Probing single nanometer-scale pores with polymeric molecular rulers

Henrickson, Sarah E.; DiMarzio, Edmund A.; Wang, Qian; Stanford, Vincent M.; Kasianowicz, John J.

doi:10.1063/1.3328875

Cited by 48 publications

(53 citation statements)

References 81 publications

(74 reference statements)

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“…After the completion of our work, a problem similar to the present work has been addressed in a recent publication. 48 There are several directions in which the experiments conducted here may be extended. While the present work clearly demonstrates the presence of entropic and enthalpic contributions to the free energy profile, it would be of particular interest to establish quantitatively their relative magnitudes by varying the temperature.…”

Section: Conclusion and Discussionmentioning

confidence: 99%

Polymer translocation through α-hemolysin pore with tunable polymer-pore electrostatic interaction

Wong

Muthukumar

2010

The Journal of Chemical Physics

120

165

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We have measured the ionic current blockages produced by single molecules of sodium poly͑styrene sulfonate͒ passing through an ␣-hemolysin protein pore under an electric field. Most of the blockage events were composed of one or two blockage levels of ionic current. By analyzing the statistics of different event types for different polymer lengths, applied voltages, and pH conditions, we have identified the molecular mechanism behind the two-level blockages. Our analysis of the data shows that not all blockages are successful translocation events and the propensity of successful translocation can be tuned by pH gradients across the protein pore. We interpret our results as the change in protein-polymer interaction via protonation of charged amino acid residues of ␣-hemolysin pore. In addition, we have constructed a stochastic theory for polymer translocation through ␣-hemolysin pore with tunable polymer-pore interactions. The theoretical calculations capture many features observed in our experiments.

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Section: Conclusion and Discussionmentioning

confidence: 99%

Polymer translocation through α-hemolysin pore with tunable polymer-pore electrostatic interaction

Wong

Muthukumar

2010

The Journal of Chemical Physics

120

165

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“…To date, several groups have developed algorithms to analyze current blockade events [22,43-45]. Herein, we developed an automated single molecule analysis system using Matlab algorithm for detailed characterization of a large number of DNA translocation events using a set of parameters ( Suppl.…”

Section: Methodsmentioning

confidence: 99%

Single pore translocation of folded, double-stranded, and tetra-stranded DNA through channel of bacteriophage phi29 DNA packaging motor

et al. 2015

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The elegant architecture of the channel of bacteriophage phi29 DNA packaging motor has inspired the development of biomimetics for biophysical and nanobiomedical applications. The reengineered channel inserted into a lipid membrane exhibits robust electrophysiological properties ideal for precise sensing and fingerprinting of dsDNA at the single-molecule level. Herein, we used single channel conduction assays to quantitatively evaluate the translocation dynamics of dsDNA as a function of the length and conformation of dsDNA. We extracted the speed of dsDNA translocation from the dwell time distribution and estimated the various forces involved in the translocation process. A ~35-fold slower speed of translocation per base pair was observed for long dsDNA, a significant contrast to the speed of dsDNA crossing synthetic pores. It was found that the channel could translocate both dsDNA with ~32% of channel current blockage and ~64% for tetra-stranded DNA (two parallel dsDNA). The calculation of both cross-sectional areas of the dsDNA and tetra-stranded DNA suggested that the blockage was purely proportional to the physical space of the channel lumen and the size of the DNA substrate. Folded dsDNA configuration was clearly reflected in their characteristic current signatures. The finding of translocation of tetra-stranded DNA with 64% blockage is in consent with the recently elucidated mechanism of viral DNA packaging via a revolution mode that requires a channel larger than the dsDNA diameter of 2 nm to provide room for viral DNA revolving without rotation. The understanding of the dynamics of dsDNA translocation in the phi29 system will enable us to design more sophisticated single pore DNA translocation devices for future applications in nanotechnology and personal medicine.

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“…The change in pore conductance is caused by the volume exclusion of mobile ions from the pore 20,21 and interactions between the ions and the analyte. 5,21,26 The change in conductance 4,20,21,26,27 and the residence time of analytes in the pore 8,20,21 are used to estimate the analyte size, 20,21 effective charge, 21 and dipole moment. 28 …”

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confidence: 99%

MOSAIC: A Modular Single-Molecule Analysis Interface for Decoding Multistate Nanopore Data

et al. 2016

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Biological and solid-state nanometer-scale pores are the basis for numerous emerging analytical technologies for use in precision medicine. We developed Modular Single-Molecule Analysis Interface (MOSAIC), an open source analysis software that improves the accuracy and throughput of nanopore-based measurements. Two key algorithms are implemented: ADEPT, which uses a physical model of the nanopore system to characterize short-lived events that do not reach their steady-state current, and CUSUM+, a version of the cumulative sum statistical method optimized for longer events that do. We show that ADEPT detects previously unreported conductance states that occur as double-stranded DNA translocates through a 2.4 nm solid-state nanopore and reveals new interactions between short single-stranded DNA and the vestibule of a biological pore. These findings demonstrate the utility of MOSAIC and the ADEPT algorithm, and offer a new tool that can improve the analysis of nanopore-based measurements.

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Probing single nanometer-scale pores with polymeric molecular rulers

Cited by 48 publications

References 81 publications

Polymer translocation through α-hemolysin pore with tunable polymer-pore electrostatic interaction

Polymer translocation through α-hemolysin pore with tunable polymer-pore electrostatic interaction

Single pore translocation of folded, double-stranded, and tetra-stranded DNA through channel of bacteriophage phi29 DNA packaging motor

MOSAIC: A Modular Single-Molecule Analysis Interface for Decoding Multistate Nanopore Data

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