DNA fragmentation in complicated flow fields created by micro-funnel shapes

Wu, Shuyi; Fu, Tengfei; Qiu, Renhui; Xu, Luping

doi:10.1039/d1sm00984b

Cited by 12 publications

(5 citation statements)

References 42 publications

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“…[28][29][30][31] Wu et al realized DNA fragmentation in microfluidic chips with funnel geometry shapes by tensile stress, indicating that the extension rate at the microscale was the main factor of DNA fragmentation. 55 Shui et al realized salmon sperm DNA fragmentation to ∼5 kbp lengths by hydrodynamic shearing in microfluidic chips. 37,38 Only shear stresses are not effective for DNA fragmentation; Dakhil et al did a well-controlled shear experiment in which the highest shear rates were in the range of ∼10 5 s −1 (shear stresses about 100 Pa) without obvious DNA shearing.…”

Section: Introductionmentioning

confidence: 99%

Polydimethylsiloxane microstructure-induced acoustic streaming for enhanced ultrasonic DNA fragmentation on a microfluidic chip

et al. 2022

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Section: Introductionmentioning

confidence: 99%

Polydimethylsiloxane microstructure-induced acoustic streaming for enhanced ultrasonic DNA fragmentation on a microfluidic chip

et al. 2022

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“…Flow across a constriction at high flow rate has been shown to result in chain scission of long DNA [ 35 , 36 , 37 , 38 ]. To test whether there is any significant hydrodynamically induced fragmentation, we collected the resulting sub fractions from a device at the highest run pressure and ran the samples again.…”

Section: Discussionmentioning

confidence: 99%

“…While we did not observe significant fragmentations, even at the highest run pressures, it is possible that longer molecules or higher pressures could lead to fragmentation. The constriction shape [ 35 ] and length [ 37 ] have been shown to affect the fragmentation. A gradual increase in the extensional rate and small constriction lengths, as occurring in our devices, has been shown to reduce the fragmentation significantly.…”

Section: Discussionmentioning

confidence: 99%

High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays

2022

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Length-based separation of DNA remains as relevant today as when gel electrophoresis was introduced almost 100 years ago. While new, long-read genomics technologies have revolutionised accessibility to powerful genomic data, the preparation of samples has not proceeded at the same pace, with sample preparation often constituting a considerable bottleneck, both in time and difficulty. Microfluidics holds great potential for automated, sample-to-answer analysis via the integration of preparatory and analytical steps, but for this to be fully realised, more versatile, powerful and integrable unit operations, such as separation, are essential. We demonstrate the displacement and separation of DNA with a throughput that is one to five orders of magnitude greater than other microfluidic techniques. Using a device with a small footprint (23 mm × 0.5 mm), and with feature sizes in the micrometre range, it is considerably easier to fabricate than parallelized nano-array-based approaches. We show the separation of 48.5 kbp and 166 kbp DNA strands achieving a significantly improved throughput of 760 ng/h, compared to previous work and the separation of low concentrations of 48.5 kbp DNA molecules from a massive background of sub 10 kbp fragments. We show that the extension of DNA molecules at high flow velocities, generally believed to make the length-based separation of long DNA difficult, does not place the ultimate limitation on our method. Instead, we explore the effects of polymer rotations and intermolecular interactions at extremely high DNA concentrations and postulate that these may have both negative and positive influences on the separation depending on the detailed experimental conditions.

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“…The simulation method was reported in previous studies ,, (Supporting Information, Sections S11–S13). Briefly, the multi-scale simulation method combining computational fluid dynamics (CFD) and Brownian dynamics simulation (BD) was used to simulate the dynamic behavior of a single KGM molecule in flow fields.…”

Section: Materials and Methodsmentioning

confidence: 99%

Adding Konjac Glucomannan for Enhancing the Whole Spraying Performance on Superhydrophobic and Hydrophilic Surfaces

Zhang

et al. 2023

ACS Appl. Mater. Interfaces

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Spraying is a common way to coat solutions onto surfaces evenly. Improving spraying effectiveness can avoid wasting solutions and reduce pollution. In this study, a trace amount of natural polysaccharide, konjac glucomannan (KGM), was added into solutions to regulate the spraying performances including the breakup of liquid jets, size of produced droplets, and collision and spreading of droplets on both superhydrophobic and hydrophilic surfaces. The shear viscosity, extensive viscosity, and surface tension of the KGM solutions were tested. The results of spraying experiments showed that adding KGM inhibited the liquid jet from breaking into small droplets, avoided the breakage of droplets on superhydrophobic surfaces, and promoted the spreading of liquid films on hydrophilic surfaces. The numerical simulation showed the stretching of single macromolecules and quantified the energy stored in molecular chains in a shear-dominated flow field during the spreading of droplets on surfaces and an elongationaldominated flow field during the breakage of a liquid bridge. The storage and dissipation of energy during the stretching and relaxing of KMG macromolecules were important origins of the increase in the colloid viscosity and molecular mechanisms of the effect of the KGM additive on spraying performances. This study provided an understanding and a strategy for optimization and application of spraying additives.

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DNA fragmentation in complicated flow fields created by micro-funnel shapes

Abstract: Micro-funnels have been widely applied to produce extensionally dominant flows for DNA manipulation, such as DNA extension for DNA mapping and DNA fragmentation for gene sequencing. However, it still lacks...

Cited by 12 publications

References 42 publications

Polydimethylsiloxane microstructure-induced acoustic streaming for enhanced ultrasonic DNA fragmentation on a microfluidic chip

Polydimethylsiloxane microstructure-induced acoustic streaming for enhanced ultrasonic DNA fragmentation on a microfluidic chip

High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays

Adding Konjac Glucomannan for Enhancing the Whole Spraying Performance on Superhydrophobic and Hydrophilic Surfaces

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