Nanopores: A journey towards DNA sequencing

Wanunu, Meni

doi:10.1016/j.plrev.2012.05.010

Cited by 558 publications

(568 citation statements)

References 139 publications

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“…Solid-state nanopores have emerged as an important tool with a large number of potential applications 22,23 at the crossroads of physics, biology and chemistry. Nanopores have provided a method to investigate various concepts in polymer physics such as polymer translocation through pores 24,25 , the Zimm relaxation time 25,26 , and the polymer capture process 27,28 .…”

Section: Abstract: Dna Knots Nanoporementioning

confidence: 99%

Direct observation of DNA knots using a solid-state nanopore

et al. 2016

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Section: Abstract: Dna Knots Nanoporementioning

confidence: 99%

Direct observation of DNA knots using a solid-state nanopore

et al. 2016

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“…1 The most commonly used detection method is that of resistive pulse sensing, where analyte molecules are electrophoretically driven across an insulating membrane, separating two sides of an electrolyte, via a nanopore. Singlemolecule detection is subsequently provided by the transient reduction in pore conductance from the steady-state whilst an analyte is present in the pore.…”

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confidence: 99%

Synchronized Optical and Electronic Detection of Biomolecules Using a Low Noise Nanopore Platform

et al. 2015

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In the past two decades there has been a tremendous amount of research into the use of nanopores as single molecule sensors, which has been inspired by the Coulter counter and molecular transport across biological pores. Recently, the desire to increase structural resolution and analytical throughput has led to the integration of additional detection methods such as fluorescence spectroscopy. For structural information to be probed electronically high bandwidth measurements are crucial due to the high translocation velocity of molecules. The most commonly used solid-state nanopore sensors consist of a silicon nitride membrane and bulk silicon substrate. Unfortunately, the photoinduced noise associated with illumination of these platforms limits their applicability to high-bandwidth, high-laser-power synchronized optical and electronic measurements. Here we present a unique low-noise nanopore platform, composed of a predominately Pyrex substrate and silicon nitride membrane, for synchronized optical and electronic detection of biomolecules. Proof of principle experiments are conducted showing that the Pyrex substrates have substantially lowers ionic current noise arising from both laser illumination and platform capacitance. Furthermore, using confocal microscopy and a partially metallic pore we demonstrate high signal-to-noise synchronized optical and electronic detection of dsDNA.

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“…The bacterial protein α-hemolysin (α-HL) has been the primary focus of several studies because of its potential to advance next-generation sequencing technology (12)(13)(14)(15). Its mushroomshaped ion channel is self-assembled across a lipid bilayer and may allow ssDNA to translocate from the cis to trans side of the protein under an electrical potential (Fig.…”

mentioning

confidence: 99%

Single-molecule investigation of G-quadruplex folds of the human telomere sequence in a protein nanocavity

Fleming

Middleton

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

102

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Human telomeric DNA consists of tandem repeats of the sequence 5′-TTAGGG-3′ that can fold into various G-quadruplexes, including the hybrid, basket, and propeller folds. In this report, we demonstrate use of the α-hemolysin ion channel to analyze these subtle topological changes at a nanometer scale by providing structuredependent electrical signatures through DNA-protein interactions. Whereas the dimensions of hybrid and basket folds allowed them to enter the protein vestibule, the propeller fold exceeds the size of the latch region, producing only brief collisions. After attaching a 25-mer poly-2′-deoxyadenosine extension to these structures, unraveling kinetics also were evaluated. Both the locations where the unfolding processes occur and the molecular shapes of the G-quadruplexes play important roles in determining their unfolding profiles. These results provide insights into the application of α-hemolysin as a molecular sieve to differentiate nanostructures as well as the potential technical hurdles DNA secondary structures may present to nanopore technology.α-hemolysin nanopore | single-molecule detection N ucleic acids can fold into a myriad of secondary structures that depend on the primary sequence as well as the physical conditions in which the structures are prepared and characterized. One prime example of a multistructural sequence is human telomeric DNA comprising the repeat sequence 5′-TTAGGG-3′. This guanine-rich single-stranded sequence is known to fold into highly ordered nanostructures in the form of G-quadruplexes that feature the coordination of two alkali cations to three layers of G-tetrads formed by Hoogsteen hydrogen-bonded assemblies of four guanine bases ( Fig. 1A) (1, 2). G-quadruplexes provide a fascinating case in which the cation and physical context play critical roles in defining the overall structural topology as well as the stability of the fold. Guanine-rich sequences also are known to present challenges to PCR amplification and sequencingby-synthesis methods that require processive analysis of singlestranded DNA (ssDNA) because of the high thermodynamic stability of these folded structures.The following studies highlight the cation and contextdependent conditions in which the topology of the natural human telomere sequence 5′-TAGGG(TTAGGG) 3 TT-3′ is affected. In NaCl solution, NMR studies revealed a structure referred to as the basket fold (Fig. 1A) (4). Key features of this structure include an antiparallel strand arrangement with alternating syn and anti orientations of the guanosine glycosidic bonds and three tetrads linked by two edgewise loops and one diagonal loop. In contrast, NMR-based studies in KCl solution show that the same sequence folds predominantly to the hybrid-1 and hybrid-2 structures (Fig. 1A) (5-8). Characteristics of this structure are an antiparallel strand orientation with a 3+1 core of syn and anti G nucleotides yielding three tetrads. The loop topology of the hybrid fold consists of a double-chain reversal loop and two edgewise loops, in which hybr...

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Nanopores: A journey towards DNA sequencing

Cited by 558 publications

References 139 publications

Direct observation of DNA knots using a solid-state nanopore

Direct observation of DNA knots using a solid-state nanopore

Synchronized Optical and Electronic Detection of Biomolecules Using a Low Noise Nanopore Platform

Single-molecule investigation of G-quadruplex folds of the human telomere sequence in a protein nanocavity

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