uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
On nanopore DNA sequencing by signal and noise analysis of ionic current
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics. Uppsala University.
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Microsystems Technology.
Show others and affiliations
2016 (English)In: Nanotechnology, ISSN 0957-4484, E-ISSN 1361-6528, Vol. 27, 215502Article in journal (Refereed) Published
Abstract [en]

DNA sequencing, i.e., the process of determining the succession of nucleotides on a DNA strand, has become a standard aid in biomedical research and is expected to revolutionize medicine. With the capability of handling single DNA molecules, nanopore technology holds high promises to become speedier in sequencing at lower cost than what are achievable with the commercially available optics-or semiconductor-based massively parallelized technologies. Despite tremendous progress made with biological and solid-state nanopores, high error rates and large uncertainties persist with the sequencing results. Here, we employ a nano-disk model to quantitatively analyze the sequencing process by examining the variations of ionic current when a DNA strand translocates a nanopore. Our focus is placed on signal-boosting and noise-suppressing strategies in order to attain the single-nucleotide resolution. Apart from decreasing pore diameter and thickness, it is crucial to also reduce the translocation speed and facilitate a stepwise translocation. Our best-case scenario analysis points to severe challenges with employing plain nanopore technology, i.e., without recourse to any signal amplification strategy, in achieving sequencing with the desired single-nucleotide resolution. A conceptual approach based on strand synthesis in the nanopore of the translocating DNA from single-stranded to double-stranded is shown to yield a 10-fold signal amplification. Although it involves no advanced physics and is very simple in mathematics, this simple model captures the essence of nanopore sequencing and is useful in guiding the design and operation of nanopore sequencing.

Place, publisher, year, edition, pages
2016. Vol. 27, 215502
Keyword [en]
nanopore; DNA sequencing; ionic current; model; series resistance; noise; signal
National Category
Other Electrical Engineering, Electronic Engineering, Information Engineering
Identifiers
URN: urn:nbn:se:uu:diva-295968DOI: 10.1088/0957-4484/27/21/215502ISI: 000374507600013PubMedID: 27095148OAI: oai:DiVA.org:uu-295968DiVA: diva2:935634
Funder
Swedish Research Council, 621-2014-6300
Available from: 2016-06-11 Created: 2016-06-11 Last updated: 2017-11-28Bibliographically approved

Open Access in DiVA

fulltext(1982 kB)171 downloads
File information
File name FULLTEXT01.pdfFile size 1982 kBChecksum SHA-512
ae493aa9b872d74a925373e5f7515b26392e0597d2da8f2a48e729ff9c47d0b16b3e0ea6d904213753f1645f93e8934774de27b923baa4b5769b3691c9bfda92
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Authority records BETA

Wen, ChenyuZeng, ShuangshuangZhang, ZhenHjort, KlasScheicher, RalphZhang, Shi-Li

Search in DiVA

By author/editor
Wen, ChenyuZeng, ShuangshuangZhang, ZhenHjort, KlasScheicher, RalphZhang, Shi-Li
By organisation
Solid State ElectronicsMicrosystems TechnologyDepartment of Physics and Astronomy
In the same journal
Nanotechnology
Other Electrical Engineering, Electronic Engineering, Information Engineering

Search outside of DiVA

GoogleGoogle Scholar
Total: 171 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 549 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf