Symposium : J
DNA Directed Programmable Self-assembly of Nanoparticles into Meta Materials for energy and other applications
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| DNA based nanotechnologies : Oleg Gang | ||
| 09:00 | The Use of DNA's Chemical Information to Direct Structure Authors : Nadrian C. Seeman Affiliations : Department of Chemistry, New York University, USA Resume : ... | 1 1 |
| 09:40 | Multiscale modeling of structural and electronic properties of DNA Authors : Efthimios Kaxiras Affiliations : Physics department, Harvard University, USA Resume : The DNA double helix plays important roles in chemistry, biology, and many areas of nanotechnology.
However, most processes of interest are beyond the computation capability of fine-grained atomic-level
calculations, which makes efficient coarse-grained models of DNA necessary for capturing the complex
behavior it exhibits under various conditions. In this talk we will review computational studies of DNA related
to its translocation, electronic sequencing, interactions with carbon nanotubes, and experiments that
probe its conformational variability under external loading. These computational studies rely on coarse-grained
models of DNA at various levels, based on first-principles calculations of energetics and electronic behavior
as a function of structural changes. | 1 2 |
| 10:15 | DNA-block copolymers: self-assembly and DNA-directed recognition Authors : F. Gauffre, R. Mayap Talom, G. Fuks Affiliations : Institut des Sciences Chimiques de Rennes; laboratoire des IIMRCP de Toulouse; Université Strasbourg Resume : We elaborate polymer nanoparticles covered with oligonucleotides for recognition applications. These nanoparticles form in water by self-assembly of block copolymers containing a short oligonucleotide strand as one block. We will first report on the formation and structure of these DNA-nanoparticles ("DNA micelles").Then we will examine their recongnition properties and their applications for the assembly of gold nanoparticles into an organic/inorganic core-shell assembly. | 1 3 |
| 10:35 | Coffee | |
| Multi-scale modelling of DNA based nanotechnologies : Efthimios Kaxiras | ||
| 10:50 | Small Interfering RNA Induces Structural Phase Transformation in a Phospholipid Bilayer Authors : Rajiv K. Kalia, Amit Choubey, Ken-ichi Nomura, Aiichiro Nakano, Priya Vashishta Affiliations : Collaboratory for Advanced Computing and Simulations; Department of Physics and Astronomy; Mork Family Department of Chemical Engineering and Materials Sciences; Department of Computer Science; University of Southern California, Los Angeles, CA 90089, USA Resume : Small interfering RNA (siRNA) molecules play a pivotal role in silencing gene expression via the RNA interference (RNAi) mechanism. Since the discovery of RNAi just over a decade ago, a tremendous amount of effort has gone into developing siRNA as a therapeutic technology. A key limitation to the widespread implementation of siRNA techniques is the difficulty of delivering siRNA-based drugs to cells. We have examined structural and mechanical barriers to siRNA passage across a phospholipid bilayer using all-atom molecular dynamics (MD) simulations. In this talk, I will present simulation results on how the siRNA induces a liquid crystalline-to-gel phase transformation. I will also discuss the nature of mechanical stresses that act as barriers to siRNA passage across the bilayer. | 2 1 |
| 11:25 | Molecular dynamics of DNA: effective charge, self-assembly and nanopore sequencing Authors : Aleksei Aksimentiev Affiliations : Department of Physics, University of Illinois, USA Resume : ... | 2 2 |
| 12:00 | Force Fluctuations in unfolding forces of biomolecules: Steered MD simulations of Contactin-1 protein Authors : Satyavani Vemparala Affiliations : The Institute of Mathematical Sciences, Chennai, India Resume : Steered molecular dynamics (SMD) simulations are routinely used for
unraveling folded domains to reveal intermediate structures and to compute
associated forces and free energies. Using the example of a neuronal
adhesion protein, Contactin, we discuss effect of pulling velocities on
unfolding forces and suggest a work-velocity scaling relation, which gives
an estimate of the non-equilibrium nature of SMD simulations performed in
complex environments. Implications of existence of such scaling relation
and validity of Jarzynski's equality in the context of fast unfolding
velocities are also discussed. Using a constant velocity pulling SMD
simulation study for protein unfolding, we confirm that the force
fluctuations of this single biomolecular system satisfy a transient-state
fluctuation-like relation analogous to well-established work fluctuation
relations. | 2 3 |
| 12:35 | Lunch | |
| DNA Origami : Maja Mataric | ||
| 14:00 | DNA-programmed assembly of molecules and materials Authors : Kurt Vesterager Gothelf Affiliations : AArhus University, Denmark Resume : ... | 1 7 |
| 14:35 | Modelling the folding of DNA origami Authors : Jean-Michel Arbona, Jean-Pierre Aime, Juan Elezgaray Affiliations : CBMN, UMR 5248, CNRS, France Resume : DNA based nanostructures built on a long single stranded DNA scaffold, known as DNA origamis, are nowadays the basis of many applications.
These applications range from the control of single-molecule chemical reaction networks to the organization at the nanometer
scale of various molecules including proteins and carbon nanotubes. However, many basic questions concerning the mechanisms
of formation of the origamis have not been addressed so far. For instance, the robustness of different designs against factors,
such as the internal topology, or the influence of the staple pattern, are handled empirically. We have built a model for
the folding and melting processes of DNA origamis that is able to reproduce accurately several thermodynamic quantities measurable from
UV absorption experiments. We show that cooperativity is key to quantitatively understand the folding
process. Based on this fact, the model can also be used to design a new distribution of crossovers that increases the
robustness of the DNA template, a necessary step for technological development. | 1 8 |
| 14:55 | Rational assembly of functional nanostructures using DNA origami Authors : Friedrich Simmel Affiliations : Biomolecular Systems and Bionanotechnology Physics Department and ZNN/WSI Technische Universität München, Germany Resume : In the past few years, the DNA origami has been proven to be a powerful technique for the
assembly of almost arbitrarily shaped nanoscale structures and objects. However, many of
the structures demonstrated so far lack a concrete function. In this talk, we will demonstrate several
potential applications for DNA origami structures: i) as a tool for single molecule biophysical studies,
ii) as functional structures residing in lipid bilayer membranes, iii) as scaffolds for the
arrangement of plasmonic structures from metallic nanoparticles. | 1 9 |
| 15:30 | Coffee | |
| DNA/RNA superstructures : Aurélien Bancaud | ||
| 15:45 | RNA auto-assembly, DNA hierarchical superstructure and nanoparticles aggregation: so far, so close Authors : Christophe Lavelle Affiliations : National Museum of Natural History, CNRS UMR7196 / INSERM U565, France Resume : DNA is organized in vivo in nucleoid structures (prokaryotes) or discrete chromosome territories (eukaryotes), each consisting of a single huge supercoiled nucleoproteic fiber. Through structural changes resulting from the transient modifications of its constituents (change in the ionic environment, recruitment of regulatory proteins and/or nucleic acids, ATP-consuming enzymatic processes), this dynamic folding of DNA plays a critical role in the regulation of cell metabolism [1,2].
RNA is a molecule that serves both as a catalyst (like proteins) and as information storage (like DNA). We recently presented evidence that small RNAs could auto-assemble in prokaryotic cells, and propose that the formation of such a structure could be involved in the regulation of non-coding RNA concentration in vivo or in a quality control mechanism used to eliminate misfolded RNAs [3,4].
We recently reported the formation by electrostatic complexation of stable clusters made of nanoparticles (nanoceria (CeO2) coated with short poly(acrylic acid) moieties) and polymers (cationic-neutral block copolymers). The cluster formation was monitored using different formulation pathways, some of them based on controlled desalting kinetics according to methods developed in molecular biology. Tuning the desalting kinetics enabled to vary the size of the clusters from 100 nm to over 1 μm [5].
From chromosome folding and dynamics to RNA auto-assembly and nanoparticles aggregation, we will show how the three above stories are related, hence demonstrating how physics can inspire biology as biology can inspire physics.
References
[1] Lavelle, C., Bancaud, A., Recouvreux, P., Barbi, M., Victor, J.M. And Viovy, J.L. (2011). Chromatin topological transitions. Prog Theor Phys 191:30-39.
[2] Lavelle, C. (2009). Force and torques in the nucleus: chromatin under mechanical constraints. Biochem Cell Biol 87:307-322.
[3] Cayrol, B., Geinguenaud, F., Lacoste, J., Busi, F., Le Derout, J., Piétrement, O., Le Cam, E., Régnier, P., Lavelle, C.+ and Arluison, V.+ (2009). Auto-assembly of E. Coli DsrA small noncoding RNA: molecular characteristics and functional consequences. RNA Biol 6:434-45.
[4] Busi, F.+, Cayrol, B.+, Lavelle, C.+, Le Derout, J., Piétrement, O., Le Cam, E., Geinguenaud, F., Lacoste, J., Régnier, P. and Arluison, V. (2009). Auto-assembly as a new regulatory mechanism of noncoding RNA. Cell Cycle 8:952-4.
[5] Fresnais, J., Lavelle, C. and Berret, J.F. (2009). Nanoparticle aggregation controlled by desalting kinetics. J Phys Chem C 113:16371-79. | 1 10 |
| 16:20 | RNA swiches and nanostructures under transcriptional control Authors : Hervé Isambert Affiliations : Institut Curie Resume : .... | 1 11 |
| 16:55 | Remodeling Peptides via Unnatural Evolution for Nanomedicine Applications Authors : Richard W. Roberts Affiliations : Departments of Chemistry, Chemical Engineering & Materials Science, and Biology, University of Southern California, USA Resume : Peptides have poor biostability and natural sequences cannot readily be converted into drug-like, stable molecules. This talk will describe our efforts to adapt mRNA display to evolve highly stabilized unnatural versions of natural peptide sequences. The results of these efforts are a new class of molecules we term SUPR peptides (Scanning Unnatural Protease Resistant) that have antibody like affinity for biomolecular targets and are highly stable to proteolysis. The potential utility of these new peptides will be demonstrated in both therapeutic and diagnostic applications relating to nanomedicine and cancer biology. | 1 12 |
| 17:30 | Exploring biological systems using integrated photonics Authors : Andrea M. Armani Ming Hsieh Affiliations : Mork Family Department of Chemical Engineering and Material Science Department of Electrical Engineering-Electrophysics, University of Southern California Resume : Innovation in technology routinely leads the way for discovery in chemistry and biology. Most notably, x-ray diffraction data was instrumental in the elucidation of the structure of DNA. To explore the inherent complexity present in biological systems, existing technologies are being pushed to their limits. Once again, scientists are looking to engineers to create innovative solutions to enable their exploration and discovery. Many of the new methods currently being developed focus on increasing the sensitivity of the detection technique by inventing new devices as well as increasing the specificity of the device by engineering synthetic targeting moieties and improved attachment methods. This talk will present an overview of a few of the more recent surface chemistry methods which have been developed in the Armani Lab to study these complex and dynamic systems. It will also delve into some of the novel biophysics experiments which have been enabled by these covalent attachment methods. Specifically, several covalent strategies for attaching antibodies and DNA to optical devices without degrading the performance of the device will be discussed. These methods have allowed us to use these photonic devices to measure protein kinetic behaviors (dissociation constants) and mass transport limitations. Additionally, a self-assembly method for attaching lipid bilayers to enable investigations into lipid bilayer behaviors has also been developed. | 1 13 |
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