SERS discrimination of single DNA bases in single oligonucleotides by electro-plasmonic trapping

Huang, Jian‐An; Mousavi, Mansoureh Z.; Zhao, Yingqi; Hubarevich, Aliaksandr; Omeis, Fatima; Giovannini, Giorgia; Schütte, Moritz; Garoli, Denis; Angelis, Francesco De

doi:10.1038/s41467-019-13242-x

Cited by 170 publications

(173 citation statements)

References 63 publications

(77 reference statements)

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“…Pioneering studies from different groups have demonstrated the capability of identifying DNA or RNA fragments and even individual nucleobases by SERS. [ 280,281 ] Moreover, recent theoretical and experimental studies have demonstrated that the spatial resolution of SERS approaches the subnanometer level in dry conditions. Researchers also demonstrated remote excitation and detection of SERS using optical nanoantenna (nanowire‐nanoparticle system, single nanowire system, crossed nanowire system, nanowire‐dimer system, etc.)…”

Section: Resultsmentioning

confidence: 99%

Optical nanoantenna for beamed and surface‐enhanced Raman spectroscopy

Awasthi

Goel

Agarwal

et al. 2020

J Raman Spectroscopy

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Optical nanoantenna is a key component in plasmonic circuitry, which can receive or transmit an electromagnetic field in the near field of an object (nanomaterials). It has wide range of applications including surface‐enhanced Raman scattering (SERS), photocatalytic reactions, remote SERS, solar cell, plasmonic nanoscopy, and quantum plasmonics. The main challenges in optical nanoantenna research include both fundamental understanding of the underlying physics and issues related to fabrication of low cost, high throughput nanostructures beyond the diffraction limit. The nanoscale feature size of optical antennas limits our ability to design, manufacture, and characterize their resonant behavior. This review investigates the fabrication methods and SERS applications of optical nanoantenna.

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Section: Resultsmentioning

confidence: 99%

Optical nanoantenna for beamed and surface‐enhanced Raman spectroscopy

Awasthi

Goel

Agarwal

et al. 2020

J Raman Spectroscopy

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“…However, there is still a long way to go, with many details remaining to be addressed. [9,90] For example, the translocation speed of molecules is still too fast for a spectrometer. Finally, it needs to be mentioned that plasmons can also modulate the FRET between a donor fluorophore and an acceptor fluorophore.…”

Section: Detection Of Plasmon Resonance Shift Sersmentioning

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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“…In the “flow-through” SERS, molecules pass the detection point so rapidly that the collected SERS signals are not sufficient for single-molecule analysis. By employing a single nanopore [ 54 ] or nanoslit [ 55 ] that allows the electrokinetic capture (i.e., electroplasmonic trapping effect) to increase the residual time of target molecules within the hot-spots, as illustrated in Figure 2 b, it is possible to trace the spectroscopic fingerprinting of a single DNA molecule. The device has also been applied in detection of all four DNA bases in a single DNA molecule, as well as in identification of single nucleobases in a single oligonucleotide.…”

Section: Optical Detectionmentioning

confidence: 99%

“…The device has also been applied in detection of all four DNA bases in a single DNA molecule, as well as in identification of single nucleobases in a single oligonucleotide. The above-mentioned results indicate the capability of nanofluidics in manipulating single molecules, as well as the light–matter interactions for single-molecule detection [ 54 , 55 ].…”

Section: Optical Detectionmentioning

confidence: 99%

“… Nanofluidic devices for SERS: ( a ) device exploiting the localization of nanoparticles and preconcentration of target molecules at micro/nanochannel junction (adapted with permission from [ 51 ]. Copyright 2011 American Chemical Society), ( b ) electrokinetic capture of a single molecule at a nanopore to increase its residual time (adapted with permission from [ 55 ]. Copyright 2019 Springer Nature), and ( c ) self-rolled nanotube integrated with Ag NPs supporting the coupling of whispering-gallery resonances and surface plasmon generated on Ag NPs that improves the enhancement factor in SERS.…”

Section: Figurementioning

confidence: 99%

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Advances in Label-Free Detections for Nanofluidic Analytical Devices

Shimizu

Morikawa

2020

Micromachines

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Nanofluidics, a discipline of science and engineering of fluids confined to structures at the 1–1000 nm scale, has experienced significant growth over the past decade. Nanofluidics have offered fascinating platforms for chemical and biological analyses by exploiting the unique characteristics of liquids and molecules confined in nanospaces; however, the difficulty to detect molecules in extremely small spaces hampers the practical applications of nanofluidic devices. Laser-induced fluorescence microscopy with single-molecule sensitivity has been so far a major detection method in nanofluidics, but issues arising from labeling and photobleaching limit its application. Recently, numerous label-free detection methods have been developed to identify and determine the number of molecules, as well as provide chemical, conformational, and kinetic information of molecules. This review focuses on label-free detection techniques designed for nanofluidics; these techniques are divided into two groups: optical and electrical/electrochemical detection methods. In this review, we discuss on the developed nanofluidic device architectures, elucidate the mechanisms by which the utilization of nanofluidics in manipulating molecules and controlling light–matter interactions enhances the capabilities of biological and chemical analyses, and highlight new research directions in the field of detections in nanofluidics.

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SERS discrimination of single DNA bases in single oligonucleotides by electro-plasmonic trapping

Cited by 170 publications

References 63 publications

Optical nanoantenna for beamed and surface‐enhanced Raman spectroscopy

Optical nanoantenna for beamed and surface‐enhanced Raman spectroscopy

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

Advances in Label-Free Detections for Nanofluidic Analytical Devices

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