In-line characterization of nanostructures produced by roll-to-roll nanoimprinting.

We present an in-line metrology solution for dimensional characterization of roll-to-roll imprinted nanostructures. The solution is based on a scatterometric analysis of optical data from a hyperspectral camera deployed at a production facility, where nanostructures are produced at speeds of 10m/min. The system combines the ease of use of a real-space imaging system with the spectral information used in scatterometry. We present nanoscale dimensional measurements on one-dimensional line gratings with various periods and orientations. The depths of the produced structures are accurately characterized with uncertainties on the scale of a few nanometers. The hyperspectral imaging capabilities of the system can also be used to avoid vibrational effects.

Single-molecule DNA-mapping and whole-genome sequencing of individual cells.

To elucidate cellular diversity and clonal evolution in tissues and tumors, one must resolve genomic heterogeneity in single cells. To this end, we have developed low-cost, mass-producible micro-/nanofluidic chips for DNA extraction from individual cells. These chips have modules that collect genomic DNA for sequencing or map genomic structure directly, on-chip, with denaturation-renaturation (D-R) optical mapping [Marie R, et al. (2013) Proc Natl Acad Sci USA 110:4893-4898]. Processing of single cells from the LS174T colorectal cancer cell line showed that D-R mapping of single molecules can reveal structural variation (SV) in the genome of single cells. In one experiment, we processed 17 fragments covering 19.8 Mb of the cell's genome. One megabase-large fragment aligned well to chromosome 19 with half its length, while the other half showed variable alignment. Paired-end single-cell sequencing supported this finding, revealing a region of complexity and a 50-kb deletion. Sequencing struggled, however, to detect a 20-kb gap that D-R mapping showed clearly in a megabase fragment that otherwise mapped well to the reference at the pericentromeric region of chromosome 4. Pericentromeric regions are complex and show substantial sequence homology between different chromosomes, making mapping of sequence reads ambiguous. Thus, D-R mapping directly, from a single molecule, revealed characteristics of the single-cell genome that were challenging for short-read sequencing.

Sequencing of human genomes extracted from single cancer cells isolated in a valveless microfluidic device.

Sequencing the genomes of individual cells enables the direct determination of genetic heterogeneity amongst cells within a population. We have developed an injection-moulded valveless microfluidic device in which single cells from colorectal cancer derived cell lines (LS174T, LS180 and RKO) and fresh colorectal tumors have been individually trapped, their genomes extracted and prepared for sequencing using multiple displacement amplification (MDA). Ninety nine percent of the DNA sequences obtained mapped to a reference human genome, indicating that there was effectively no contamination of these samples from non-human sources. In addition, most of the reads are correctly paired, with a low percentage of singletons (0.17 ± 0.06%) and we obtain genome coverages approaching 90%. To achieve this high quality, our device design and process shows that amplification can be conducted in microliter volumes as long as the lysis is in sub-nanoliter volumes. Our data thus demonstrates that high quality whole genome sequencing of single cells can be achieved using a relatively simple, inexpensive and scalable device. Detection of genetic heterogeneity at the single cell level, as we have demonstrated for freshly obtained single cancer cells, could soon become available as a clinical tool to precisely match treatment with the properties of a patient's own tumor.

Concentrating and labeling genomic DNA in a nanofluidic array.

Nucleotide incorporation by DNA polymerase forms the basis of DNA sequencing-by-synthesis. In current platforms, either the single-stranded DNA or the enzyme is immobilized on a solid surface to locate the incorporation of individual nucleotides in space and/or time. Solid-phase reactions may, however, hinder the polymerase activity. We demonstrate a device and a protocol for the enzymatic labeling of genomic DNA arranged in a dense array of single molecules without attaching the enzyme or the DNA to a surface. DNA molecules accumulate in a dense array of pits embedded within a nanoslit due to entropic trapping. We then perform ϕ29 polymerase extension from single-strand nicks created on the trapped molecules to incorporate fluorescent nucleotides into the DNA. The array of entropic traps can be loaded with λ-DNA molecules to more than 90% of capacity at a flow rate of 10 pL min-1. The final concentration can reach up to 100 µg mL-1, and the DNA is eluted from the array by increasing the flow rate. The device may be an important preparative module for carrying out enzymatic processing on DNA extracted from single-cells in a microfluidic chip.

Enrichment of megabase-sized DNA molecules for single-molecule optical mapping and next-generation sequencing.

Next-generation sequencing (NGS) has caused a revolution, yet left a gap: long-range genetic information from native, non-amplified DNA fragments is unavailable. It might be obtained by optical mapping of megabase-sized DNA molecules. Frequently only a specific genomic region is of interest, so here we introduce a method for selection and enrichment of megabase-sized DNA molecules intended for single-molecule optical mapping: DNA from a human cell line is digested by the NotI rare-cutting enzyme and size-selected by pulsed-field gel electrophoresis. For demonstration, more than 600 sub-megabase- to megabase-sized DNA molecules were recovered from the gel and analysed by denaturation-renaturation optical mapping. Size-selected molecules from the same gel were sequenced by NGS. The optically mapped molecules and the NGS reads showed enrichment from regions defined by NotI restriction sites. We demonstrate that the unannotated genome can be characterized in a locus-specific manner via molecules partially overlapping with the annotated genome. The method is a promising tool for investigation of structural variants in enriched human genomic regions for both research and diagnostic purposes. Our enrichment method could potentially work with other genomes or target specified regions by applying other genomic editing tools, such as the CRISPR/Cas9 system.

Optothermally actuated capillary burst valve.

We demonstrate the optothermal actuation of individual capillary burst valves in an all-polymer microfluidic device. The capillary burst valves are realised in a planar design by introducing a fluidic constriction in a microfluidic channel of constant depth. We show that a capillary burst valve can be burst by raising the temperature due to the temperature dependence of the fluid surface tension. We address individual valves by using a local heating platform based on a thin film of near infrared absorber dye embedded in the lid used to seal the microfluidic device [L. H. Thamdrup et al., Nano Lett. 10, 826-832 (2010)]. An individual valve is burst by focusing the laser in its vicinity. We demonstrate the capture of single polystyrene 7 µm beads in the constriction triggered by the bursting of the valve.

Design of Hierarchical Surfaces for Tuning Wetting Characteristics.

Patterned surfaces with tunable wetting properties are described. A hybrid hierarchical surface realized by combining two different materials exhibits different wetting states, depending on the speed of impingement of the water droplets. Both "lotus" (high contact angle and low adhesion) and "petal" (high contact angle and high adhesion) states were observed on the same surface without the need of any modification of the surface. The great difference between the capillary pressures exerted by the microstructures and nanostructures was the key factor that allowed us to tailor effectively the adhesiveness of the water droplets. Having a low capillary pressure for the microstructures and a high capillary pressure for the nanostructures, we allow to the surface the possibility of being in a lotus state or in a petal state.

Separation of cancer cells from white blood cells by pinched flow fractionation.

In this paper, the microfluidic size-separation technique pinched flow fractionation (PFF) is used to separate cancer cells from white blood cells (WBCs). The cells are separated at efficiencies above 90% for both cell types. Circulating tumor cells (CTCs) are found in the blood of cancer patients and can form new tumors. CTCs are rare cells in blood, but they are important for the understanding of metastasis. There is therefore a high interest in developing a method for the enrichment of CTCs from blood samples, which also enables further analysis of the separated cells. The separation is challenged by the size overlap between cancer cells and the 10(6) times more abundant WBCs. The size overlap prevents high efficiency separation, however we demonstrate that cell deformability can be exploited in PFF devices to gain higher efficiencies than expected from the size distribution of the cells.

Well-defined microapertures for ion channel biosensors.

Gated ion channels are excitable nanopores in biological membranes. They sense and respond to different triggers in nature. The sensory characteristics of these channels can be modified by protein engineering tools and the channels can be functionally reconstituted into synthetic lipid bilayer membranes. The combination of the advances in protein engineering with electrical and/or optical signal detection possibilities makes ion channels perfect detection modules for sensory devices. However, their integration into analytical devices is problematic due to the instability of lipid bilayers. Here, we report on developing a stable sensory chip containing a mechanosensitive channel in a Si/SiO(2) chip with a 3 µm pore. Our new fabrication strategy was straightforward. It required only lithography and dry etching for the pore definition and membrane release and reduced the risk of membrane rupture in the fabrication process. A gated ion channel could be inserted, with the retention of its function, into the pores of Si/SiO(2) chips and be detectable at the single channel level upon activation. Excitable ion channels in stable small pores can serve as very sensitive detectors of specific molecules.

Imprinted silicon-based nanophotonics.

We demonstrate and optically characterize silicon-on-insulator based nanophotonic devices fabricated by nanoimprint lithography. In our demonstration, we have realized ordinary and topology-optimized photonic crystal waveguide structures. The topology-optimized structures require lateral pattern definition on a sub 30-nm scale in combination with a deep vertical silicon etch of the order of ~300 nm. The nanoimprint method offers a cost-efficient parallel fabrication process with state-of-the-art replication fidelity, comparable to direct electron beam writing.