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Prof. Fred Kramer (Public Health Research Institute)25/05/2011, 17:00Molecular beacons are hairpin-shaped oligonucleotide probes that undergo a fluorogenic conformational change upon binding to PCR amplicons. They can be labeled with differently colored fluorophores, enabling multiplex assays to be carried out in sealed reaction tubes. They can be designed to be “finicky”, so that they only bind to amplicons from a single species, or they can be designed...Go to contribution page
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Prof. Hendrik Dietz (Technische Universität München)25/05/2011, 18:45Advanced molecular self-assembly with ‘DNA origami’ offers a unique route for building custom shaped high-complexity objects that are commensurate in size to biological macromolecules. DNA origami objects can be used as platforms for placing, orienting, and even manipulating biological molecules in user defined ways. Thus, DNA origami objects can not only help improve existing...Go to contribution page
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Prof. William Shih (Harvard Medical School)26/05/2011, 09:15I will present a general method for solving a key challenge for nanotechnology: programmable self-assembly of complex, three-dimensional nanostructures. Previously, scaffolded DNA origami had been used to build arbitrary flat shapes 100 nm in diameter and almost twice the mass of a ribosome. We have succeeded in building custom three-dimensional structures that can be conceived as stacks...Go to contribution page
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Prof. Päivi Törmä (Aalto University)26/05/2011, 10:30I present work where we propose a novel method for the controlled positioning of carbon nanotubes on DNA self-assembled structures. The method is based on the use of streptavidin (STV)–biotin interaction. Precise assembly of both a single CNT and CNT cross-junctions on DNA-origami templates with relatively high yield is demonstrated. The results thus make an essential contribution to the...Go to contribution page
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Prof. Erez Dekel (Weizmann Institute of Science)26/05/2011, 11:15
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Prof. Björn Högberg (Karolinska Institute)26/05/2011, 14:30CAD software for the design of 3D DNA origami nanostructures have been reported previously. In caDNAno by Shawn Douglas, and the more recent CanDo package by Castro and co-workers the focus has been on designing structures where parallel helices are packed in a square-, or honeycomb-lattice. In our recent efforts in building a DNA nanopore, there has been a need for a design software...Go to contribution page
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Dr Lukas Bogunovic (Universität Bielefeld)26/05/2011, 15:15We present our recent studies concerning micro-and nanofluidic devices that are capable of detecting, manipulating and separating single DNAs with different lengths and conformations [1,2] and with complexed molecules such as polymerases or chemotherapeutics [3,4]. The first device consists of a straight microchannel structured with an array of non-conducting posts, which create...Go to contribution page
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Dr Josep Maria Huguet (Universitat de Barcelona)26/05/2011, 16:30We have recently developed a methodology to infer the free energy of hybridization of DNA with a single molecule technique (Huguet et al., PNAS 107, 15431 (2010)). It consists in unzipping a molecule of DNA of a few thousands of base pairs with optical tweezers. These pulling experiments provide a force vs. distance curve that is analyzed to obtain the free energy of formation of...Go to contribution page
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Dr Thomas Ouldridge (Oxford University)26/05/2011, 17:15We have recently proposed a coarse-grained model of DNA [1] which captures much of the thermodynamic and physical changes associated with DNA duplex formation from isolated single strands, in particular representing double-stranded hybridization, hairpin formation and single-stranded stacking consistently for the first time. Despite this, the model is suciently simple to allow the study...Go to contribution page
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Prof. David Soloveichik (University of Washington)27/05/2011, 09:15What challenges must be overcome before engineers can design molecules and their interactions with ease? The ideas of abstraction and modularity allowed the creation of software and hardware systems of extreme complexity consisting of millions of lines of code and hundreds of millions of transistors. Mimicking software and hardware engineering, an approach to the molecular challenge is...Go to contribution page
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Prof. Jarkko Kari (University of Turku)27/05/2011, 10:30We consider the algorithmic problem of determining if a given self-assembly system is terminating, that is, if an unbounded growth may happen or not. We prove that this question is undecidable even in the simple tiling model of self-assembly, by showing that no algorithm is able to determine if a given set of Wang tiles can form on the plane an infinite path where consecutive tiles match...Go to contribution page
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Prof. Max Garzon (The University of Memphis)27/05/2011, 11:15Finding large sets of single DNA strands that do not crosshybridize to themselves or to their complements is an important problem in DNA computing, self-assembly, DNA memories and phylogenetic analyses, because of their error correction and prevention properties. The problem is in itself NP-complete, even in very simplified versions using any single reasonable measure that approximates...Go to contribution page
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Prof. Anne Condon (University of British Columbia)27/05/2011, 14:30We consider recycling, or reuse of molecules, in chemical reaction systems and their DNA strand displacement realizations. Recycling happens when a product of one reaction is a reactant in a later reaction. Recycling has the benefits of reducing consumption, or waste, of molecules and of avoiding fuel depletion. We will describe a binary counter that recycles molecules efficiently while...Go to contribution page
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Dr Lulu Qian (Caltech)27/05/2011, 15:15Not long after Adleman showed that DNA can serve as a computing substrate, Baum proposed using DNA to build an associative memory larger than the brain. Attempts to bring these ideas to fruition have been hindered by requirements for enzymes or manual experimental steps. Here our interest is in DNA strand displacement circuits that can perform neural network computation autonomously. We...Go to contribution page
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Dr Eugen Czeizler (Aalto University)27/05/2011, 16:30Recent years have witnessed a burst of experimental activity concerning algorithmic self-assembly of nanostructures, motivated at least in part by the potential of this approach as a radically new manufacturing technology. Our specific interest is in the self-assembly of Carbon-Nanotube Field Effect Transistor (CNFET) circuits. In the present work, we propose a generic framework for the...Go to contribution page
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Prof. Tim Liedl (LMU München)28/05/2011, 09:15The directed metallization of DNA origami nanostructures could give rise to self-assembling materials with novel optical and electronic properties. We show that three-dimensional (3D) DNA origami structures can be converted into gold nanoparticles of designed shapes by a two- step metallization process: Positively charged 1.4 nm gold nanoclusters adsorb to the negatively charged...Go to contribution page
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Prof. Erik Winfree (Caltech)28/05/2011, 10:30Self-assembly is a fundamental process in the self-organization of biological as well as non-biological structures. Passive self-assembly of molecular units, being driven just by thermodynamic binding energies and the geometrical structure of the molecules, would seem to be the simplest case to study -- but it can be remarkably complicated. In fact, in a model of generalized...Go to contribution page
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Prof. Friedrich Simmel (TU Munchen)28/05/2011, 11:15The highly predictable interactions between DNA or RNA molecules have been utilized for the construction of a large variety of molecular structures and devices. For instance, the recently developed DNA origami technique facilitates the molecular assembly of two- and even three-dimensional nano-objects with almost arbitrary shape - and with nanometric precision. These structures can be...Go to contribution page
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