Fluctuation Tolerant Charge-Integration Read Scheme for Ultrafast DNA Sequencing with Nanopore Device

Kazuo ONO; Yoshimitsu YANAGAWA; Akira KOTABE; Riichiro TAKEMURA; Tatsuo NAKAGAWA; Tomio IWASAKI; Takayuki KAWAHARA

doi:10.1587/transele.E95.C.651

Fluctuation Tolerant Charge-Integration Read Scheme for Ultrafast DNA Sequencing with Nanopore Device

Kazuo ONO, Yoshimitsu YANAGAWA, Akira KOTABE, Riichiro TAKEMURA, Tatsuo NAKAGAWA, Tomio IWASAKI, Takayuki KAWAHARA

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A charge-integration read scheme has been developed for a solid-nanopore DNA-sequencer that determines a genome by direct and electrical measurements of transverse tunneling current in single-stranded DNA. The magnitude of the current was simulated with a first-principles molecular dynamics method. It was found that the magnitude is as small as in the sub-pico ampere range, and signals from four bases represent wide distributions with overlaps between each base. The distribution is believed to originate with translational and rotational motion of DNA in a nanopore with a frequency of over 10⁵ Hz. A sequence scheme is presented to distinguish the distributed signals. The scheme makes widely distributed signals time-integrated convergent by cumulating charge at the capacitance of a nanopore device and read circuits. We estimated that an integration time of 1.4 ms is sufficient to obtain a signal difference of over 10 mV for distinguishing between each DNA base. Moreover, the time is shortened if paired bases, such as A-T and C-G in double-stranded DNA, can be measured simultaneously with two nanopores. Circuit simulations, which included the capacitance of a nanopore calculated with a device simulator, successfully distinguished between DNA bases in less than 2.0 ms. The speed is roughly six orders faster than that of a conventional DNA sequencer. It is possible to determine the human genome in one day if 100-nanopores are operated in parallel.

Publication: IEICE TRANSACTIONS on Electronics Vol.E95-C No.4 pp.651-660

Publication Date: 2012/04/01

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Online ISSN: 1745-1353

DOI: 10.1587/transele.E95.C.651

Type of Manuscript: Special Section PAPER (Special Section on Solid-State Circuit Design – Architecture, Circuit, Device and Design Methodology)

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Kazuo ONO, Yoshimitsu YANAGAWA, Akira KOTABE, Riichiro TAKEMURA, Tatsuo NAKAGAWA, Tomio IWASAKI, Takayuki KAWAHARA, "Fluctuation Tolerant Charge-Integration Read Scheme for Ultrafast DNA Sequencing with Nanopore Device" in IEICE TRANSACTIONS on Electronics, vol. E95-C, no. 4, pp. 651-660, April 2012, doi: 10.1587/transele.E95.C.651.
Abstract: A charge-integration read scheme has been developed for a solid-nanopore DNA-sequencer that determines a genome by direct and electrical measurements of transverse tunneling current in single-stranded DNA. The magnitude of the current was simulated with a first-principles molecular dynamics method. It was found that the magnitude is as small as in the sub-pico ampere range, and signals from four bases represent wide distributions with overlaps between each base. The distribution is believed to originate with translational and rotational motion of DNA in a nanopore with a frequency of over 10⁵ Hz. A sequence scheme is presented to distinguish the distributed signals. The scheme makes widely distributed signals time-integrated convergent by cumulating charge at the capacitance of a nanopore device and read circuits. We estimated that an integration time of 1.4 ms is sufficient to obtain a signal difference of over 10 mV for distinguishing between each DNA base. Moreover, the time is shortened if paired bases, such as A-T and C-G in double-stranded DNA, can be measured simultaneously with two nanopores. Circuit simulations, which included the capacitance of a nanopore calculated with a device simulator, successfully distinguished between DNA bases in less than 2.0 ms. The speed is roughly six orders faster than that of a conventional DNA sequencer. It is possible to determine the human genome in one day if 100-nanopores are operated in parallel.
URL: https://globals.ieice.org/en_transactions/electronics/10.1587/transele.E95.C.651/_p

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@ARTICLE{e95-c_4_651,
author={Kazuo ONO, Yoshimitsu YANAGAWA, Akira KOTABE, Riichiro TAKEMURA, Tatsuo NAKAGAWA, Tomio IWASAKI, Takayuki KAWAHARA, },
journal={IEICE TRANSACTIONS on Electronics},
title={Fluctuation Tolerant Charge-Integration Read Scheme for Ultrafast DNA Sequencing with Nanopore Device},
year={2012},
volume={E95-C},
number={4},
pages={651-660},
abstract={A charge-integration read scheme has been developed for a solid-nanopore DNA-sequencer that determines a genome by direct and electrical measurements of transverse tunneling current in single-stranded DNA. The magnitude of the current was simulated with a first-principles molecular dynamics method. It was found that the magnitude is as small as in the sub-pico ampere range, and signals from four bases represent wide distributions with overlaps between each base. The distribution is believed to originate with translational and rotational motion of DNA in a nanopore with a frequency of over 10⁵ Hz. A sequence scheme is presented to distinguish the distributed signals. The scheme makes widely distributed signals time-integrated convergent by cumulating charge at the capacitance of a nanopore device and read circuits. We estimated that an integration time of 1.4 ms is sufficient to obtain a signal difference of over 10 mV for distinguishing between each DNA base. Moreover, the time is shortened if paired bases, such as A-T and C-G in double-stranded DNA, can be measured simultaneously with two nanopores. Circuit simulations, which included the capacitance of a nanopore calculated with a device simulator, successfully distinguished between DNA bases in less than 2.0 ms. The speed is roughly six orders faster than that of a conventional DNA sequencer. It is possible to determine the human genome in one day if 100-nanopores are operated in parallel.},
keywords={},
doi={10.1587/transele.E95.C.651},
ISSN={1745-1353},
month={April},}

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TY - JOUR
TI - Fluctuation Tolerant Charge-Integration Read Scheme for Ultrafast DNA Sequencing with Nanopore Device
T2 - IEICE TRANSACTIONS on Electronics
SP - 651
EP - 660
AU - Kazuo ONO
AU - Yoshimitsu YANAGAWA
AU - Akira KOTABE
AU - Riichiro TAKEMURA
AU - Tatsuo NAKAGAWA
AU - Tomio IWASAKI
AU - Takayuki KAWAHARA
PY - 2012
DO - 10.1587/transele.E95.C.651
JO - IEICE TRANSACTIONS on Electronics
SN - 1745-1353
VL - E95-C
IS - 4
JA - IEICE TRANSACTIONS on Electronics
Y1 - April 2012
AB - A charge-integration read scheme has been developed for a solid-nanopore DNA-sequencer that determines a genome by direct and electrical measurements of transverse tunneling current in single-stranded DNA. The magnitude of the current was simulated with a first-principles molecular dynamics method. It was found that the magnitude is as small as in the sub-pico ampere range, and signals from four bases represent wide distributions with overlaps between each base. The distribution is believed to originate with translational and rotational motion of DNA in a nanopore with a frequency of over 10⁵ Hz. A sequence scheme is presented to distinguish the distributed signals. The scheme makes widely distributed signals time-integrated convergent by cumulating charge at the capacitance of a nanopore device and read circuits. We estimated that an integration time of 1.4 ms is sufficient to obtain a signal difference of over 10 mV for distinguishing between each DNA base. Moreover, the time is shortened if paired bases, such as A-T and C-G in double-stranded DNA, can be measured simultaneously with two nanopores. Circuit simulations, which included the capacitance of a nanopore calculated with a device simulator, successfully distinguished between DNA bases in less than 2.0 ms. The speed is roughly six orders faster than that of a conventional DNA sequencer. It is possible to determine the human genome in one day if 100-nanopores are operated in parallel.
ER -