanoparticles designed specifically for delivery of N-methyl-D-aspartate receptor 2B(NR2B)-specific small interference RNA(siRNA) into neuronal cells, in which the effects has been previously proved to enhance cell survival and ameliorate the symptoms in Parkinsonian models [DOI: 10.1159/000334720]. Previous studies demonstrated that the magnetic field could facilitate the particle internalization through endocytosis so as to increase the effectiveness of siRNA uptake [DOI: 10.2147/IJN.S1608]. In the present study, magnetic nanoparticles was allowed to self assemble under a magnetic field, and siRNA was conjugated with by electrostatic force. The efficiency in terms of signal intensity was examined with using a laser scan confocal microscope. Our findings strongly supports the magnetic nanoparticles are extremely useful for the delivery of NR2B siRNA which could achieve the goal of neuroprotection by regulating the NR2B protein expression. They are effective and efficient. The present findings also demonstrate a high potential in future applications of drug delivery.
Team: Columbia University, New York, NY — The Kinesin Kings
Title: Three Dimensional Microtubule Assembly in the presence of Poly-L-Lysine
Abstract: Microtubules are filaments of the cytoskeleton which are polymerized from tubulin dimers and have a diameter of 25nm and lengths on the order of a few microns. By association with the motor proteins kinesin and dynein, microtubules form “highways” for molecular transport in cells. Microtubules have been used as “molecular shuttles” in lab-on-chip devices such as smart dust biosensors by coating a surface with motor proteins, which propel the microtubules on the horizontal plane. We designed a 3D mesh of rhodamine-labeled microtubules by utilizing electrostatic interactions of the polymer poly-L-lysine with the microtubules. After introducing a microtubule solution into a poly-L-lysine-coated glass flow chamber, we observed microtubules oriented perpendicular to the surface and the formation of web-like structures spanning the height of the chamber. These structures maintained their structural integrity over several days. The poly-L-lysine in solution is conjectured to have acted as a bridging mechanism between the microtubules that created the observed structures. This new mesh has potential to contribute to the biosensing field in physical filtration devices.
Team: Harvard University, Cambridge, MA — Harvard BioDesign 2012
Title: Into the mirror world: using an information-rich but nuclease-sensitive self-assembled D-DNA scaffold to template an information-poor but nuclease-resistant L-DNA nano-structure
Abstract: It is now possible to create fully-addressable nanostructures from hundreds of unique synthetic DNA strands. Such structures, being made of biologically-natural D-DNA, are easily degraded by nucleases, posing a potential problem for in-vivo applications such as drug delivery. The oppositely-chiral L-DNA cannot be so degraded due to the inability of chiral nucleases to recognize and attack its mirror-image structure. Unfortunately, L-DNA is currently much more expensive than D-DNA. Here we demonstrate a method for inexpensively creating L-DNA structures with controlled shapes: a repetitive L-DNA structure is templated on an inexpensive, all-unique D-DNA layer. The D-DNA layer forms first, exposing D-DNA handles at defined locations. Subsequently, alternating rows of identical L-DNA/D-DNA chimerical strands are added through hybridization of complementary handles. The D-DNA template can then be enzymatically degraded while the assembled L-DNA structure stays intact, resulting in an economical yet nuclease-resistant nanostructure.
Team: TU Dresden, Dresden, Germany — Dresden Nanosaurs
Title: Signal-Driven Tethering System based on DNA-Origami linked to Lipid Bilayers
Abstract: Considerable work has been put into building DNA-origami structures for a variety of applications and into linking oligonucleotides to lipid membranes. By bringing these systems together, we devise a ‘novel biological tethering system based on a controllable DNA origami box coupled to a vesicle’. This system combines the appeal of vesicles as transport vehicles and the versatility of DNA-origami structures. Our system comprises of a three-dimensional hexagonal DNA origami box that is attached to a lipid vesicle by cholesterol-modified oligonucleotidic 'anchor strands’. Opening of the DNA-origami box can be controlled by the binding of specific ligands to aptamer locks on the origami. Upon opening, several single-stranded DNA 'catcher strands’ are exposed. These strands are complementary to 'receiver strands’ linked to target species present in solution. Consequently, these target species bind to the DNA- origami box only in the presence of a signal establishing a signal-driven tethering system. The applications of such a signal-driven tethering system are diverse because the underlying concept can be adapted and applied to a wide range of scenarios and environments. Most strikingly, the system may be used as a signal-driven targeted drug delivery system in which drugs or compounds encapsulated in vesicles are delivered to specific targets like cancer cells. Other potential applications include vesicle fusion by membrane destabilization, using the system to ‘fish’ for a specific target in solution and forming highly ordered vesicle networks which may be extended to artificial tissue.
Team: University of Tokyo, Komaba, Meguro-ku, Tokyo — UT-Komaba
Title: DNA Tablet
Abstract: Inspired by tablet computers, we propose a DNA origami (tablet) that can display alternative pictures or show a short molecular movie. Our approach combines DNA nanotechnology and DNA dynamic circuits. To demonstrate the unveiling of different images, we created a DNA origami with two latent designs and connected it with a dynamic network having two stables states. This bistability ensures that only one of the two images is displayed at a time, and no intermediate erroneous displays are produced. The user can browse his library of images, by introducing a small amount of an image-specific tag sequence to switch the bistable system. The size of the library, currently two, could be extended by using a n-stable system to show n different pictures. Images on the DNA-tablet are created by hybridization with the state-dependent products of the bistable network and can be observed by AFM. The DNA tablet can also be modified to cycle through several pictures autonomously, by adapting it to a DNA oscillator.
Team: Tokyo Institute of Technology, Tokyo, Japan — Titech Nano-Jugglers
Title: Biomolecular Rocket
Abstract: We propose an extremely high-speed, controllable and rail-free biomolecular rocket. Our rocket moves faster than a naturalhigh-speed molecular motor, kinesin, by taking advantage of catalytic O2 production that progresses anywhere in a dilute H2O2 solution. For increasing the emission of O2 bubbles from the rocket, we conjugated numerous catalytic engines to a micrometer-sized rocket body with the use of DNA. In addition, direction of the rail-free movement of our rocket can be controlled, since we designed the photoresponsive DNA for allowing detachment of the engines from the body upon the UV light irradiation in a region-specific manner. The present study embodies the concept to utilize and control non-biological reactions by designing biomolecules for achieving novel functions implemented by synthetic molecular systems. We believe our biomolecular rocket is a step toward advanced molecular robots that can move on long and rugged fields such as the inside of human body.
Team: Kansai University, Osaka, Japan — UT Kansei Runners
Title: Autonomous DNA runner: a DNA-kinesin hybrid nano-robot
Abstract: Recent progress in nanotechnology has accelerated the development of life science devices. Micro-Total Analysis Systems (μ-TAS) is one such micro fluidic device enabling us to analyze various kinds of biological molecules rapidly and precisely. Narrowing the flow channel improves the performance of this system. However, this will require higher pressure to transport the cargo. To resolve this problem, we chose a biologically inspired method using kinesin motor proteins. As a first step, we present a transportation system combing kinesin and DNA nanostructure called "DNA runner". In our system, the key strands trigger the conformational change of the DNA nanostructure, and induce the synthesis of kinesin. The produced kinesins then bind to the DNA nanostructure, and the formed DNA-kinesin hybrids receive the cargos for transportation along the microtubule filaments. Our study might be the basis for DNA nano-robots working in nano-devices and biological bodies.
Team: The Ohio State University — OhioMOD
Title: A Framework for Assembling and Reconfiguring DNA Origami Containers
Abstract:Previous DNA origami research has illustrated a wide array of 3D structures. Typically, folding multiple objects requires ordering a new set of DNA components for each desired structure. This project seeks to overcome this limitation by developing a hierarchical assembly framework where multiple 3D shapes can be constructed from a single base DNA origami structure. The basic shape is constructed by folding four equilateral triangles from a single DNA origami scaffold and then arranging them into a parallelogram. Schematics were created to fold these parallelograms into four nanoscale container-like shapes: a tetrahedron, an octahedron, an icosahedron, and a wheel. These final shapes are composed of triangles joined by double stranded DNA connections that can be disrupted utilizing DNA strand displacement to ultimately reconfigure a given shape into a different 3D shape (i.e. reconfigure an octahedron to an icosahedron). This project will enable an economic framework to fabrication of multiple DNA origami structures. Furthermore, this approach could be used to develop DNA structures that can reconfigure in response to a biological stimulus, for example cancer cell microenvironments, for drug delivery applications.
Team: Tohoku University, Sendai, Japan — Team Sendai
Title: Cell gate
Abstract: All the creatures on Earth are made of cells. The exterior and the interior of the cell are compartmentalized by biomembranes. A nanodevice that is able to actively transport only the specific oligonucleotide through the biomembrane has a great potential to deliver siRNA into the cell or to extract mRNA expressed in the cell. Here, we decided to create a novel device with such a function. We have designed a cylindrical injector/extractor device made of DNA origami. Inside the cylinder, a cascade of single stranded DNAs is planted. Once the outer-most ssDNA binds to a target oligonucleotide, the target is passed to the inner-ones one by one because of the higher bonding energy assigned to the inner ones. We also investigate how the cylinder penetrates the biomembrane by using liposome as a model membrane.
Team: The University of Texas at Austin — NanoWranglers
Title: An autonomous DNA biped walker powered by catalyzed hairpin assembly
Abstract: Functional biological machines carrying out useful work are ubiquitous in cells. Molecular motors such as kinesins and dyneins can walk along microtubules and transport molecules when powered by adenosine triphosphate hydrolysis. However, these systems have all evolved. Given the control over matter that can be exercised using DNA nanotechnology, it is an intrinsically interesting question to determine to what extent similar motors could be designed. To this end, we propose a DNA biped motor that can walk autonomously along a one-dimensional track when powered by a couple of fuel hairpins. In our design, the two fuel hairpins can not directly interact with one another without the opening of the specific anchor hairpins on the track, and the release of the second leg depends on the release of the first leg, allowing unidirectional locomotion. The anchor hairpins will not be destroyed and thus the track can be reused. The chemical energy provided by the hybridization during strand displacement drives the continuous motion of this walker. This system can be embedded into DNA 2D or 3D substrates, and has the potential to be endowed with multiple functions.
Team: University of California, San Diego — tRiton Nano Architects
Title: Fluorescent DNA Aptamer for lysozyme detection Abstract: Combining previous work on structure-switching signaling aptamers and fluorescent signaling we design a DNA based aptamer modified with fluorophores and quenchers to detect and signal the presence of lysozyme. This device is then compared against the same attached with a nanoparticle. We verify the device’s behavior using polyacrylamide gel electrophoresis, atomic force microscopy, and fluorescent spectroscopy. Our device demonstrates that DNA nano-structures can be designed to meet detection of specific and trace quantities of proteins and this can have important applications such as low cost sensors for detecting deadly viruses via viral capsid proteins.
Team: École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland — EPFL NanoBioTailors
Title: Smart Nanofibers as Nanomuscles
Abstract: Adapting themselves with surrounding environments, regulating transport of ions and molecules, changing wettability and adhesion of different species on the external stimuli, or convert chemical and biochemical signals into optical, electrical, thermal and mechanical signals, and vice versa, are the capabilities that responsive nanostructures give us. Diverse range of applications, such as drug delivery, diagnostics, tissue engineering and optical systems, as well as biosensors, microelectromechanical systems, coatings and textiles. Stimuli-responsive electrospun nanofibers are gaining considerable attention as highly versatile tools that offer great potential in biomedical field. On the other side, enzymes are key components of the bionanotechnology toolbox that possess brilliant recognition capabilities and great catalytic properties. When combined with the unique physical properties of nanostructures such as nanofibers, the resulting enzyme-responsive nanofibers can be designed to perform functions efficiently and with high specificity for the triggering stimulus. In this project we are going to fabricate glucose responsive mats of organized electrospun nanofibers to mimic function of a natural muscle in nanoscale. To do this the glucose oxidase enzyme (GOx) is conjugated on the surface of polyelectrolyte decorated carbon nanotube and these functionalized carbon structures are introduced into the solution of pH sensitive polymer. This nanocomposite solution then was used to make orientated arrays of nanofibers by electrospinning on micropatterned substrate. The resulted mat will be responsive to the presence of glucose molecules. Upon reaction of glucose with GOx enzyme, the fibers will be swelled or shrinked based on their charge states.
Team: Kansai University, Osaka, Japan — Team Kansai
Title: Molecular NINJA Returns
Abstract: Last year, our team tried to construct new molecular walker system named "molecular NINJA". However, we could not accomplish the project. In BIOMOD2012, we will fabricate new molecular robot. This project's name is "Molecular NINJA Returns". In this project, DNA origami can be transformed like NINJA's skill, "ninjutsu". The transformation is based on π- π stacking interaction between intramolecular blant-ends. By making DNA origami without staple strands on few vertical lines, shrunk DNA origami is formed. If this method is used, it will be possible to make DNA origami having a capability of shape selective capturing. We designed shape selective capturing DNA origami which is consist of two U shaped regions connected by single stranded DNA. The DNA origami can selectively catch another complementary shaped DNA origami to maximize π- π stacking interaction. We expect this system can be used for constructing molecular robots.
Team: University of Potsdam, Potsdam, BB, Germany — DnanoPROT
Title: DnanoPROT: Nanostructuring by Combining DNA Origami and Proteins
Abstract: DNA origami are based on rational design principles and provide versatile structures. However, in nature examples of protein structures with diverse shapes and functions are more common. Therefore, we aim at testing and providing methods to combine DNA origami technology with proteins structures. Positioning of chemical modifications at the edges of flat DNA origami recognized by bivalent binding antibodies enabled us link the DNA origami to dimers and in the case of multiple chemical modifications to higher order oligomers. For a more general approach to link proteins in a directed manner to DNA origami we added a tag to recombinantly expressed proteins. This allows for enzymatic linkage of chemical modifications and subsequent click chemistry of proteins with alkyne modified DNA origami. Next to small proteins, we are testing the linkage of DNA origami with virus like particles.