The potential and challenges of nanopore sequencing

Branton, Daniel; Deamer, David W.; Marziali, Andre; Bayley, Hagan; Benner, Steven A.; Butler, Thomas J.; Ventra, Massimiliano Di; Garaj, Slaven; Hibbs, Andrew D.; Huang, Xiaoxia; Jovanovich, Stevan; Krstić, Predrag; Lindsay, Stuart; Ling, Xinsheng; Mastrangelo, Carlos H.; Meller, A.; Oliver, John S.; Pershin, Yuriy V.; Ramsey, J. Michael; Riehn, Robert; Soni, Gautam V.; Tabard‐Cossa, Vincent; Wanunu, Meni; Wiggin, Matthew; Schloss, Jeffery A.

doi:10.1038/nbt.1495

Cited by 2,276 publications

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References 86 publications

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“…1B) by mechanical exfoliation from graphite on SiO 2 13 . Monolayer graphene is identified by its particular optical contrast 14 in the optical microscope and by Raman measurements (Fig.…”

Section: -3 -mentioning

confidence: 99%

DNA Translocation through Graphene Nanopores

Schneider¹,

Kowalczyk²,

Calado³

et al. 2010

Nano Lett.

940

930

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In the past few years, nanopores have emerged as a new powerful tool to interrogate single molecules. They have been successfully used to rapidly characterize biopolymers like DNA 3,4 , RNA 5 , as well as DNA-ligand complexes 6 and local protein structures along DNA 7 at the single-molecule level. A key driving force for nanopore research in the past decade has been the prospect of DNA sequencing. However, a major roadblock for achieving high-resolution DNA sequencing with pores is the finite length of the channel constituting the pore (Fig. 1A). In a long nanopore, the current blockade resulting from DNA translocation is due to a large number of bases (for typical devices ~10-100 bases) present in the pore. Here, we demonstrate that this limitation can be overcome by realizing an ultimately thin nanopore in a graphene monolayer. We obtain single-layer graphene (Fig. 1B) by mechanical exfoliation from graphite on SiO 2 13 . Monolayer graphene is identified by its particular optical contrast 14 in the optical microscope and by Raman measurements (Fig. 1C). At ~ 1590 cm -1 , we measure the socalled G resonance peak and at ~2690 cm -1 the 2D resonance peak. In the case of multilayer graphene, the 2D resonance peak splits off in multiple peaks in contrast to monolayer graphene which has a very sharp single resonance peak. In this way, we are well able to distinguish single-layer graphene from multilayer graphene 15 .Next we select a monolayer of graphene and transfer it onto a SiN support membrane with a 5 micron sized hole 16 by use of our recently developed 'wedging transfer' technique 17 . This transfer procedure is straightforward: flakes can be overlaid to support membranes in less than an hour. Briefly, a hydrophobic polymer is spun onto a hydrophilic substrate (here plasma-oxidized SiO 2 ) with graphene flakes, and wedged off the substrate by sliding it at an angle in water. Graphene flakes are peeled off the SiO 2 along with the -4 -polymer. The polymer is then floating on the water surface, located near a target SiN substrate, the water level is lowered, and the flakes are positioned onto the SiN membrane with micrometer lateral precision. In the final step the polymer is dissolved.We then drill a nanopore into the graphene monolayer using the highly focused electron beam of a transmission electron microscope (TEM). The acceleration voltage is 300 kV, well above the 80-140 kV knock-out voltage for carbon atoms in graphene 18 (see Methods).Drilling the holes by TEM is a robust well-reproducible procedure (we drilled 31 holes with diameters ranging from 2 to 40 nm, in monolayer as well as in multilayer graphene; some examples of pores are shown in Fig. 2). Because of the high acceleration voltage of the electron beam, drilling could potentially induce damage to the graphene around the pore. However, electron beam diffraction measurements across the hole ( Fig. 2B and C) confirm the crystallinity of the monolayer surrounding the hole, as evidenced by the well-defined hexagonal diffraction patterns (Fig. 2C).Su...

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“…1B) by mechanical exfoliation from graphite on SiO 2 13 . Monolayer graphene is identified by its particular optical contrast 14 in the optical microscope and by Raman measurements (Fig.…”

Section: -3 -mentioning

confidence: 99%

DNA Translocation through Graphene Nanopores

Schneider¹,

Kowalczyk²,

Calado³

et al. 2010

Nano Lett.

940

930

View full text Add to dashboard Cite

show abstract

“…In particular, the longest strand of DNA that can be effectively read with electrophoresis is restricted to around 1,000 base pairs. Of all the alternative technologies being explored, DNA sequencing with nanopores is arguably the most revolutionary 6 .…”

Section: Editorialmentioning

confidence: 99%

Quantum steps to better sequencing

2010

Nature Nanotech

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“…L'idée est de faire passer la molécule d'ADN à travers un tel canal et de détecter de subtiles modifications électriques lors de ce passage -et, encore plus subtilement, de différencier les modifications produites par chacune des quatre bases… La chose n'est nullement chimérique, et il existe déjà tout un corpus de résultats montrant les potentialités de cette approche [5]. Le problème principal semble être actuellement de trouver une manière de ralentir la molécule d'ADN lorsqu'elle traverse le nanopore sous l'influence d'un champ électrique, afin de pouvoir effectivement enregistrer le signal qui donnera la séquence (Figure 1).…”

Section: Les Espoirs Des Nanoporesunclassified

“…Le problème principal semble être actuellement de trouver une manière de ralentir la molécule d'ADN lorsqu'elle traverse le nanopore sous l'influence d'un champ électrique, afin de pouvoir effectivement enregistrer le signal qui donnera la séquence (Figure 1). Parmi les firmes les plus avancées, on peut citer Oxford Nanopore (Royaume-Uni), Nabsys et Sequenom (États-Unis), ainsi que plusieurs laboratoires académiques principalement aux États-Unis (voir [5]). …”

Section: Les Espoirs Des Nanoporesunclassified

La génération suivante, déjà…

Jordan

2009

Med Sci (Paris)

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The potential and challenges of nanopore sequencing

Cited by 2,276 publications

References 86 publications

DNA Translocation through Graphene Nanopores

DNA Translocation through Graphene Nanopores

Quantum steps to better sequencing

La génération suivante, déjà…

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