Fragmentation of DNA in a sub-microliter microfluidic sonication device

Abstract

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.

Microfluidics for genome-wide studies involving next generation sequencing

“…described a DNA/chromatin shearing device within a microfluidic chip 186 . The acoustic field is generated by attaching a piezoelectric Langevin-type composite transducer to a microfluidic chip.…”

Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics

“…Rather than manual pipetting and multistep protocols with significant sample losses, miniature-interconnecting chambers and channels manipulate samples and fluids in a repeatable, rapid manner that reduces sample consumption. This level of integration can also be coupled with on-chip sonication 66 and fragmentation 67 to further automate the ChIP-Seq workflow. The microfluidic-ChIP devices have recently been used to screen antibody efficacy 68 and used to gain insights into dynamic chromatin-remodeling processes.…”

A high-power ultrasonic microreactor and its application in gas–liquid mass transfer intensification

“…34 To overcome this issue, Hubner et al 17 designed a vessel filled with pressured water (ca. Tseng et al 50 recently built a USMR by using a glass plate to connect the LUT and a PDMS microfluidic chip. This indirect energy input method has advantages of modularity and temperature control, 15,17,49 while the energy transfer efficiency is relatively low, due to the attenuation in the transmission medium and reflection at the liquid/solid interface.…”

“…4.5 bar, the cavitation of the water was suppressed) to transmit the ultrasound from a LUT to the microreactor. 50 In this paper, we present a novel high-power USMR with a microreactor plate directly coupled with LUT. Directly coupling LUT with a microreactor is the most efficient way to deliver ultrasound into microreactors.…”