DNA confinement in nanochannels: physics and biological applications

Publication: Research - peer-reviewJournal article – Annual report year: 2012

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DNA confinement in nanochannels: physics and biological applications. / Reisner, Walter ; Pedersen, Jonas Nyvold; Austin, Robert H .

In: Reports on Progress in Physics, Vol. 75, No. 10, 2012.

Publication: Research - peer-reviewJournal article – Annual report year: 2012

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Reisner, Walter ; Pedersen, Jonas Nyvold; Austin, Robert H / DNA confinement in nanochannels: physics and biological applications.

In: Reports on Progress in Physics, Vol. 75, No. 10, 2012.

Publication: Research - peer-reviewJournal article – Annual report year: 2012

Bibtex

@article{a96b2026d45e4e958dcc52a5a2b48488,
title = "DNA confinement in nanochannels: physics and biological applications",
author = "Walter Reisner and Pedersen, {Jonas Nyvold} and Austin, {Robert H}",
year = "2012",
doi = "10.1088/0034-4885/75/10/106601",
volume = "75",
journal = "Reports on Progress in Physics",
issn = "0034-4885",
publisher = "Institute of Physics Publishing Ltd.",
number = "10",

}

RIS

TY - JOUR

T1 - DNA confinement in nanochannels: physics and biological applications

AU - Reisner,Walter

AU - Pedersen,Jonas Nyvold

AU - Austin,Robert H

PY - 2012

Y1 - 2012

N2 - DNA is the central storage molecule of genetic information in the cell, and reading that information is a centralproblem in biology. While sequencing technology has made enormous advances over the past decade, there isgrowing interest in platforms that can readout genetic information directly from long single DNA molecules,with the ultimate goal of single-cell, single-genome analysis. Such a capability would obviate the need forensemble averaging over heterogeneous cellular populations and eliminate uncertainties introduced by cloningand molecular amplification steps (thus enabling direct assessment of the genome in its native state). In thisreview, we will discuss how the information contained in genomic-length single DNA molecules can beaccessed via physical confinement in nanochannels. Due to self-avoidance interactions, DNA molecules willstretch out when confined in nanochannels, creating a linear unscrolling of the genome along the channel foranalysis. We will first review the fundamental physics of DNA nanochannel confinement—including the effectof varying ionic strength—and then discuss recent applications of these systems to genomic mapping. Apartfrom the intense biological interest in extracting linear sequence information from elongated DNA molecules,from a physics view these systems are fascinating as they enable probing of single-molecule conformation inenvironments with dimensions that intersect key physical length-scales in the 1 nm to 100μm range.(Some figures may appear in colour only in the online journal)

AB - DNA is the central storage molecule of genetic information in the cell, and reading that information is a centralproblem in biology. While sequencing technology has made enormous advances over the past decade, there isgrowing interest in platforms that can readout genetic information directly from long single DNA molecules,with the ultimate goal of single-cell, single-genome analysis. Such a capability would obviate the need forensemble averaging over heterogeneous cellular populations and eliminate uncertainties introduced by cloningand molecular amplification steps (thus enabling direct assessment of the genome in its native state). In thisreview, we will discuss how the information contained in genomic-length single DNA molecules can beaccessed via physical confinement in nanochannels. Due to self-avoidance interactions, DNA molecules willstretch out when confined in nanochannels, creating a linear unscrolling of the genome along the channel foranalysis. We will first review the fundamental physics of DNA nanochannel confinement—including the effectof varying ionic strength—and then discuss recent applications of these systems to genomic mapping. Apartfrom the intense biological interest in extracting linear sequence information from elongated DNA molecules,from a physics view these systems are fascinating as they enable probing of single-molecule conformation inenvironments with dimensions that intersect key physical length-scales in the 1 nm to 100μm range.(Some figures may appear in colour only in the online journal)

U2 - 10.1088/0034-4885/75/10/106601

DO - 10.1088/0034-4885/75/10/106601

M3 - Journal article

VL - 75

JO - Reports on Progress in Physics

T2 - Reports on Progress in Physics

JF - Reports on Progress in Physics

SN - 0034-4885

IS - 10

ER -