Prof.
Fred Kramer
(Public Health Research Institute)
25/05/2011, 17:00
Molecular 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...
Prof.
Hendrik Dietz
(Technische Universität München)
25/05/2011, 18:45
Advanced 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...
Prof.
William Shih
(Harvard Medical School)
26/05/2011, 09:15
I 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...
Prof.
Päivi Törmä
(Aalto University)
26/05/2011, 10:30
I 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...
Prof.
Erez Dekel
(Weizmann Institute of Science)
26/05/2011, 11:15
Prof.
Björn Högberg
(Karolinska Institute)
26/05/2011, 14:30
CAD 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...
Dr
Lukas Bogunovic
(Universität Bielefeld)
26/05/2011, 15:15
We 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...
Dr
Josep Maria Huguet
(Universitat de Barcelona)
26/05/2011, 16:30
We 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...
Dr
Thomas Ouldridge
(Oxford University)
26/05/2011, 17:15
We 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...
Prof.
David Soloveichik
(University of Washington)
27/05/2011, 09:15
What 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...
Prof.
Jarkko Kari
(University of Turku)
27/05/2011, 10:30
We 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...
Prof.
Max Garzon
(The University of Memphis)
27/05/2011, 11:15
Finding 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...
Prof.
Anne Condon
(University of British Columbia)
27/05/2011, 14:30
We 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...
Dr
Eugen Czeizler
(Aalto University)
27/05/2011, 16:30
Recent 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...
Prof.
Tim Liedl
(LMU München)
28/05/2011, 09:15
The 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...
Prof.
Erik Winfree
(Caltech)
28/05/2011, 10:30
Self-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...
Prof.
Friedrich Simmel
(TU Munchen)
28/05/2011, 11:15
The 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...
