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Polydimethylsiloxane microstructure-induced acoustic streaming for enhanced ultrasonic DNA fragmentation on a microfluidic chip
Lab on a Chip ( IF 6.1 ) Pub Date : 2022-09-30 , DOI: 10.1039/d2lc00366j Lin Sun 1, 2 , Thomas Lehnert 2 , Martin A M Gijs 2 , Songjing Li 1
Lab on a Chip ( IF 6.1 ) Pub Date : 2022-09-30 , DOI: 10.1039/d2lc00366j Lin Sun 1, 2 , Thomas Lehnert 2 , Martin A M Gijs 2 , Songjing Li 1
Affiliation
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Next-generation sequencing (NGS) is an essential technology for DNA identification in genomic research. DNA fragmentation is a critical step for NGS and doing this on-chip is of great interest for future integrated genomic solutions. Here we demonstrate fast acoustofluidic DNA fragmentation via ultrasound-actuated elastic polydimethylsiloxane (PDMS) microstructures that induce acoustic streaming and associated shear forces when placed in the field of an ultrasonic transducer. Indeed, acoustic streaming locally generates high tensile stresses that can mechanically stretch and break DNA molecule chains. The improvement in efficiency of the on-chip DNA fragmentation is due to the synergistic effect of these tensile stresses and ultrasonic cavitation phenomena. We tested these microstructure-induced effects in a DNA-containing microfluidic channel both experimentally and by simulation. The DNA fragmentation process was evaluated by measuring the change in the DNA fragment size over time. The chip works well with both long and short DNA chains; in particular, purified lambda (λ) DNA was cut from 48.5 kbp to 3 kbp in one minute with selected microstructures and further down to 300 bp within two and a half minutes. The fragment size of mouse genomic DNA was reduced from 1.4 kbp to 400 bp in one minute and then to 200 bp in two and a half minutes. The DNA fragmentation efficiency of the chip equipped with the PDMS microstructures was twice that of the chip without the microstructures. Exhaustive comparison shows that the on-chip fragmentation performance reaches the level of high-end professional standards. Recently, DNA fragmentation was shown to be enhanced using vibrating air microbubbles when the chip was placed in an acoustic field. We think the microbubble-free microstructure-based device we present is easier to operate and more reliable, as it avoids microbubble preparation and maintenance, while showing high DNA fragmentation performance.
中文翻译：
聚二甲基硅氧烷微结构诱导的声流用于增强微流控芯片上的超声 DNA 碎裂
新一代测序 (NGS) 是基因组研究中 DNA 鉴定的一项基本技术。DNA 片段化是 NGS 的关键步骤，在芯片上进行此操作对未来的集成基因组解决方案具有重要意义。在这里，我们通过超声驱动的弹性聚二甲基硅氧烷 (PDMS) 微结构，当放置在超声换能器的场中时会引起声流和相关的剪切力。事实上，声流局部产生高拉伸应力，可以机械拉伸和破坏 DNA 分子链。片上 DNA 片段化效率的提高是由于这些张应力和超声空化现象的协同作用。我们通过实验和模拟在含有 DNA 的微流体通道中测试了这些微观结构诱导的效应。通过测量 DNA 片段大小随时间的变化来评估 DNA 片段化过程。该芯片适用于长链和短链 DNA；特别是，从 48 中切割纯化的 lambda (λ) DNA。使用选定的微结构在一分钟内从 5 kbp 到 3 kbp，并在两分半钟内进一步降低到 300 bp。小鼠基因组 DNA 的片段大小在一分钟内从 1.4 kbp 减少到 400 bp，然后在两分半钟内减少到 200 bp。配备PDMS微结构的芯片的DNA断裂效率是没有微结构的芯片的两倍。详尽对比，片上分片性能达到高端专业标准水平。最近，当芯片被放置在声场中时，DNA 碎片被证明使用振动空气微泡得到增强。我们认为我们提出的无微泡微结构装置更易于操作且更可靠，因为它避免了微泡制备和维护，
更新日期：2022-09-30
中文翻译：
聚二甲基硅氧烷微结构诱导的声流用于增强微流控芯片上的超声 DNA 碎裂
新一代测序 (NGS) 是基因组研究中 DNA 鉴定的一项基本技术。DNA 片段化是 NGS 的关键步骤，在芯片上进行此操作对未来的集成基因组解决方案具有重要意义。在这里，我们通过超声驱动的弹性聚二甲基硅氧烷 (PDMS) 微结构，当放置在超声换能器的场中时会引起声流和相关的剪切力。事实上，声流局部产生高拉伸应力，可以机械拉伸和破坏 DNA 分子链。片上 DNA 片段化效率的提高是由于这些张应力和超声空化现象的协同作用。我们通过实验和模拟在含有 DNA 的微流体通道中测试了这些微观结构诱导的效应。通过测量 DNA 片段大小随时间的变化来评估 DNA 片段化过程。该芯片适用于长链和短链 DNA；特别是，从 48 中切割纯化的 lambda (λ) DNA。使用选定的微结构在一分钟内从 5 kbp 到 3 kbp，并在两分半钟内进一步降低到 300 bp。小鼠基因组 DNA 的片段大小在一分钟内从 1.4 kbp 减少到 400 bp，然后在两分半钟内减少到 200 bp。配备PDMS微结构的芯片的DNA断裂效率是没有微结构的芯片的两倍。详尽对比，片上分片性能达到高端专业标准水平。最近，当芯片被放置在声场中时，DNA 碎片被证明使用振动空气微泡得到增强。我们认为我们提出的无微泡微结构装置更易于操作且更可靠，因为它避免了微泡制备和维护，
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