μLAS technology for DNA isolation coupled to Cas9-assisted targeting for sequencing and assembly of a 30 kb region in plant genome

Size Fractionation of Milliliter DNA Samples in Minutes Controlled by an Electric Field of ∼10 V

DNA size fractionation is an essential tool in molecular biology and is used to isolate targets in a mixture characterized by a broad molecular-weight distribution. Microfluidics was thought to provide the opportunity to create devices capable of enhancing and speeding up the classical fractionation processes. However, this conjecture met limited success due to the low mass or volume throughput of these technologies. We describe the μLAF (μ-laboratory for DNA fractionation) technology for DNA size selection based on the stacking of molecules on films of ∼100 μm in thickness with 105 cm-2 pores ∼2 μm in diameter. Size selection is achieved by controlling the regime of electrohydrodynamic migration through the temporal modulation of an electric field. This technology allows the processing of milliliter-scale samples containing a DNA mass of several hundreds of ng within ∼10 min and the selection of DNA in virtually any size window spanning 200 to 1000 bp. We demonstrate that one operation suffices to fractionate sheared genomic DNA in up to six fractions with collection efficiencies of ∼20-40% and enrichment factors of ∼1.5-3-fold. These performances compare favorably in terms of speed and versatility to those of the current standards.

Hybridization-based DNA biosensing with a limit of detection of 4 fM in 30 s using an electrohydrodynamic concentration module fabricated by grayscale lithography

Speeding up and enhancing the performances of nucleic acid biosensing technologies have remained drivers for innovation. Here, we optimize a fluorimetry-based technology for DNA detection based on the concentration of linear targets paired with probes. The concentration module consists of a microfluidic channel with the shape of a funnel in which we monitor a viscoelastic flow and a counter-electrophoretic force. We report that the technology performs better with a target longer than 100 nucleotides (nt) and a probe shorter than 30 nt. We also prove that the control of the funnel geometry in 2.5D using grayscale lithography enhances sensitivity by 100-fold in comparison to chips obtained by conventional photolithography. With these optimized settings, we demonstrate a limit of detection of 4 fM in 30 s and a detection range of more than five decades. This technology hence provides an excellent balance between sensitivity and time to result.

Recent Advances in Strategies for the Cloning of Natural Product Biosynthetic Gene Clusters

Microbial natural products (NPs) are a major source of pharmacological agents. Most NPs are synthesized from specific biosynthetic gene clusters (BGCs). With the rapid increase of sequenced microbial genomes, large numbers of NP BGCs have been discovered, regarded as a treasure trove of novel bioactive compounds. However, many NP BGCs are silent in native hosts under laboratory conditions. In order to explore their therapeutic potential, a main route is to activate these silent NP BGCs in heterologous hosts. To this end, the first step is to accurately and efficiently capture these BGCs. In the past decades, a large number of effective technologies for cloning NP BGCs have been established, which has greatly promoted drug discovery research. Herein, we describe recent advances in strategies for BGC cloning, with a focus on the preparation of high-molecular-weight DNA fragment, selection and optimization of vectors used for carrying large-size DNA, and methods for assembling targeted DNA fragment and appropriate vector. The future direction into novel, universal, and high-efficiency methods for cloning NP BGCs is also prospected.

Single-step electrohydrodynamic separation of 1-150 kbp in less than 5 min using homogeneous glass/adhesive/glass microchips

Electrohydrodynamic migration, which is based on hydrodynamic actuation with an opposing electrophoretic force, enables the separation of DNA molecules of 3-100 kbp in glass capillary within 1 h. Here, we wish to enhance these performances using microchip technologies. This study starts with the fabrication of microchips with uniform surfaces, as motivated by our observation that band splitting occurs in microchannels made out of heterogeneous materials such as glass and silicon. The resulting glass-adhesive-glass microchips feature the highest reported bonding strength of 11 MPa for such materials (115 kgf/cm²), a high lateral resolution of critical dimension 5 μm, and minimal auto-fluorescence. These devices enable us to report the separation of 13 DNA bands in the size range of 1-150 kbp in one experiment of 5 min, i.e. 13 times faster than with capillary. In turn, we observe that bands split during electrohydrodynamic migration in heterogeneous glass-silicon but not in homogeneous glass-adhesive-glass microchips. We suggest that this effect arises from differential Electro-Osmotic Flow (EOF) in between the upper and lower walls of heterogeneous channels, and provide evidence that this phenomenon of differential EOF causes band broadening in electrophoresis during microchip electrophoresis. We finally prove that our electrohydrodynamic separation compares very favorably to microchip technologies in terms of resolution length and features the broadest analytical range reported so far.

Characterization and minimization of band broadening in DNA electrohydrodynamic migration for enhanced size separation

The combination of hydrodynamic actuation with an opposing electrophoretic force in viscoelastic liquids enables the separation, concentration, and purification of DNA. Obtaining good analytical performances despite the use of hydrodynamic flow fields, which dramatically enhance band broadening due to Taylor dispersion, constitutes a paradox that remains to be clarified. Here, we study the mechanism of band broadening in electrohydrodynamic migration with an automated microfluidic platform that allows us to track the migration of a 600 bp band in the pressure-electric field parameter space. We demonstrate that diffusion in the electrohydrodynamic regime is controlled predominantly by the electric field and marginally by the hydrodynamic flow velocity. We explain this response with an analytical model of diffusion based on Taylor dispersion arguments. Furthermore, we demonstrate that the electric field can be modulated over time to monitor and minimize the breadth of a DNA band, and suggest guidelines to enhance the resolution of DNA separation experiments. Altogether, our report is a leap towards to the development of high-performance analytical technologies based on electrohydrodynamic actuation.

A tunable filter for high molecular weight DNA selection and linked-read sequencing

In third generation sequencing, the production of quality data requires the selection of molecules longer than ∼20 kbp, but the size selection threshold of most purification technologies is smaller than this target. Here, we describe a technology operated in a capillary with a tunable selection threshold in the range of 3 to 40 kbp controlled by an electric field. We demonstrate that the selection cut-off is sharp, the purification yield is high, and the purification throughput is scalable. We also provide an analytical model that the actuation settings of the filter. The selection of high molecular weight genomic DNA from the melon Cucumis melo L., a diploid organism of ∼0.45 Gbp, is then reported. Linked-read sequencing data show that the N50 phase block size, which scores the correct representation of two chromosomes, is enhanced by a factor of 2 after size selection, establishing the relevance and versatility of our technology.