Exploiting biased reptation for continuous flow preparative DNA fractionation in a versatile microfluidic platform

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Abstract

A new approach is presented for preparative, continuous flow fractionation of sub-10-kbp DNA fragments, which exploits the variation in the field-dependent mobility of the DNA molecules based on their length. Orthogonally pulsed electric fields of significantly different magnitudes are applied to a microchip filled with a sieving matrix of 1.2% agarose gel. Using this method, we demonstrate a high-resolution separation of 0.5, 1, 2, 5, and 10 kbp DNA fragments within 2 min. During the separation, DNA fragments are also purified from other ionic species. Preparative fractionation of sub-10-kbp DNA molecules plays an important role in second-generation sequencing. The presented device performs rapid high-resolution fractionation and it can be reliably manufactured with simple microfabrication procedures.
Original languageEnglish
Article number17001
Number of pages9
JournalMicrosystems & nanoengineering
Volume3
DOIs
Publication statusPublished - 22 May 2017

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Fractionation
Microfluidics
fractionation
DNA
deoxyribonucleic acid
platforms
fragments
Molecules
sequencing
Microfabrication
high resolution
Sepharose
molecules
Gels
Electric fields
gels
electric fields
matrices

Cite this

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title = "Exploiting biased reptation for continuous flow preparative DNA fractionation in a versatile microfluidic platform",
abstract = "A new approach is presented for preparative, continuous flow fractionation of sub-10-kbp DNA fragments, which exploits the variation in the field-dependent mobility of the DNA molecules based on their length. Orthogonally pulsed electric fields of significantly different magnitudes are applied to a microchip filled with a sieving matrix of 1.2{\%} agarose gel. Using this method, we demonstrate a high-resolution separation of 0.5, 1, 2, 5, and 10 kbp DNA fragments within 2 min. During the separation, DNA fragments are also purified from other ionic species. Preparative fractionation of sub-10-kbp DNA molecules plays an important role in second-generation sequencing. The presented device performs rapid high-resolution fractionation and it can be reliably manufactured with simple microfabrication procedures.",
author = "B. G{\"u}m{\"u}sc{\"u} and Bomer, {Johan G.} and {de Boer}, {Hans L.} and {van den Berg}, Albert and Eijkel, {Jan C.T.}",
year = "2017",
month = "5",
day = "22",
doi = "10.1038/micronano.2017.1",
language = "English",
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journal = "Microsystems & nanoengineering",
issn = "2055-7434",
publisher = "Nature Publishing Group",

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TY - JOUR

T1 - Exploiting biased reptation for continuous flow preparative DNA fractionation in a versatile microfluidic platform

AU - Gümüscü, B.

AU - Bomer, Johan G.

AU - de Boer, Hans L.

AU - van den Berg, Albert

AU - Eijkel, Jan C.T.

PY - 2017/5/22

Y1 - 2017/5/22

N2 - A new approach is presented for preparative, continuous flow fractionation of sub-10-kbp DNA fragments, which exploits the variation in the field-dependent mobility of the DNA molecules based on their length. Orthogonally pulsed electric fields of significantly different magnitudes are applied to a microchip filled with a sieving matrix of 1.2% agarose gel. Using this method, we demonstrate a high-resolution separation of 0.5, 1, 2, 5, and 10 kbp DNA fragments within 2 min. During the separation, DNA fragments are also purified from other ionic species. Preparative fractionation of sub-10-kbp DNA molecules plays an important role in second-generation sequencing. The presented device performs rapid high-resolution fractionation and it can be reliably manufactured with simple microfabrication procedures.

AB - A new approach is presented for preparative, continuous flow fractionation of sub-10-kbp DNA fragments, which exploits the variation in the field-dependent mobility of the DNA molecules based on their length. Orthogonally pulsed electric fields of significantly different magnitudes are applied to a microchip filled with a sieving matrix of 1.2% agarose gel. Using this method, we demonstrate a high-resolution separation of 0.5, 1, 2, 5, and 10 kbp DNA fragments within 2 min. During the separation, DNA fragments are also purified from other ionic species. Preparative fractionation of sub-10-kbp DNA molecules plays an important role in second-generation sequencing. The presented device performs rapid high-resolution fractionation and it can be reliably manufactured with simple microfabrication procedures.

U2 - 10.1038/micronano.2017.1

DO - 10.1038/micronano.2017.1

M3 - Article

VL - 3

JO - Microsystems & nanoengineering

JF - Microsystems & nanoengineering

SN - 2055-7434

M1 - 17001

ER -