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The evolution of nanopore sequencing.

Wang Y, Yang Q, Wang Z - Front Genet (2015)

Bottom Line: Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors.A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards.In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China.

ABSTRACT
The "$1000 Genome" project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the "$1000 Genome" while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.

No MeSH data available.


Schematic illustration of SBET. (A) Illustration of ssDNA traveling between a pair of tunneling electrodes in a nanochannel. (B) The upper left inset shows top view of the pore cross section embedded with two pairs of electrodes (gold rectangles). The upper right inset illustrates ssDNA and a pair of gold electrodes at atomic level. Lower shows the simulation result of a tunneling diagram of the ssDNA (sequence: AGCATCGCTC) (Lagerqvist et al., 2006). Reproduced by copyright permission of American Chemical Society.
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Figure 8: Schematic illustration of SBET. (A) Illustration of ssDNA traveling between a pair of tunneling electrodes in a nanochannel. (B) The upper left inset shows top view of the pore cross section embedded with two pairs of electrodes (gold rectangles). The upper right inset illustrates ssDNA and a pair of gold electrodes at atomic level. Lower shows the simulation result of a tunneling diagram of the ssDNA (sequence: AGCATCGCTC) (Lagerqvist et al., 2006). Reproduced by copyright permission of American Chemical Society.

Mentions: In 2003, Lee and Thundat disclosed a nanoelectrode-gated tunneling method for DNA sequencing (Lee and Thundat, 2003). The hypothesis is based on the principle that each base has its distinct structure, and has specific perturbation effect on tunneling signals when each base is translocating between a pair of nanoelectrode tips (gate) perpendicular to DNA backbone. Lee et al. theoretically showed that the four bases have significant charge conductance which could possibly be detected when they are passing through a 1.5-nm gap between the nanoelectrodes (Lee, 2007). Theoretical calculation by di Ventra's group also supported this concept (Zwolak and Di Ventra, 2005). Their theoretical analysis showed that sequencing speed could reach up to 106–107 bases/s (Lee and Thundat, 2003; Lagerqvist et al., 2006). It has attracted increasing number of groups to develop new technologies to fabricate such devices. One example is shown in Figure 8.


The evolution of nanopore sequencing.

Wang Y, Yang Q, Wang Z - Front Genet (2015)

Schematic illustration of SBET. (A) Illustration of ssDNA traveling between a pair of tunneling electrodes in a nanochannel. (B) The upper left inset shows top view of the pore cross section embedded with two pairs of electrodes (gold rectangles). The upper right inset illustrates ssDNA and a pair of gold electrodes at atomic level. Lower shows the simulation result of a tunneling diagram of the ssDNA (sequence: AGCATCGCTC) (Lagerqvist et al., 2006). Reproduced by copyright permission of American Chemical Society.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4285804&req=5

Figure 8: Schematic illustration of SBET. (A) Illustration of ssDNA traveling between a pair of tunneling electrodes in a nanochannel. (B) The upper left inset shows top view of the pore cross section embedded with two pairs of electrodes (gold rectangles). The upper right inset illustrates ssDNA and a pair of gold electrodes at atomic level. Lower shows the simulation result of a tunneling diagram of the ssDNA (sequence: AGCATCGCTC) (Lagerqvist et al., 2006). Reproduced by copyright permission of American Chemical Society.
Mentions: In 2003, Lee and Thundat disclosed a nanoelectrode-gated tunneling method for DNA sequencing (Lee and Thundat, 2003). The hypothesis is based on the principle that each base has its distinct structure, and has specific perturbation effect on tunneling signals when each base is translocating between a pair of nanoelectrode tips (gate) perpendicular to DNA backbone. Lee et al. theoretically showed that the four bases have significant charge conductance which could possibly be detected when they are passing through a 1.5-nm gap between the nanoelectrodes (Lee, 2007). Theoretical calculation by di Ventra's group also supported this concept (Zwolak and Di Ventra, 2005). Their theoretical analysis showed that sequencing speed could reach up to 106–107 bases/s (Lee and Thundat, 2003; Lagerqvist et al., 2006). It has attracted increasing number of groups to develop new technologies to fabricate such devices. One example is shown in Figure 8.

Bottom Line: Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors.A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards.In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China.

ABSTRACT
The "$1000 Genome" project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the "$1000 Genome" while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.

No MeSH data available.