DNA‐Based Nanopore Sensing

Liu, Lei; Wu, Hai‐Chen

doi:10.1002/anie.201604405

Cited by 96 publications

(74 citation statements)

References 84 publications

(100 reference statements)

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“…Inability to clarify this issue has long been a barrier to understanding the delicate function of biomimetic nanochannels. In addition, this is also a problem in nanochannel-based DNA sequencing 22 – 29 and single-molecule sensing 30 – 36 . For instance, discriminating a nucleotide base typically relies on characteristic channel-blockade current and dwell-time signatures, which, however, cannot be actualized when the base has no access to the inner of nanochannel.…”

Section: Introductionmentioning

confidence: 99%

Role of outer surface probes for regulating ion gating of nanochannels

et al. 2018

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Nanochannels with functional elements have shown promise for DNA sequencing, single-molecule sensing, and ion gating. Ionic current measurement is currently a benchmark, but is focused solely on the contribution from nanochannels’ inner-wall functional elements (NIWFE); the attributes of functional elements at nanochannels’ outer surface (NOSFE) are nearly ignored, and remain elusive. Here we show that the role of NOSFE and NIWFE for ion gating can be distinguished by constructing DNA architectures using dual-current readout. The established molecular switches have continuously tunable and reversible ion-gating ability. We find that NOSFE exhibits negligible ion-gating behavior, but it can produce a synergistic effect in alliance with NIWFE. Moreover, the high-efficiency gating systems display more noticeable synergistic effect than the low-efficiency ones. We also reveal that the probe amount of NOSFE and NIWFE is almost equally distributed in our biomimetic nanochannels, which is potentially a premise for the synergistic ion-gating phenomena.

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Section: Introductionmentioning

confidence: 99%

Role of outer surface probes for regulating ion gating of nanochannels

et al. 2018

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“…Nanopores have been applied to single molecule detection and DNA sequencing based on a principle of ionic or transverse tunneling current sensing through a nanopore. The materials, fabrication, and applications of nanopores have been well described in recent review articles and will not be considered here.…”

Section: Materials and Methods For Fabricating Nanofluidic Devicesmentioning

confidence: 99%

Nanofluidics: A New Arena for Materials Science

2017

Advanced Materials

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A significant growth of research in nanofluidics is achieved over the past decade, but the field is still facing considerable challenges toward the transition from the current physics-centered stage to the next application-oriented stage. Many of these challenges are associated with materials science, so the field of nanofluidics offers great opportunities for materials scientists to exploit. In addition, the use of unusual effects and ultrasmall confined spaces of well-defined nanofluidic environments would offer new mechanisms and technologies to manipulate nanoscale objects as well as to synthesize novel nanomaterials in the liquid phase. Therefore, nanofluidics will be a new arena for materials science. In the past few years, burgeoning progress has been made toward this trend, as overviewed in this article, including materials and methods for fabricating nanofluidic devices, nanofluidics with functionalized surfaces and functional material components, as well as nanofluidics for manipulating nanoscale materials and fabricating new nanomaterials. Many critical challenges as well as fantastic opportunities in this arena lie ahead. Some of those, which are of particular interest, are also discussed.

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“…Nanopore is a promising label-free, single-molecule-based, next-generation sequencing technology 11 – 15 . By taking advantage of the ability to electrically detect charged biomolecules through a nanometer-wide channel, various nanopore biosensors have been developed, with targets including DNAs 16 , 17 , microRNA biomarkers 18 – 20 , tRNA 21 , peptides 22 , 23 , and proteins 24 , 25 as well as epigenetic changes such as DNA methylation 26 – 28 . In another important application, nanopores have been used as a precise force instrument to explore biomolecular mechanisms such as protein unfolding 29 , DNA unzipping 11 , 30 , 31 , RNA unfolding 32 , and the binding of nucleic acids to enzymes 33 .…”

Section: Introductionmentioning

confidence: 99%

Nanopore electric snapshots of an RNA tertiary folding pathway

et al. 2017

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The chemical properties and biological mechanisms of RNAs are determined by their tertiary structures. Exploring the tertiary structure folding processes of RNA enables us to understand and control its biological functions. Here, we report a nanopore snapshot approach combined with coarse-grained molecular dynamics simulation and master equation analysis to elucidate the folding of an RNA pseudoknot structure. In this approach, single RNA molecules captured by the nanopore can freely fold from the unstructured state without constraint and can be programmed to terminate their folding process at different intermediates. By identifying the nanopore signatures and measuring their time-dependent populations, we can “visualize” a series of kinetically important intermediates, track the kinetics of their inter-conversions, and derive the RNA pseudoknot folding pathway. This approach can potentially be developed into a single-molecule toolbox to investigate the biophysical mechanisms of RNA folding and unfolding, its interactions with ligands, and its functions.

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DNA‐Based Nanopore Sensing

Cited by 96 publications

References 84 publications

Role of outer surface probes for regulating ion gating of nanochannels

Role of outer surface probes for regulating ion gating of nanochannels

Nanofluidics: A New Arena for Materials Science

Nanopore electric snapshots of an RNA tertiary folding pathway

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