Fast, Label-Free Force Spectroscopy of Histone–DNA Interactions in Individual Nucleosomes Using Nanopores

Ivankin, Andrey; Carson, Spencer; Kinney, Shannon R. Morey; Wanunu, Meni

doi:10.1021/ja408354s

Cited by 45 publications

(58 citation statements)

References 32 publications

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“…12 Furthermore, nanopores may be exploited to characterize and separate synthetic macromolecules. The various charged macromolecules used in the health care and materials industries typically start out highly polydisperse.…”

Section: Beyond Sequencingmentioning

confidence: 99%

Single-molecule sensing with nanopores

Muthukumar¹,

Plesa²,

Dekker³

2015

Physics Today

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Section: Beyond Sequencingmentioning

confidence: 99%

Single-molecule sensing with nanopores

Muthukumar¹,

Plesa²,

Dekker³

2015

Physics Today

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“…[37] Wanunu and co-workers reported an approach for the fast, label-free probing of DNA-histone interactions in individual nucleosomes by unraveling the DNA-histone complexes with an SSnanopore. [38] Yu et al demonstrated the identification of zinc finger binding site within ad sDNAt oas ingle protein resolution using alow noise solid-state nanopore. [39] Similarly, Bashir and co-workers used methyl-binding proteins (MBPs) to selectively label the methylated DNAa nd accomplished the detection of methylation in dsDNAf ragments.…”

Section: Methodsmentioning

confidence: 99%

DNA‐Based Nanopore Sensing

Liu

2016

Angew Chem Int Ed

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Nanopore sensing is an attractive, label-free approach that can measure single molecules. Although initially proposed for rapid and low-cost DNA sequencing, nanopore sensors have been successfully employed in the detection of a wide variety of substrates. Early successes were mostly achieved based on two main strategies by 1) creating sensing elements inside the nanopore through protein mutation and chemical modification or 2) using molecular adapters to enhance analyte recognition. Over the past five years, DNA molecules started to be used as probes for sensing rather than substrates for sequencing. In this Minireview, we highlight the recent research efforts of nanopore sensing based on DNA-mediated characteristic current events. As nanopore sensing is becoming increasingly important in biochemical and biophysical studies, DNA-based sensing may find wider applications in investigating DNA-involving biological processes.

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“…Different kinds of proteins, [97,98] DNA-protein complexes, [99,100] biomarkers, enzyme flexibilities, [101] and biochemical processes [5] have been widely studied through the electrical signals obtained from nanopores. Now, with the help of high-sensitivity and specific optical signals, more detailed research on those biochemical processes and molecules in suit can be conducted.…”

Section: Identification Of Complexes and Biochemical Processes At Thementioning

confidence: 99%

Electro‐Optical Detection of Single Molecules Based on Solid‐State Nanopores

Tong

et al. 2020

Small Structures

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Solid-state nanopore-based biosensors have received considerable attention in the past two decades and are promising for the next-generation single-molecule detection and sequencing platforms. Typically, the sensor is comprised of a thin inorganic membrane that separates two chambers containing an ion conductive solution. A nanoscale pore is drilled in the membrane as the only channel connecting the two chambers (cis chamber and trans chamber). The charged molecules are driven through the nanopore by an electric field applied across the membrane. At the same time, as the molecules block a fraction of the ionic current that flows through the pore, there will be a set of current pulses. The characteristics of the pulses, such as dwell time (duration of the pulses) and current blockages, give us a wealth of information about the passing analytes. Typically, excluded volumes, charges, capture rates, configurations, dynamics, and possible interactions of the analyte molecules can be concluded from electrical signals. Biological nanopores have been commercially used for DNA sequencing. [1] However, for solid-state nanopores, there are still challenges that need to be addressed for commercial use: specifically, spatial resolution, temporal resolution, and reproducibility. To achieve the identification of nucleotides during a stepwise displacement of DNA through the nanopores, our sensors must have a spatial resolution of 0.34 nm, considering the distance between adjacent base pairs of a double-stranded DNA chain. [2] Such a spatial resolution is a real challenge for nanofabrication of solid-state pores. Temporal resolution depends on the maximum bandwidth of the platforms and translocation speed of the analyte molecules. Limited temporal resolution leads to anomalously low event rates and distorted signals of proteins. [3] Signal reproducibility is another problem for solid-state nanopores compared with their biological counterparts. Biological nanopores, such as α-hemolysin [4] and mycobacterium smegmatis porin A, [5] serve as reliable sensors with excellent signal reproducibility because of the same genetically encoded structure. In comparison, due to the nonuniformity of the fabrication process or other unknown reasons, each solid-state nanopore is slightly different from one to another. In addition, there are other limitations for conventional solid-state nanopore sensors, such as low throughput, background noise, and lack of external handles to manipulate the analytes. Several strategies have been proposed to address these challenges, among which the combination of solid-state nanopores and optical detection has obvious advantages. Introducing a synchronized optical detection would help to improve the spatial resolution of solid-state nanopore platforms. Optical detection, in particular fluorescence [6] and surface-enhanced Raman spectroscopy (SERS), [7,8] has been widely used for

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Fast, Label-Free Force Spectroscopy of Histone–DNA Interactions in Individual Nucleosomes Using Nanopores

Cited by 45 publications

References 32 publications

Single-molecule sensing with nanopores

Single-molecule sensing with nanopores

DNA‐Based Nanopore Sensing

Electro‐Optical Detection of Single Molecules Based on Solid‐State Nanopores

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