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Literature DB >> 25642629

Challenges in DNA motion control and sequence readout using nanopore devices.

Abstract

Nanopores are being hailed as a potential next-generation DNA sequencer that could provide cheap, high-throughput DNA analysis. In this review we present a detailed summary of the various sensing techniques being investigated for use in DNA sequencing and mapping applications. A crucial impasse to the success of nanopores as a reliable DNA analysis tool is the fast and stochastic nature of DNA translocation. We discuss the incorporation of biological motors to step DNA through a pore base-by-base, as well as the many experimental modifications attempted for the purpose of slowing and controlling DNA transport.

Entities: Chemical Disease Gene Species

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Year: 2015 PMID： 25642629 PMCID： PMC4710574 DOI： 10.1088/0957-4484/26/7/074004

Source DB: PubMed Journal: Nanotechnology ISSN： 0957-4484 Impact factor: 3.874

119 in total

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Journal: Nature Date: 2001-07-12 Impact factor: 49.962

2. Identifying single bases in a DNA oligomer with electron tunnelling.

Authors: Shuo Huang; Jin He; Shuai Chang; Peiming Zhang; Feng Liang; Shengqin Li; Michael Tuchband; Alexander Fuhrmann; Robert Ros; Stuart Lindsay
Journal: Nat Nanotechnol Date: 2010-11-14 Impact factor: 39.213

3. Slowing DNA translocation in a solid-state nanopore.

Authors: Daniel Fologea; James Uplinger; Brian Thomas; David S McNabb; Jiali Li
Journal: Nano Lett Date: 2005-09 Impact factor: 11.189

4. DNA translocation governed by interactions with solid-state nanopores.

Authors: Meni Wanunu; Jason Sutin; Ben McNally; Andrew Chow; Amit Meller
Journal: Biophys J Date: 2008-08-15 Impact factor: 4.033

5. Electrophoretic force on a protein-coated DNA molecule in a solid-state nanopore.

Authors: Adam R Hall; Stijn van Dorp; Serge G Lemay; Cees Dekker
Journal: Nano Lett Date: 2009-12 Impact factor: 11.189

6. Smooth DNA transport through a narrowed pore geometry.

Authors: Spencer Carson; James Wilson; Aleksei Aksimentiev; Meni Wanunu
Journal: Biophys J Date: 2014-11-18 Impact factor: 4.033

7. The effects of diffusion on an exonuclease/nanopore-based DNA sequencing engine.

Authors: Joseph E Reiner; Arvind Balijepalli; Joseph W F Robertson; Bryon S Drown; Daniel L Burden; John J Kasianowicz
Journal: J Chem Phys Date: 2012-12-07 Impact factor: 3.488

8. Nanopore detection of 8-oxo-7,8-dihydro-2'-deoxyguanosine in immobilized single-stranded DNA via adduct formation to the DNA damage site.

Authors: Anna E P Schibel; Na An; Qian Jin; Aaron M Fleming; Cynthia J Burrows; Henry S White
Journal: J Am Chem Soc Date: 2010-12-07 Impact factor: 15.419

9. Graphene quantum point contact transistor for DNA sensing.

Authors: Anuj Girdhar; Chaitanya Sathe; Klaus Schulten; Jean-Pierre Leburton
Journal: Proc Natl Acad Sci U S A Date: 2013-09-30 Impact factor: 11.205

10. Effect of an Electrolyte Cation on Detecting DNA Damage with the Latch Constriction of α-Hemolysin.

Authors: Robert P Johnson; Aaron M Fleming; Cynthia J Burrows; Henry S White
Journal: J Phys Chem Lett Date: 2014-10-14 Impact factor: 6.475

24 in total

Review 1. Nanopore Sensing.

Authors: Wenqing Shi; Alicia K Friedman; Lane A Baker
Journal: Anal Chem Date: 2016-11-18 Impact factor: 6.986

2. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.

Authors: Melanie P Muller; Tao Jiang; Chang Sun; Muyun Lihan; Shashank Pant; Paween Mahinthichaichan; Anda Trifan; Emad Tajkhorshid
Journal: Chem Rev Date: 2019-04-12 Impact factor: 60.622

Challenges in DNA motion control and sequence readout using nanopore devices.

1. Ion-beam sculpting at nanometre length scales.

2. Identifying single bases in a DNA oligomer with electron tunnelling.

3. Slowing DNA translocation in a solid-state nanopore.

4. DNA translocation governed by interactions with solid-state nanopores.

5. Electrophoretic force on a protein-coated DNA molecule in a solid-state nanopore.

6. Smooth DNA transport through a narrowed pore geometry.

7. The effects of diffusion on an exonuclease/nanopore-based DNA sequencing engine.

8. Nanopore detection of 8-oxo-7,8-dihydro-2'-deoxyguanosine in immobilized single-stranded DNA via adduct formation to the DNA damage site.

9. Graphene quantum point contact transistor for DNA sensing.

10. Effect of an Electrolyte Cation on Detecting DNA Damage with the Latch Constriction of α-Hemolysin.

Review 1. Nanopore Sensing.

2. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.

3. Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores.

Review 4. Flow of DNA in micro/nanofluidics: From fundamentals to applications.

5. Effects of Nanopore Charge Decorations on the Translocation Dynamics of DNA.

6. Construction of an aerolysin nanopore in a lipid bilayer for single-oligonucleotide analysis.

7. Monolithic Fabrication of NPN/SiN_x Dual Membrane Cavity for Nanopore-based DNA Sensing.

8. Fabrication and practical applications of molybdenum disulfide nanopores.

Review 9. Studies of RNA Sequence and Structure Using Nanopores.

10. Base Flipping within the α-Hemolysin Latch Allows Single-Molecule Identification of Mismatches in DNA.