Subangstrom single-molecule measurements of motor proteins using a nanopore

Derrington, Ian M.; Craig, Jonathan M.; Stava, Eric; Laszlo, Andrew H.; Ross, Benjamin; Brinkerhoff, Henry; Nova, Ian C.; Doering, Kenji; Tickman, Benjamin I.; Ronaghi, Mostafa; Mandell, Jeffrey G.; Gunderson, Kevin L.; Gundlach, Jens H.

doi:10.1038/nbt.3357

Cited by 112 publications

(185 citation statements)

References 19 publications

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“…Derrington et al (Derrington et al, 2015) applied SPRNT to study the Hel308 helicase from Thermococcus gammatolerans (hereafter referred to as Hel308). Hel308 is an ATP-dependent Ski2-like superfamility II (SF2) helicase/translocase that unwinds duplex DNA in the 3′ to 5′ direction.…”

Section: Application Of Sprnt: Helicase Hel308mentioning

confidence: 99%

“…Such scaling converts the raw SNR into the scaled SNR (sSNR), the SNR that would be observed for a 1 nm step at 1 Hz bandwidth (Moffitt, Chemla, Izhaky, & Bustamante, 2006). Using comparisons of sSNR from various experiments (Abbondanzieri, Greenleaf, Shaevitz, Landick, & Block, 2005; Derrington et al, 2015; Dulin et al, 2015; Holden et al, 2010) we generated Figure 9, which shows a log-log sensitivity plot, highlighting the large new phase-space available to SPRNT experiments. Specifically figure 9 was constructed as follows:

The diagonal line representing the spatiotemporal resolution limit for OT comes from (Moffitt et al, 2008).

…”

Section: Comparison To Other Single-molecule Techniquesmentioning

confidence: 99%

“…2) This spline provides a direct mapping from current to DNA position and we can use it to measure sub-nucleotide movement of DNA. Figure modified from (Derrington et al, 2015). …”

Section: Figurementioning

confidence: 99%

“…With the ability to resolve such small substates and observe their chemical dependencies, SPRNT has the potential to shed light on how such motors actually do their work. Modified from (Derrington et al, 2015). …”

Section: Figurementioning

confidence: 99%

“…We call the method SPRNT, which stands for Single-molecule Picometer Resolution Nanopore Tweezers (Derrington et al, 2015). This method is ideally suited to enzymes that process along DNA, RNA or other charged polymers.…”

Section: Introduction To Sprntmentioning

confidence: 99%

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Subangstrom Measurements of Enzyme Function Using a Biological Nanopore, SPRNT

Laszlo

Derrrington

Gundlach

2017

Methods in Enzymology

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Nanopores are emerging as new single-molecule tools in the study of enzymes. Based on progress in nanopore sequencing of DNA, a tool called Single-molecule Picometer Resolution Nanopore Tweezers (SPRNT) was developed to measure the movement of enzymes along DNA in real time. In this new method, an enzyme is loaded onto a DNA (or RNA) molecule. A single stranded DNA end of this complex is drawn into a nanopore by an electrostatic potential that is applied across the pore. The single-stranded DNA passes through the pore’s constriction until the enzyme comes into contact with the pore. Further progression of the DNA through the pore is then controlled by the enzyme. An ion current that flows through the pore’s constriction is modulated by the DNA in the constriction. Analysis of ion current changes reveals the advance of the DNA with high spatiotemporal precision, thereby providing a real-time record of the enzyme’s activity. Using an engineered version of the protein nanopore MspA, SPRNT has spatial resolution as small as 40 pm at milliseconds time scales, while simultaneously providing the DNA’s sequence within the enzyme. In this chapter SPRNT is introduced and its extraordinary potential is exemplified using the helicase Hel308. Two distinct sub-states are observed for each one-nucleotide advance; one of these about half-nucleotide long steps is ATP-dependent and the other is ATP-independent. The spatiotemporal resolution of this low-cost single-molecule technique lifts the study of enzymes to a new level of precision, enabling exploration of hitherto unobservable enzyme dynamics in real-time.

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Section: Application Of Sprnt: Helicase Hel308mentioning

confidence: 99%

The diagonal line representing the spatiotemporal resolution limit for OT comes from (Moffitt et al, 2008).

…”

Section: Comparison To Other Single-molecule Techniquesmentioning

confidence: 99%

“…2) This spline provides a direct mapping from current to DNA position and we can use it to measure sub-nucleotide movement of DNA. Figure modified from (Derrington et al, 2015). …”

Section: Figurementioning

confidence: 99%

Section: Figurementioning

confidence: 99%

Section: Introduction To Sprntmentioning

confidence: 99%

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Subangstrom Measurements of Enzyme Function Using a Biological Nanopore, SPRNT

Laszlo

Derrrington

Gundlach

2017

Methods in Enzymology

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A Multiparameter pH‐Sensitive Nanodevice Based on Plasmonic Nanopores

Liu

Jiang

Pang

et al. 2017

Adv Funct Materials

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With controllable mass transfer and special optical properties, plasmonic nanopores may be applied as a nanodevice and possibly create a new generation of single molecule detection technique based on plasmon-enhanced spectra. In the present study, gold nanoparticles self-assemble into a gold porous sphere (GPS) on the tip of a glass nanopipette with the help of i-motif DNA thiolated by both ends as linker molecules. The gaps among neighboring gold nanoparticles are considered as plasmonic nanopores. The size of the formed nanopores can be tuned by the folded-unfolded conformational change of i-motif DNA upon pH adjustment from 4.5 to 7.0. Based on its tunable structural property, the GPS shows reversible changes in ionic current, potential, and surface-enhanced Raman scattering signal. The GPS is further used to probe regional pH in single cells. The successful application of GPS in multiparameter pH probing and single cell analysis suggests that the new physical properties of the self-assembled plasmonic nanopores can be used for fabricating multiple types of nanodevices and nanosensors.

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Super‐Resolution Detection of DNA Nanostructures Using a Nanopore

et al. 2023

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High‐resolution analysis of biomolecules has brought unprecedented insights into fundamental biological processes and dramatically advanced biosensing. Notwithstanding the ongoing resolution revolution in electron microscopy and optical imaging, only a few methods are presently available for high‐resolution analysis of unlabeled single molecules in their native states. Here, label‐free electrical sensing of structured single molecules with a spatial resolution down to single‐digit nanometers is demonstrated. Using a narrow solid‐state nanopore, the passage of a series of nanostructures attached to a freely translocating DNA molecule is detected, resolving individual nanostructures placed as close as 6 nm apart and with a surface‐to‐surface gap distance of only 2 nm. Such super‐resolution ability is attributed to the nanostructure‐induced enhancement of the electric field at the tip of the nanopore. This work demonstrates a general approach to improving the resolution of single‐molecule nanopore sensing and presents a critical advance towards label‐free, high‐resolution DNA sequence mapping, and digital information storage independent of molecular motors.

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Subangstrom single-molecule measurements of motor proteins using a nanopore

Cited by 112 publications

References 19 publications

Subangstrom Measurements of Enzyme Function Using a Biological Nanopore, SPRNT

Subangstrom Measurements of Enzyme Function Using a Biological Nanopore, SPRNT

A Multiparameter pH‐Sensitive Nanodevice Based on Plasmonic Nanopores

Super‐Resolution Detection of DNA Nanostructures Using a Nanopore

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