Search results for "nanopore"
showing 10 items of 99 documents
Direct RNA nanopore sequencing of SARS-CoV-2 extracted from critical material from swabs
2020
ABSTRACTBackgroundIn consideration of the increasing prevalence of COVID-19 cases in several countries and the resulting demand for unbiased sequencing approaches, we performed a direct RNA sequencing experiment using critical oropharyngeal swab samples collected from Italian patients infected with SARS-CoV-2 from the Palermo region in Sicily.MethodsHere, we identified the sequences SARS-CoV-2 directly in RNA extracted from critical samples using the Oxford Nanopore MinION technology without prior cDNA retro-transcription.ResultsUsing an appropriate bioinformatics pipeline, we could identify mutations in the nucleocapisid (N) gene, which have been reported previously in studies conducted in…
A redox-sensitive nanofluidic diode based on nicotinamide-modified asymmetric nanopores
2017
[EN] We demonstrate a redox-sensitive nanofluidic diode whose ion rectification is modulated by the oxidation and reduction of chemical moieties incorporated on its surface. To achieve this goal, we have first synthesized the chemical compounds 1-(4-aminobutyl)-3-carbamoylpyridin-1-ium (Nic-BuNH2) and 3-carbamoyl-1-(2,4-dinitrophenyl)pyridinium (Nic-DNP). Then, the surface of track-etched single asymmetric nanopores is decorated with the redox-sensitive Nic-BuNH2 and Nic-DNP molecules using carbodiimide coupling chemistry and Zincke reaction, respectively. The success of the modification reactions is monitored through the changes in the current¿voltage (I¿V) curves prior to and after pore f…
Protein transport through gold-coated, charged nanopores: Effects of applied voltage
2006
The flux of bovine serum albumin and bovine hemoglobin through charged nanopores inside polymeric membranes is analysed as a function of the applied voltage to the nanopore surface, the solution ionic strength and pH. The electrostatic interaction of the protein with the nanopore surface gives low transport rates except at the protein isoelectric point and the minimum of the effective, voltage-induced nanopore charge. This electrostatic sieving effect allows for the separation of proteins with similar molecular weights.
Ionic transport characteristics of negatively and positively charged conical nanopores in 1:1, 2:1, 3:1, 2:2, 1:2, and 1:3 electrolytes
2019
We study experimentally the current (I)-voltage (V) curves of 1:1, 2:1, 3:1, 2:2, 1:2, and 1:3 electrolytes in positively and negatively charged conically-shaped pores of nanoscale dimensions. The positive charges are poly(allylamine hydrochloride) chains functionalized on the pore surface by electrostatic interactions while the negative charges are carboxylic acid groups. Under physiological conditions, these fixed-charge groups are ionized and strongly interact with the different monovalent, divalent, and trivalent ions in the pore solution. The current rectification of the I-V curves and the membrane potentials provide fundamental information on the interaction of the pore charge groups …
Adsorption-induced polymer translocation through a nanopore: a Monte Carlo investigation
2005
Abstract We study the translocation of a coarse-grained flexible polymer through a nanopore in a membrane induced by its adsorption on the trans side of the membrane. Dramatic differences in the threading behavior are observed if the adhesion to the membrane wall, e w , is below or above the adsorption threshold e c r . For e w e c r (weak adsorption) the activation barrier for translocation is at c cis 0 ≈ N / 2 (in terms of the fraction of chain c cis = N cis / N before the pore), independent of chain length N. For e w > e c r this barrier is at a constant (vanishing) number of passed trans monomers for all N. The mean time of chain passage τ trans ∝ c cis 1.3 when c cis c cis 0 . It scal…
Fabrication of Single Cylindrical Au-Coated Nanopores with Non-Homogeneous Fixed Charge Distribution Exhibiting High Current Rectifications
2014
We have designed and characterized a cylindrical nanopore that exhibits high electrochemical current rectification ratios at low and intermediate electrolyte concentrations. For this purpose, the track-etched single cylindrical nanopore in polymer membrane is coated with a gold (Au) layer via electroless plating technique. Then, a non-homogeneous fixed charge distribution inside the Au-coated nanopore is obtained by incorporating thiol-terminated uncharged poly(N-isopropylacrylamide) (PNIPAM) chains in series to poly(4-vinyl pyridine) (PVP) chains, which are positively charged at acidic pH values. The functionalization reaction is checked by measuring the current–voltage (I–V) curves prior …
Metal ion affinity-based biomolecular recognition and conjugation inside synthetic polymer nanopores modified with iron-terpyridine complexes.
2011
Here we demonstrate a novel biosensing platform for the detection of lactoferrin (LFN) via metal-organic frameworks, in which the metal ions have accessible free coordination sites for binding, inside the single conical nanopores fabricated in polymeric membrane. First, monolayer of amine-terminated terpyridine (metal-chelating ligand) is covalently immobilized on the inner walls of the nanopore via carbodiimide coupling chemistry. Second, iron-terpyridine (iron-terPy) complexes are obtained by treating the terpyridine modified-nanopores with ferrous sulfate solution. The immobilized iron-terPy complexes can be used as recognition elements to fabricate biosensing nanodevice. The working pri…
Conformation of Polyethylene Glycol inside Confined Space: Simulation and Experimental Approaches
2021
The modification of the inner nanopore wall by polymers is currently used to change the specific properties of the nanosystem. Among them, the polyethylene glycol (PEG) is the most used to prevent the fouling and ensure the wettability. However, its properties depend mainly on the chain structure that is very difficult to estimate inside this confined space. Combining experimental and simulation approaches, we provide an insight to the consequence of the PEG presence inside the nanopore on the nanopore properties. We show, in particular, that the cation type in the electrolyte, together with the type of electrolyte (water or urea), is at the origin of the ion transport modification in the n…
Surface charge regulation of functionalized conical nanopore conductance by divalent cations and anions
2019
Abstract The surface charge regulation in nanoscale volumes is a subject of wide interest to biological and chemical soft matter systems. Also, electrolyte mixtures with monovalent and divalent ions are commonplace in practical applications with micro and nanoporous ion-exchange membranes. We have studied experimentally and theoretically the conductance of conical nanopores functionalized with negative and positive surface charges that are bathed by electrolyte mixtures of the monovalent ions K+ and Cl− and the divalent ions Mg2+, Ba2+, Ca2+, and SO42−. Small concentrations of these ions can modulate the nanopore selectivity and conductance because of their interaction with the charged grou…
KINETICS OF POLYMER EJECTION FROM CAPSID CONFINEMENT: SCALING CONSIDERATIONS AND COMPUTER EXPERIMENT
2012
We investigate the ejection dynamics of a flexible polymer chain out of confined environment by means of scaling considerations and Monte Carlo simulations. Situations of this kind arise in different physical contexts, including a flexible synthetic polymer partially confined in a nanopore and a viral genome partially ejected from its capsid. In the case of cylindric confinement the entropic driving force which pulls the chain out of the pore is argued to be constant once a few persistent lengths are out of the pore. We demonstrate that in this case the ejection dynamics follows a [Formula: see text]-law with elapsed time t. The mean ejection time τ depends nonmonotonically on chain length…