Hydrodynamic shearing of DNA in a polymeric microfluidic device

Nesterova, Irina V.; Hupert, Mateusz L.; Witek, Małgorzata A.

doi:10.1039/c2lc21122j

Cited by 13 publications

(12 citation statements)

References 29 publications

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“…10 Hydrodynamic shearing of DNA in microfluidic system has been reported recently, but did not allow the generation of sub-kilobase fragments essential for most NGS devices. 11,12 This limitation could be circumvented by sonication, which is the most widely used method for bulk DNA shearing experiments including applications, such as Chromatin Immunoprecipitation (ChIP), 13 for which small fragment sizes are absolutely crucial to obtain high resolution. The physical shearing mechanism of sonication generates DNA fragments in an unbiased fashion and is quite robust in regard to sample type and concentration.…”

Section: Introductionmentioning

confidence: 99%

Fragmentation of DNA in a sub-microliter microfluidic sonication device

et al. 2012

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Fragmentation of DNA is an essential step for many biological applications including the preparation of next-generation sequencing (NGS) libraries. As sequencing technologies push the limits towards single cell and single molecule resolution, it is of great interest to reduce the scale of this upstream fragmentation step. Here we describe a miniaturized DNA shearing device capable of processing sub-microliter samples based on acoustic shearing within a microfluidic chip. A strong acoustic field was generated by a Langevin-type piezo transducer and coupled into the microfluidic channel via the flexural lamb wave mode. Purified genomic DNA, as well as covalently cross-linked chromatin were sheared into various fragment sizes ranging from ∼180 bp to 4 kb. With the use of standard PDMS soft lithography, our approach should facilitate the integration of additional microfluidic modules and ultimately allow miniaturized NGS workflows.

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Section: Introductionmentioning

confidence: 99%

Fragmentation of DNA in a sub-microliter microfluidic sonication device

et al. 2012

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“…Sample loss is a problem for some DNA sample treatment methods1114192021. In this bubbling DNA fragmentation process, water evaporates quickly and DNA sample loss can occur due to sample splashed out and stuck on tube/cuvette surface.…”

Section: Resultsmentioning

confidence: 99%

“…Methods available for DNA fragmentation include enzymatic digestion6789, sonication101112, nebulization1314 and hydrodynamic shearing15161718192021. These methods have been widely used to produce DNA fragments for different applications.…”

mentioning

confidence: 99%

High Efficiency Hydrodynamic DNA Fragmentation in a Bubbling System

Jin

Sun

et al. 2017

Sci Rep

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DNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling system. We expect that hydrodynamic forces generated during the bubbling process shear the DNA molecules, extending and breaking them at the points where shearing forces are larger than the strength of the phosphate backbone. Factors of applied pressure, bubbling time and temperature have been investigated. Genomic DNA could be fragmented down to controllable 1–10 Kbp fragment lengths with a yield of 75.30–91.60%. We demonstrate that the ends of the genomic DNAs generated from hydrodynamic shearing can be ligated by T4 ligase and the fragmented DNAs can be used as templates for polymerase chain reaction. Therefore, in the bubbling system, DNAs could be hydrodynamically sheared to achieve smaller pieces in dsDNAs available for further processes. It could potentially serve as a DNA sample pretreatment technique in the future.

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“…The ability to apply well-defined flow types is essential for the study of flow induced structures in materials such as drop deformation and coalescence in multiphase systems, [1][2][3][4][5] alignment and stretching of molecules, [6][7][8][9] or flow-induced changes in colloidal dispersions. [10][11][12][13] Flow application is also relevant in the study of biological processes such as tissue organization and cell sorting.…”

Section: Introductionmentioning

confidence: 99%

Simple microfluidic stagnation point flow geometries

et al. 2016

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A geometrically simple flow cell is proposed to generate different types of stagnation flows, using a separation flow and small variations of the geometric parameters. Flows with high local deformation rates can be changed from purely rotational, over simple shear flow, to extensional flow in a region surrounding a stagnation point. Computational fluid dynamic calculations are used to analyse how variations of the geometrical parameters affect the flow field. These numerical calculations are compared to the experimentally obtained streamlines of different designs, which have been determined by high speed confocal microscopy. As the flow type is dictated predominantly by the geometrical parameters, such simple separating flow devices may alleviate the requirements for flow control, while offering good stability for a wide variety of flow types.

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Hydrodynamic shearing of DNA in a polymeric microfluidic device

Cited by 13 publications

References 29 publications

Fragmentation of DNA in a sub-microliter microfluidic sonication device

Fragmentation of DNA in a sub-microliter microfluidic sonication device

High Efficiency Hydrodynamic DNA Fragmentation in a Bubbling System

Simple microfluidic stagnation point flow geometries

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