Nanopore analysis

Madampage, Claudia; Tavassoly, Omid; Christensen, Chris; Kumari, Meena; Lee, Jeremy S.

doi:10.4161/pri.18665

Cited by 49 publications

(38 citation statements)

References 69 publications

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“…35 As well, it was demonstrated that the event profiles after pre-incubation in 1.5 M guanidinium hydrochloride (Gdn-HCl) of wild-type bPrP and mutant bPrP(T194A) were different as were those of full length human PrP(23-231) and truncated PrP(90-231). 38 Thus the electronic signal at the instant that the protein interacts with the pore is very sensitive to the protein's structure and conformation. [39][40][41] A complete profile for wild-type bovine prion protein bPrP, could be accumulated in about 3 h (Fig.…”

Section: Resultsmentioning

confidence: 99%

Binding of bovine T194A PrP^Cby PrP^Sc-specific antibodies

Madampage

Määttänen

Marciniuk

et al. 2013

Prion

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Section: Resultsmentioning

confidence: 99%

Binding of bovine T194A PrP^Cby PrP^Sc-specific antibodies

Madampage

Määttänen

Marciniuk

et al. 2013

Prion

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“…Hence, nanopores can, in principle, provide precise information on a single-molecule level. Significant efforts have been devoted to nanopore DNA sequencing [2] and only recently possible proteomic applications have started being explored [3][4][5][6][7][8][9][10][11][12] using both solid-state and biological pores.…”

Section: Introductionmentioning

confidence: 99%

“…The protein passage across a narrow pore, like α-hemolysin [3,5,7], occurs via a capture stage followed by single-file translocation. Folded proteins are extremely hard, if not impossible, to capture [5] in standard voltage-driven experiments with biopores, requiring a prior chemical unfolding in the bulk before translocating.…”

Section: Introductionmentioning

confidence: 99%

“…[16] for a rod-coil polymer passing through a model nanopore. Moreover, experimental studies [5][6][7] have shown that certain translocation can be characterized by long tails in the blockade time distributions with the suspect that, besides the capture, some other kind of rate-limiting mechanism could be at work during the migration determining the bottlenecks.…”

Section: Introductionmentioning

confidence: 99%

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Protein translocation in narrow pores: Inferring bottlenecks from native structure topology

et al. 2013

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Coarse-grained simulations of protein translocation across narrow pores suggest that the transport is characterized by long stall events. The translocation bottlenecks and the associated free-energy barriers are found to be strictly related to the structural properties of the protein native structure. The ascending ramps of the free-energy profile systematically correspond to regions of the chain denser in long range native contacts formed with the untranslocated portion of the protein. These very regions are responsible for the stalls occurring during the protein transport along the nanopore. The decomposition of the free energy in internal energyand entropic terms shows that the dominant energetic contribution can be estimated on the base of the protein native structure only. Interestingly, the essential features of the dynamics are retained in a reduced phenomenological model of the process describing the evolution of a suitable collective variable in the associated free-energy landscape.

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“…Translocation of DNA is the most studied process [6] being a promising technology for low cost/high throughput DNA analysis, its realization is still confronted with challenges [7][8][9][10]. In parallel, a separate set of studies have focused on protein and polypeptide translocation, with the goal of structural characterization [11][12][13][14][15].…”

mentioning

confidence: 99%

Modulation of current through a nanopore induced by a charged globule: Implications for DNA-docking

Chinappi¹,

Casciola²,

Cecconi³

et al. 2014

EPL

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H--Macromolecular and polymers solutions; polymer meltsAbstract -The passage of DNA through a nanopore can be effectively decomposed into two distinct phases, docking and actual translocation. In experiments each phase is characterized by a distinct current signature which allows the discrimination of the two events. However, at low voltages a clear distinction of the two phases is lost. By using numerical simulations we clarify how the current signature associated to the docking events depends on the applied voltage. The simulations show that at small voltage the DNA globule enhances the pore conductance due to an enrichment of charge carriers. At high voltage, the globule drains substantial charge carriers from the pore region, thereby reducing the overall conductance. The results provide a new interpretation to the experimental data on conductance and show how docking interferes with the translocation signal, of potential interest for sequencing applications.Introduction. -In the last decade, nanopore-based biosensing has become a burgeoning research field thanks to the impressive burst in the capability to fabricate devices based on solid state [1,2] and biological pores [3][4][5]. The working principle of the device is, in essence, simple. The nanopore connects two chambers containing an electrolyte solution. Under an electric voltage, ions migrate from one chamber to the other, with a conductance that depends on the details of the pore and the electrolytic solution. Since a translocating macromolecule alters the ionic flux, its passage can be detected and possibly the local nature of its monomers can be read off. Translocation of DNA is the most studied process [6] being a promising technology for low cost/high throughput DNA analysis, its realization is still confronted with challenges [7][8][9][10]. In parallel, a separate set of studies have focused on protein and polypeptide translocation, with the goal of structural

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Nanopore analysis

Cited by 49 publications

References 69 publications

Binding of bovine T194A PrP^Cby PrP^Sc-specific antibodies

Binding of bovine T194A PrP^Cby PrP^Sc-specific antibodies

Protein translocation in narrow pores: Inferring bottlenecks from native structure topology

Modulation of current through a nanopore induced by a charged globule: Implications for DNA-docking

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Nanopore analysis

Cited by 49 publications

References 69 publications

Binding of bovine T194A PrPCby PrPSc-specific antibodies

Binding of bovine T194A PrPCby PrPSc-specific antibodies

Protein translocation in narrow pores: Inferring bottlenecks from native structure topology

Modulation of current through a nanopore induced by a charged globule: Implications for DNA-docking

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Binding of bovine T194A PrP^Cby PrP^Sc-specific antibodies

Binding of bovine T194A PrP^Cby PrP^Sc-specific antibodies