2,238 research outputs found
Self-assembling DNA-caged particles: nanoblocks for hierarchical self-assembly
DNA is an ideal candidate to organize matter on the nanoscale, primarily due
to the specificity and complexity of DNA based interactions. Recent advances in
this direction include the self-assembly of colloidal crystals using DNA
grafted particles. In this article we theoretically study the self-assembly of
DNA-caged particles. These nanoblocks combine DNA grafted particles with more
complicated purely DNA based constructs. Geometrically the nanoblock is a
sphere (DNA grafted particle) inscribed inside a polyhedron (DNA cage). The
faces of the DNA cage are open, and the edges are made from double stranded
DNA. The cage vertices are modified DNA junctions. We calculate the
equilibriuim yield of self-assembled, tetrahedrally caged particles, and
discuss their stability with respect to alternative structures. The
experimental feasability of the method is discussed. To conclude we indicate
the usefulness of DNA-caged particles as nanoblocks in a hierarchical
self-assembly strategy.Comment: v2: 21 pages, 8 figures; revised discussion in Sec. 2, replaced 2
figures, added new reference
New Methods for Depositing and Imaging Molecules in Scanning Tunneling Microscopy
Methods and apparatus are described to deposit and image molecules by scanning tunneling microscopy (STM) under an inert atmosphere. Three methods of applying molecules have been evaluated: equilibrium adsorption from the vapor phase, sublimation, and electrospraying. Using these methods, a variety of organic and biopolymer molecules have been deposited and imaged on graphite and on gold (111), grown epitaxially on mica. Compared with alternatives, such as the use of high vacuum apparatus or glove boxes, these procedures offer some important advantages: they are inexpensive, convenient, and more rapid. Mercaptoethanol, ethanolamine, ethanol, acetic acid, and water produce two-dimensional crystalline adlayers on gold substrates, when they are introduced into the scanning cell as vapors. These adlayers are assumed to involve hydrogen bonding of the molecules to an oxide of gold formed on the surface. Electrospraying protein solutions on gold surfaces yielded images of individual protein molecules with lateral dimensions close to those measured by X-ray analysis, and thicknesses of 0.6-1.3 nm. In the case of metallothionein, the known internal domain structure of the molecule was reproducibly observed. No detailed internal structure could be resolved in the other examples examined
Elasticity of entangled polymer loops: Olympic gels
In this note we present a scaling theory for the elasticity of olympic gels,
i.e., gels where the elasticity is a consequence of topology only. It is shown
that two deformation regimes exist. The first is the non affine deformation
regime where the free energy scales linear with the deformation. In the large
(affine) deformation regime the free energy is shown to scale as where is the deformation ratio. Thus a highly non
Hookian stress - strain relation is predicted.Comment: latex, no figures, accepted in PRE Rapid Communicatio
Controlled assembly of SNAP-PNA-fluorophore systems on DNA templates to produce fluorescence resonance energy transfer
The SNAP protein is a widely used self-labeling tag that can be used for tracking protein localization and trafficking in living systems. A model system providing controlled alignment of SNAP-tag units can provide a new way to study clustering of fusion proteins. In this work, fluorescent SNAP-PNA conjugates were controllably assembled on DNA frameworks forming dimers, trimers, and tetramers. Modification of peptide nucleic acid (PNA) with the O6-benzyl guanine (BG) group allowed the generation of site-selective covalent links between PNA and the SNAP protein. The modified BG-PNAs were labeled with fluorescent Atto dyes and subsequently chemo-selectively conjugated to SNAP protein. Efficient assembly into dimer and oligomer forms was verified via size exclusion chromatography (SEC), electrophoresis (SDS-PAGE), and fluorescence spectroscopy. DNA directed assembly of homo- and hetero-dimers of SNAP-PNA constructs induced homo- and hetero-FRET, respectively. Longer DNA scaffolds controllably aligned similar fluorescent SNAP-PNA constructs into higher oligomers exhibiting homo-FRET. The combined SEC and homo-FRET studies indicated the 1:1 and saturated assemblies of SNAP-PNA-fluorophore:DNA formed preferentially in this system. This suggested a kinetic/stoichiometric model of assembly rather than binomially distributed products. These BG-PNA-fluorophore building blocks allow facile introduction of fluorophores and/or assembly directing moieties onto any protein containing SNAP. Template directed assembly of PNA modified SNAP proteins may be used to investigate clustering behavior both with and without fluorescent labels which may find use in the study of assembly processes in cells
Status of the Super-B factory Design
The SuperB international team continues to optimize the design of an
electron-positron collider, which will allow the enhanced study of the origins
of flavor physics. The project combines the best features of a linear collider
(high single-collision luminosity) and a storage-ring collider (high repetition
rate), bringing together all accelerator physics aspects to make a very high
luminosity of 10 cm sec. This asymmetric-energy collider
with a polarized electron beam will produce hundreds of millions of B-mesons at
the (4S) resonance. The present design is based on extremely low
emittance beams colliding at a large Piwinski angle to allow very low
without the need for ultra short bunches. Use of crab-waist
sextupoles will enhance the luminosity, suppressing dangerous resonances and
allowing for a higher beam-beam parameter. The project has flexible beam
parameters, improved dynamic aperture, and spin-rotators in the Low Energy Ring
for longitudinal polarization of the electron beam at the Interaction Point.
Optimized for best colliding-beam performance, the facility may also provide
high-brightness photon beams for synchrotron radiation applications
Tetraspanin (TSP-17) Protects Dopaminergic Neurons against 6-OHDA-Induced Neurodegeneration in <i>C. elegans</i>
Parkinson's disease (PD), the second most prevalent neurodegenerative disease after Alzheimer's disease, is linked to the gradual loss of dopaminergic neurons in the substantia nigra. Disease loci causing hereditary forms of PD are known, but most cases are attributable to a combination of genetic and environmental risk factors. Increased incidence of PD is associated with rural living and pesticide exposure, and dopaminergic neurodegeneration can be triggered by neurotoxins such as 6-hydroxydopamine (6-OHDA). In C. elegans, this drug is taken up by the presynaptic dopamine reuptake transporter (DAT-1) and causes selective death of the eight dopaminergic neurons of the adult hermaphrodite. Using a forward genetic approach to find genes that protect against 6-OHDA-mediated neurodegeneration, we identified tsp-17, which encodes a member of the tetraspanin family of membrane proteins. We show that TSP-17 is expressed in dopaminergic neurons and provide genetic, pharmacological and biochemical evidence that it inhibits DAT-1, thus leading to increased 6-OHDA uptake in tsp-17 loss-of-function mutants. TSP-17 also protects against toxicity conferred by excessive intracellular dopamine. We provide genetic and biochemical evidence that TSP-17 acts partly via the DOP-2 dopamine receptor to negatively regulate DAT-1. tsp-17 mutants also have subtle behavioral phenotypes, some of which are conferred by aberrant dopamine signaling. Incubating mutant worms in liquid medium leads to swimming-induced paralysis. In the L1 larval stage, this phenotype is linked to lethality and cannot be rescued by a dop-3 null mutant. In contrast, mild paralysis occurring in the L4 larval stage is suppressed by dop-3, suggesting defects in dopaminergic signaling. In summary, we show that TSP-17 protects against neurodegeneration and has a role in modulating behaviors linked to dopamine signaling
SuperB: a linear high-luminosity B Factory
This paper is based on the outcome of the activity that has taken place
during the recent workshop on "SuperB in Italy" held in Frascati on November
11-12, 2005. The workshop was opened by a theoretical introduction of Marco
Ciuchini and was structured in two working groups. One focused on the machine
and the other on the detector and experimental issues.
The present status on CP is mainly based on the results achieved by BaBar and
Belle. Estabilishment of the indirect CP violation in B sector in 2001 and of
the direct CP violation in 2004 thanks to the success of PEP-II and KEKB e+e-
asymmetric B Factories operating at the center of mass energy corresponding to
the mass of the Y(4s). With the two B Factories taking data, the Unitarity
Triangle is now beginning to be overconstrained by improving the measurements
of the sides and now also of the angles alpha, and gamma. We are also in
presence of the very intriguing results about the measurements of sin(2 beta)
in the time dependent analysis of decay channels via penguin loops, where b -->
s sbar s and b --> s dbar d. Tau physics, in particular LFV search, as well as
charm and ISR physics are important parts of the scientific program of a SuperB
Factory. The physics case together with possible scenarios for the high
luminosity SuperB Factory based on the concepts of the Linear Collider and the
related experimental issues are discussed.Comment: 22 pages, 22 figures, INFN Roadmap Repor
DNA-based Self-Assembly of Chiral Plasmonic Nanostructures with Tailored Optical Response
Surface plasmon resonances generated in metallic nanostructures can be
utilized to tailor electromagnetic fields. The precise spatial arrangement of
such structures can result in surprising optical properties that are not found
in any naturally occurring material. Here, the designed activity emerges from
collective effects of singular components equipped with limited individual
functionality. Top-down fabrication of plasmonic materials with a predesigned
optical response in the visible range by conventional lithographic methods has
remained challenging due to their limited resolution, the complexity of
scaling, and the difficulty to extend these techniques to three-dimensional
architectures. Molecular self-assembly provides an alternative route to create
such materials which is not bound by the above limitations. We demonstrate how
the DNA origami method can be used to produce plasmonic materials with a
tailored optical response at visible wavelengths. Harnessing the assembly power
of 3D DNA origami, we arranged metal nanoparticles with a spatial accuracy of 2
nm into nanoscale helices. The helical structures assemble in solution in a
massively parallel fashion and with near quantitative yields. As a designed
optical response, we generated giant circular dichroism and optical rotary
dispersion in the visible range that originates from the collective
plasmon-plasmon interactions within the nanohelices. We also show that the
optical response can be tuned through the visible spectrum by changing the
composition of the metal nanoparticles. The observed effects are independent of
the direction of the incident light and can be switched by design between left-
and right-handed orientation. Our work demonstrates the production of complex
bulk materials from precisely designed nanoscopic assemblies and highlights the
potential of DNA self-assembly for the fabrication of plasmonic nanostructures.Comment: 5 pages, 4 figure
- …