672 research outputs found
Unzipping Kinetics of Double-Stranded DNA in a Nanopore
We studied the unzipping kinetics of single molecules of double-stranded DNA
by pulling one of their two strands through a narrow protein pore. PCR analysis
yielded the first direct proof of DNA unzipping in such a system. The time to
unzip each molecule was inferred from the ionic current signature of DNA
traversal. The distribution of times to unzip under various experimental
conditions fit a simple kinetic model. Using this model, we estimated the
enthalpy barriers to unzipping and the effective charge of a nucleotide in the
pore, which was considerably smaller than previously assumed.Comment: 10 pages, 5 figures, Accepted: Physics Review Letter
Reduction of aldehydes and hydrogen cyanide yields in mainstream cigarette smoke using an amine functionalised ion exchange resin
<p>Abstract</p> <p>Background</p> <p>Cigarette smoking is a well recognized cause of diseases such as lung cancer, chronic obstructive pulmonary disease and cardiovascular disease. Of the more than 5000 identified species in cigarette smoke, at least 150 have toxicological activity. For example, formaldehyde and acetaldehyde have been assigned as Group 1 and Group 2B carcinogens by IARC, and hydrogen cyanide has been identified as a respiratory and cardiovascular toxicant. Active carbon has been shown to be an effective material for the physical adsorption of many of the smoke volatile species. However, physical adsorption of acetaldehyde, formaldehyde and also hydrogen cyanide from smoke is less effective using carbon. Alternative methods for the removal of these species from cigarette smoke are therefore of interest. A macroporous, polystyrene based ion-exchange resin (Diaion<sup>®</sup>CR20) with surface amine group functionality has been investigated for its ability to react with aldehydes and HCN in an aerosol stream, and thus selectively reduce the yields of these compounds (in particular formaldehyde) in mainstream cigarette smoke.</p> <p>Results</p> <p>Resin surface chemistry was characterized using vapour sorption, XPS, TOF-SIMS and <sup>15</sup>N NMR. Diaion<sup>®</sup>CR20 was found to have structural characteristics indicating weak physisorption properties, but sufficient surface functionalities to selectively remove aldehydes and HCN from cigarette smoke. Using 60 mg of Diaion<sup>®</sup>CR20 in a cigarette cavity filter gave reductions in smoke formaldehyde greater than 50% (estimated to be equivalent to >80% of the formaldehyde present in the smoke vapour phase) independent of a range of flow rates. Substantial removal of HCN (>80%) and acetaldehyde (>60%) was also observed. The performance of Diaion<sup>®</sup>CR20 was found to be consistent over a test period of 6 months. The overall adsorption for the majority of smoke compounds measured appeared to follow a pseudo-first order approximation to second order kinetics.</p> <p>Conclusions</p> <p>This study has shown that Diaion<sup>®</sup>CR20 is a highly selective and efficient adsorbent for formaldehyde, acetaldehyde and HCN in cigarette smoke. The reductions for these compounds were greater than those achieved using an active carbon. The results also demonstrate that chemisorption can be an effective mechanism for the removal of certain vapour phase toxicants from cigarette smoke.</p
Graphene: A sub-nanometer trans-electrode membrane
Isolated, atomically thin conducting membranes of graphite, called graphene,
have recently been the subject of intense research with the hope that practical
applications in fields ranging from electronics to energy science will emerge.
Here, we show that when immersed in ionic solution, a layer of graphene takes
on new electrochemical properties that make it a trans-electrode. The
trans-electrode's properties are the consequence of the atomic scale proximity
of its two opposing liquid-solid interfaces together with graphene's well known
in-plane conductivity. We show that several trans-electrode properties are
revealed by ionic conductivity measurements on a CVD grown graphene membrane
that separates two aqueous ionic solutions. Despite this membrane being only
one to two atomic layers thick, we find it is a remarkable ionic insulator with
a very small stable conductivity that depends on the ion species in solution.
Electrical measurements on graphene membranes in which a single nanopore has
been drilled show that the membrane's effective insulating thickness is less
than one nanometer. This small effective thickness makes graphene an ideal
substrate for very high-resolution, high throughput nanopore based single
molecule detectors. Sensors based on modulation of graphene's in-plane
electronic conductivity in response to trans-electrode environments and voltage
biases will provide new insights into atomic processes at the electrode
surfaces.Comment: Submitted 12 April 2010 to Nature, where it is under revie
Chaperone-assisted translocation of a polymer through a nanopore
Using Langevin dynamics simulations, we investigate the dynamics of
chaperone-assisted translocation of a flexible polymer through a nanopore. We
find that increasing the binding energy between the chaperone and
the chain and the chaperone concentration can greatly improve the
translocation probability. Particularly, with increasing the chaperone
concentration a maximum translocation probability is observed for weak binding.
For a fixed chaperone concentration, the histogram of translocation time
has a transition from long-tailed distribution to Gaussian distribution with
increasing . rapidly decreases and then almost saturates with
increasing binding energy for short chain, however, it has a minimum for longer
chains at lower chaperone concentration. We also show that has a minimum
as a function of the chaperone concentration. For different , a
nonuniversal dependence of on the chain length is also observed.
These results can be interpreted by characteristic entropic effects for
flexible polymers induced by either crowding effect from high chaperone
concentration or the intersegmental binding for the high binding energy.Comment: 10 pages, to appear in J. Am. Chem. So
Transverse Electronic Transport through DNA Nucleotides with Functionalized Graphene Electrodes
Graphene nanogaps and nanopores show potential for the purpose of electrical
DNA sequencing, in particular because single-base resolution appears to be
readily achievable. Here, we evaluated from first principles the advantages of
a nanogap setup with functionalized graphene edges. To this end, we employed
density functional theory and the non-equilibrium Green's function method to
investigate the transverse conductance properties of the four nucleotides
occurring in DNA when located between the opposing functionalized graphene
electrodes. In particular, we determined the electrical tunneling current
variation as a function of the applied bias and the associated differential
conductance at a voltage which appears suitable to distinguish between the four
nucleotides. Intriguingly, we observe for one of the nucleotides a negative
differential resistance effect.Comment: 19 pages, 7 figure
Effects of active carbon pore size distributions on adsorption of toxic organic compounds
Cryo-electron microscopy of viruses
Thin vitrified layers of unfixed, unstained and unsupported virus suspensions can be prepared for observation by cryo-electron microscopy in easily controlled conditions. The viral particles appear free from the kind of damage caused by dehydration, freezing or adsorption to a support that is encountered in preparing biological samples for conventional electron microscopy. Cryo-electron microscopy of vitrified specimens offers possibilities for high resolution observations that compare favourably with any other electron microscopical method
Nanopore surface coating delivers nanopore size and shape through conductance-based sizing
The performance of nanopore single-molecule sensing elements depends intimately on their physical dimensions and surface chemical properties. These factors underpin the dependence of the nanopore ionic conductance on electrolyte concentration, yet the measured, or modeled, dependence only partially illuminates the details of geometry and surface chemistry. Using the electrolyte-dependent conductance data before and after selective surface functionalization of solid-state nanopores, however, introduces more degrees of freedom and improves the performance of conductance-based nanopore characterizations. Sets of representative nanopore profiles were used to generate conductance data, and the nanopore shape and exact dimensions were identified, through conductance alone, by orders-of-magnitude 3 reductions in the geometry optimization metrics. The optimization framework could similarly be used to evaluate the nanopore surface coating thickness
Fusion of secretory vesicles isolated from rat liver
Secretory vesicles isolated from rat liver were found to fuse after exposure to Ca2+. Vescle fusion is characterized by the occurrence of twinned vesicles with a continuous cleavage plane between two vesicles in freeze-fracture electron microscopy. The number of fused vesicles increases with increasing Ca2+-concentrations and is half maximal around 10–6 m. Other divalent cations (Ba2+, Sr2+, and Mg2+) were ineffective. Mg2+ inhibits Ca2+-induced fusion. Therefore, the fusion of secretory vesiclesin vitro is Ca2+ specific and exhibits properties similar to the exocytotic process of various secretory cells.
Various substances affecting secretionin vivo (microtubular inhibitors, local anethetics, ionophores) were tested for their effect on membrane fusion in our system.
The fusion of isolated secretory vesicles from liver was found to differ from that of pure phospholipid membranes in its temperature dependence, in its much lower requirement for Ca2+, and in its Ca2+-specificity. Chemical and enzymatic modifications of the vesicle membrane indicate that glycoproteins may account for these differences
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