Electro-osmotic capture and ionic discrimination of peptide and protein biomarkers with FraC nanopores

Huang, Gang; Willems, Kherim; Soskine, Misha; Wloka, Carsten; Maglia, Giovanni

doi:10.1038/s41467-017-01006-4

Cited by 221 publications

(295 citation statements)

References 78 publications

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“…To decrease the difficulty of protein sequencing, some investigators tried to understand the translocation process in virtue of denaturant, pH change, enzyme, or aptamer . In addition, the protein can be fragmented by chemical cleavage or enzymatic digestion, then peptide fragments can be analyzed by biological nanopores, for instance, α‐hemolysin, OmpF, Phi29, Frac . According to our recent results, aerolysin, a β‐pore‐forming toxin from Aeromonas hydrophila , performed a high sensing ability for molecular detection .…”

Section: Properties Of the Peptides Used In The Workmentioning

confidence: 99%

Detection of Peptides with Different Charges and Lengths by Using the Aerolysin Nanopore

Cao

Yang

et al. 2018

ChemElectroChem

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The aerolysin nanopore has a high sensitivity for molecular sensing, owing to its super‐narrow diameter and highly charged lumen structure. Here, taking advantages of its high sensitivity, we investigated peptides with comparable size and mass but different charges. Based on the blockade current and duration time, we found that the charge distribution at the entrance of the aerolysin nanopore governs the capture of peptides. Moreover, peptides with the same charge density but different lengths were measured by the aerolysin nanopore. In comparison to the short peptides, longer peptides gave a larger blockade current and a longer duration time. Our findings demonstrate that both the charge and length of peptides affect the translocation process simultaneously, which improve our understanding of peptides’ translocation through the aerolysin nanopore and suggest that aerolysin is an excellent candidate for peptides/protein sequencing.

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Section: Properties Of the Peptides Used In The Workmentioning

confidence: 99%

Detection of Peptides with Different Charges and Lengths by Using the Aerolysin Nanopore

Cao

Yang

et al. 2018

ChemElectroChem

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“…More specifically, biological and solid‐state nanopores are nanoscale openings in a thin membrane that electrophoretically transport biomolecules toward the sensing region via an externally applied bias voltage. This active transport results in great sensor response times and has been used in the past decade to characterize protein, DNA, and protein–DNA interactions . However, the mode of transport unavoidably leads to an uncontrollably fast passage of the molecules through the sensing region and high translocation speeds that lead to a limited temporal resolution in the ionic‐current readout .…”

Section: Introductionmentioning

confidence: 99%

“…Ultimately, the proposed single‐molecule manipulator enables to grab single molecules from solution, and then trap them in the sensor to observe their structural characteristics and native dynamics, and finally expel them after investigation. This creates opportunities for the characterization of protein solutions for diagnostics, the study of protein–ligand interactions for drug screening, and a system for biophysical investigation of protein folding, all without any need for labeling.…”

Section: Introductionmentioning

confidence: 99%

Nano‐Optical Tweezing of Single Proteins in Plasmonic Nanopores

2019

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Single‐molecule sensing technologies aim to detect and characterize single biomolecules, but generally need labeling while the measurement times and throughput are severely restricted by a lack of positional control over the molecule. Here, a plasmonic nanopore biosensor is reported where single molecules can be electrophoretically delivered into a nanopore sensor with a plasmonic nanoantenna that is used to optically trap single molecules for extended measurement times. Using the light transmission through the antenna as read‐out, optical trapping of 20 nm diameter polystyrene nanoparticles and individual beta‐amylase proteins, a 200 kDa enzyme, in the plasmonic nanoantenna are demonstrated. Application of an electrical bias voltage allows the increase of the event rate over an order of magnitude as well as shorten the residence time of the proteins in the plasmonic nanopore as they can controllably be drawn out of the trap by electrical forces. Trapping is found to be assisted by protein–surface interactions and trapped proteins can denature on the nanopore surface. The integration of two single‐molecule sensors, a plasmonic nanoantenna and solid‐state nanopore, creates independent control handles at the single‐molecule level—the optical trapping force and electrophoretic force—which provides augmented control over single molecules.

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“…[1][2][3][4][5][6] One of the primary driving forces behind this research is the development of nanopores as label-free, stochastic sensors at the ultimate analytical limit (i.e., single molecule). 7-10 Such detectors have applications ranging from the analysis of biopolymers such as DNA [11][12][13][14][15][16][17][18] or proteins, [19][20][21][22][23] to the detection and quantification of biomarkers, [24][25][26][27][28][29][30] to the fundamental study of chemical or enzymatic reactions at the single molecular level. 22,[31][32][33][34] Nanopores are typically operated in the resistive-pulse mode, where the fluctuations of their ionic conductance are monitored over time.…”

Section: Introductionmentioning

confidence: 99%

Modeling of Ion and Water Transport in the Biological Nanopore ClyA

Willems

Ruić

Lucas

et al. 2020

Preprint

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In recent years, the protein nanopore cytolysin A (ClyA) has become a valuable tool for the detection, characterization and quantification of biomarkers, proteins and nucleic acids at the single-molecule level. Despite this extensive experimental utilization, a comprehensive computational study of ion and water transport through ClyA is currently lacking. Such a study yields a wealth of information on the electrolytic conditions inside the pore and on the scale the electrophoretic forces that drive molecular transport. To this end we have built a computationally efficient continuum model of ClyA which, together with an extended version of Poison-Nernst-Planck-Navier-Stokes (ePNP-NS) equations, faithfully reproduces its ionic conductance over a wide range of salt concentrations. These ePNP-NS equations aim to tackle the shortcomings of the traditional PNP-NS models by self-consistently taking into account the influence of both the ionic strength and the nanoscopic scale of the pore on all relevant electrolyte properties. In this study, we give both a detailed description of our ePNP-NS 1 model and apply it to the ClyA nanopore. This enabled us to gain a deeper insight into the influence of ionic strength and applied voltage on the ionic conductance through ClyA and a plethora of quantities difficult to assess experimentally. The latter includes the cation and anion concentrations inside the pore, the shape of the electrostatic potential landscape and the magnitude of the electro-osmotic flow. Our work shows that continuum models of biological nanopores-if the appropriate corrections are applied-can make both qualitatively and quantitatively meaningful predictions that could be valuable tool to aid in both the design and interpretation of nanopore experiments.

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Electro-osmotic capture and ionic discrimination of peptide and protein biomarkers with FraC nanopores

Cited by 221 publications

References 78 publications

Detection of Peptides with Different Charges and Lengths by Using the Aerolysin Nanopore

Detection of Peptides with Different Charges and Lengths by Using the Aerolysin Nanopore

Nano‐Optical Tweezing of Single Proteins in Plasmonic Nanopores

Modeling of Ion and Water Transport in the Biological Nanopore ClyA

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