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.

Nanoscale Plasmonic V-Groove Waveguides for the Interrogation of Single Fluorescent Bacterial Cells

We experimentally demonstrate the interrogation of an individual Escherichia coli cell using a nanoscale plasmonic V-groove waveguide. Several different configurations were studied. The first involved the excitation of the cell in a liquid environment because it flows on top of the waveguide nanocoupler, while the obtained fluorescence is coupled into the waveguide and collected at the other nanocoupler. The other two configurations involved the positioning of the bacterium within the nanoscale waveguide and its excitation in a dry environment either directly from the top or through waveguide modes. This is achieved by taking advantage of the waveguide properties not only for light guiding but also as a mechanical tool for trapping the bacteria within the V-grooves. The obtained results are supported by a set of numerical simulations, shedding more light on the mechanism of excitation. This demonstration paves the way for the construction of an efficient bioplasmonic chip for diverse cell-based sensing applications.

Photothermal Transport of DNA in Entropy-Landscape Plasmonic Waveguides

The ability to handle single, free molecules in lab-on-a-chip systems is key to the development of advanced biotechnologies. Entropic confinement offers passive control of polymers in nanofluidic systems by locally asserting a molecule's number of available conformation states through structured landscapes. Separately, a range of plasmonic configurations have demonstrated active manipulation of nano-objects by harnessing concentrated electric fields. The integration of these two independent techniques promises a range of sophisticated and complementary functions to handle, for example, DNA, but numerous difficulties, in particular, conflicting requirements of channel size, have prevented progress. Here, we show that metallic V-groove waveguides, embedded in fluidic nanoslits, form entropic potentials that trap and guide DNA molecules over well-defined routes while simultaneously promoting photothermal transport of DNA through the losses of plasmonic modes. The propulsive forces, assisted by in-coupling to propagating channel plasmon polaritons, extend along the V-grooves with a directed motion up to ≈0.5 μm·mW^-1 away from the input beam and λ-DNA velocities reaching ≈0.2 μm·s^-1·mW^-1. The entropic trapping enables the V-grooves to be flexibly loaded and unloaded with DNA by variation of transverse fluid flow, a process that is selective to biopolymers versus fixed-shape objects and also allows the technique to address the challenges of nanoscale interaction volumes. Our self-aligning, light-driven actuator provides a convenient platform to filter, route, and manipulate individual molecules and may be realized wholly by wafer-scale fabrication suitable for parallelized investigation.

Resonant laser printing of structural colors on high-index dielectric metasurfaces

Man-made structural colors, which originate from resonant interactions between visible light and manufactured nanostructures, are emerging as a solution for ink-free color printing. We show that non-iridescent structural colors can be conveniently produced by nanostructures made from high-index dielectric materials. Compared to plasmonic analogs, color surfaces with high-index dielectrics, such as germanium (Ge), have a lower reflectance, yielding a superior color contrast. Taking advantage of band-to-band absorption in Ge, we laser-postprocess Ge color metasurfaces with morphology-dependent resonances. Strong on-resonance energy absorption under pulsed laser irradiation locally elevates the lattice temperature (exceeding 1200 K) in an ultrashort time scale (1 ns). This forms the basis for resonant laser printing, where rapid melting allows for surface energy-driven morphology changes with associated modification of color appearance. Laser-printable high-index dielectric color metasurfaces are scalable to a large area and open a new paradigm for printing and decoration with nonfading and vibrant colors.

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.

Abstract A49: Transcription factor upregulation after mTOR inhibition by Torin1 induces growth factor receptor expression

Introduction: mTOR (mammalian target of rapamycin) integrates signals from cellular nutrient status and growth factors, to regulate cell growth, proliferation, and metabolism. mTOR is a part of the PI3K-Akt-mTOR signalling pathway, the components of which are frequently mutated in human cancers. Various inhibitors of mTOR activity have been developed to target this pathway, including rapamycin and its analogs sirolimus, everolimus, temsirolimus. These inhibitors are currently approved for the treatment of certain cancers, and under investigation in clinical trials for the treatment of others. Despite displaying initial effectiveness in delaying tumor progression, mTOR inhibitors eventually lose efficacy and patients relapse due to development of resistance.

Due to the regulation of cap-dependent translation by mTOR, treatment of cells with mTOR inhibitors inhibits general protein translation. However, a subset of proteins exhibit increased translation in response to mTOR inhibitors. We postulate that these proteins that exhibit upregulation in response to mTOR inhibition play a role in conferring mTOR inhibitor resistance. In this study, we aim to characterize the landscape of proteins that are upregulated in response to mTOR inhibition, in order to identify pathways that contribute to resistance. We use a second-generation mTOR inhibitor Torin1, which targets both mTORC1 and mTORC2 complexes.

Methods: In order to study newly translated proteins after mTOR inhibition by Torin1 on a proteomic scale, we combined the methods of click chemistry with SILAC (stable isotopic labelling of amino acids in cell culture) and tandem mass spectrometry. The translatome was studied through click-pulse-SILAC experiments conducted at 2 hours and 24 hours post Torin1 treatment in MEFs (mouse embryonic fibroblasts) as well as PC3 prostate carcinoma cells. The total proteome of MEF and PC3 cells 24 hours after Torin1 treatment was studied using SILAC and tandem mass spectrometry. Proteomics data processing and pathway enrichment analysis was performed using the Perseus software, and upregulated proteins were subject to analysis by RNA silencing, qPCR, and click chemistry.

Results: Translatome analysis after Torin1 treatment showed general translation inhibition as expected, except for a small subset of proteins with increased translation. Increased translation of growth factor receptors was observed 24 hours post-Torin1 treatment, and of many transcription factors 2 hours post-treatment. Total proteome analysis 24 hours post-treatment revealed an increase in total protein levels of many of these growth factor receptors as well as transcription factors. qPCR experiments revealed increased transcripts levels of these growth factor receptors as early as 2 hours post-treatment, suggesting transcriptional upregulation. Through cross-referencing our 2 hour translatome data with genome-wide ChIP-seq datasets accessed through Cscan, we determined candidate transcription factors that may be responsible for upregulating the expression of growth factor receptors. Knockdown studies suggest that some of these transcription factors are indeed responsible for the upregulation of growth factor receptors.

Conclusion: mTOR inhibition by Torin1 suppresses general translation, but many transcription factors escape this suppression and exhibit increased expression. These transcription factors induce expression of growth factor receptors, consequently enhancing their signaling. These studies identify an axis which potentially reduces the efficacy of mTOR inhibitors in cancer therapy, as well as targets that may require simultaneous inhibition.

Citation Format: Tianqing T. Yang, Gian L. Negri, Anders Kristensen, Poul H. B. Sorensen. Transcription factor upregulation after mTOR inhibition by Torin1 induces growth factor receptor expression. [abstract]. In: Proceedings of the AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; 2016 Oct 27-30; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2017;77(6 Suppl):Abstract nr A49.

How to determine local stretching and tension in a flow-stretched DNA molecule

We determine the nonuniform stretching of and tension in a mega base pairs-long fragment of deoxyribonucleic acid (DNA) that is flow stretched in a nanofluidic chip. We use no markers, do not know the contour length of the DNA, and do not have the full DNA molecule inside our field of view. Instead, we analyze the transverse thermal motion of the DNA. Tension at the center of the DNA adds up to 16 pN, giving almost fully stretched DNA. This method was devised for optical mapping of DNA, specifically, DNA denaturation patterns. It may be useful also for other studies, e.g., DNA-protein interactions, specifically, their tension dependence. Generally, wherever long strands of DNA-e.g., native DNA extracted from human cells or bacteria-must be stretched with ease for inspection, this method applies.

Plasmonic colour laser printing

Colour generation by plasmonic nanostructures and metasurfaces has several advantages over dye technology: reduced pixel area, sub-wavelength resolution and the production of bright and non-fading colours. However, plasmonic colour patterns need to be pre-designed and printed either by e-beam lithography (EBL) or focused ion beam (FIB), both expensive and not scalable processes that are not suitable for post-processing customization. Here we show a method of colour printing on nanoimprinted plasmonic metasurfaces using laser post-writing. Laser pulses induce transient local heat generation that leads to melting and reshaping of the imprinted nanostructures. Depending on the laser pulse energy density, different surface morphologies that support different plasmonic resonances leading to different colour appearances can be created. Using this technique we can print all primary colours with a speed of 1 ns per pixel, resolution up to 127,000 dots per inch (DPI) and power consumption down to 0.3 nJ per pixel.

Does chemotherapy improve health-related quality of life in advanced pancreatic cancer? A systematic review

Chemotherapy is increasingly being used in advanced pancreatic cancer, but side-effects are common. The aim of this systematic review was to assess whether chemotherapy improves health-related quality of life (HRQoL), pain or cachexia. Thirty studies were reviewed. Four of 23 studies evaluating HRQoL, 7 of 24 studies evaluating pain and 0 of 8 studies evaluating cachexia found differences between treatment arms. Change in HRQoL from baseline was evaluated in 14 studies: five studies reported an improvement in at least one treatment arm; three a worsening and the remaining stable scores. Change in pain intensity from baseline was evaluated in eight studies, and improvement was observed in seven. Of the four studies reporting improved survival, three reported improved HRQoL or pain. In conclusion, chemotherapy can stabilize HRQoL and improve pain control. Effects on cachexia are hard to elucidate. Improved survival does not come at the expense of HRQoL or pain control.

Transition state theory demonstrated at the micron scale with out-of-equilibrium transport in a confined environment

Transition state theory (TST) provides a simple interpretation of many thermally activated processes. It applies successfully on timescales and length scales that differ several orders of magnitude: to chemical reactions, breaking of chemical bonds, unfolding of proteins and RNA structures and polymers crossing entropic barriers. Here we apply TST to out-of-equilibrium transport through confined environments: the thermally activated translocation of single DNA molecules over an entropic barrier helped by an external force field. Reaction pathways are effectively one dimensional and so long that they are observable in a microscope. Reaction rates are so slow that transitions are recorded on video. We find sharp transition states that are independent of the applied force, similar to chemical bond rupture, as well as transition states that change location on the reaction pathway with the strength of the applied force. The states of equilibrium and transition are separated by micrometres as compared with angstroms/nanometres for chemical bonds.

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.

Polarization-dependent aluminum metasurface operating at 450 nm

We report on a polarization-dependent plasmonic aluminum-based high-density metasurface operating at blue wavelengths. The fabricated sub-wavelength structures, tailored in size and geometry, possess strong, localized, plasmonic resonances able to control linear polarization. Best performance is achieved by rotating an elongated rectangular structure of length 180 nm and width 110 nm inside a square lattice of period 250 nm. In the case of 45 degrees rotation of the structure with respect to the lattice, the normal-incidence reflectance drops around the resonance wavelength of 457 nm from about 60 percent to below 2 percent.

New technologies for DNA analysis--a review of the READNA Project

The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 41/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.

All-polymer photonic crystal slab sensor

An all-polymer photonic crystal slab sensor is presented, and shown to exhibit narrow resonant reflection with a FWHM of less than 1 nm and a sensitivity of 31 nm/RIU when sensing media with refractive indices around that of water. This results in a detection limit of 4.5 × 10(-6) RIU when measured in conjunction with a spectrometer of 12 pm/pixel resolution. The device is a two-layer structure, composed of a low refractive index polymer with a periodically modulated surface height, covered with a smooth upper-surface high refractive index inorganic-organic hybrid polymer modified with ZrO2based nanoparticles. Furthermore, it is fabricated using inexpensive vacuum-less techniques involving only UV nanoreplication and polymer spin-casting, and is thus well suited for single-use biological and refractive index sensing applications.

Gap and channeled plasmons in tapered grooves: a review

Tapered metallic grooves have been shown to support plasmons - electromagnetically coupled oscillations of free electrons at metal-dielectric interfaces - across a variety of configurations and V-like profiles. Such plasmons may be divided into two categories: gap-surface plasmons (GSPs) that are confined laterally between the tapered groove sidewalls and propagate either along the groove axis or normal to the planar surface, and channeled plasmon polaritons (CPPs) that occupy the tapered groove profile and propagate exclusively along the groove axis. Both GSPs and CPPs exhibit an assortment of unique properties that are highly suited to a broad range of cutting-edge nanoplasmonic technologies, including ultracompact photonic circuits, quantum-optics components, enhanced lab-on-a-chip devices, efficient light-absorbing surfaces and advanced optical filters, while additionally affording a niche platform to explore the fundamental science of plasmon excitations and their interactions. In this Review, we provide a research status update of plasmons in tapered grooves, starting with a presentation of the theory and important features of GSPs and CPPs, and follow with an overview of the broad range of applications they enable or improve. We cover the techniques that can fabricate tapered groove structures, in particular highlighting wafer-scale production methods, and outline the various photon- and electron-based approaches that can be used to launch and study GSPs and CPPs. We conclude with a discussion of the challenges that remain for further developing plasmonic tapered-groove devices, and consider the future directions offered by this select yet potentially far-reaching topic area.

Automation of a single-DNA molecule stretching device

We automate the manipulation of genomic-length DNA in a nanofluidic device based on real-time analysis of fluorescence images. In our protocol, individual molecules are picked from a microchannel and stretched with pN forces using pressure driven flows. The millimeter-long DNA fragments free flowing in micro- and nanofluidics emit low fluorescence and change shape, thus challenging the image analysis for machine vision. We demonstrate a set of image processing steps that increase the intrinsically low signal-to-noise ratio associated with single-molecule fluorescence microscopy. Furthermore, we demonstrate how to estimate the length of molecules by continuous real-time image stitching and how to increase the effective resolution of a pressure controller by pulse width modulation. The sequence of image-processing steps addresses the challenges of genomic-length DNA visualization; however, they should also be general to other applications of fluorescence-based microfluidics.

Refractometric monitoring of dissolution and fluid flow with distributed feedback dye laser sensor

Monitoring the dissolution of solid material in liquids and monitoring of fluid flow is of significant interest for applications in chemistry, food production, medicine, and especially in the fields of microfluidics and lab on a chip. Here, real-time refractometric monitoring of dissolution and fast fluid flow with DFB dye laser sensors with an optical imaging spectroscopy setup is presented. The dye laser sensors provide both low detection limits and high spatial resolution. It is demonstrated how the materials NaCl, sucrose, and bovine serum albumin show characteristic dissolution patterns. The unique feature of the presented method is a high frame rate of up to 20 Hz, which is proven to enable the monitoring of fast flow of a sucrose solution jet into pure water.

Thermophoretic forces on DNA measured with a single-molecule spring balance

We stretch a single DNA molecule with thermophoretic forces and measure these forces with a spring balance: the DNA molecule itself. It is an entropic spring which we calibrate, using as a benchmark its Brownian motion in the nanochannel that contains and prestretches it. This direct measurement of the thermophoretic force in a static configuration finds forces up to 130 fN. This is eleven times stronger than the force experienced by the same molecule in the same thermal gradient in bulk, where the molecule shields itself. Our stronger forces stretch the middle of the molecule up to 80% of its contour length. We find the Soret coefficient per unit length of DNA at various ionic strengths. It agrees, with novel precision, with results obtained in bulk for DNA too short to shield itself and with the thermodynamic model of thermophoresis.

Random-cavity lasing from electrospun polymer fiber networks

Lasing emission from random cavities formed in networks of electrospun Rhodamine-doped polymer fibers is presented. Spatially resolved spectroscopy and spectral analysis prove that the observed laser emission stems from individual ring resonators randomly distributed throughout the network. These electrospun fiber lasers represent a facile and straightforward configuration for developing novel photonic devices that may advantageously utilize the network morphology.

Plasmonic metasurfaces for coloration of plastic consumer products

We present reflective plasmonic colors based on the concept of localized surface plasmon resonances (LSPR) for plastic consumer products. In particular, we bridge the widely existing technological gap between clean-room fabricated plasmonic metasurfaces and the practical call for large-area structurally colored plastic surfaces robust to daily life handling. We utilize the hybridization between LSPR modes in aluminum nanodisks and nanoholes to design and fabricate bright angle-insensitive colors that may be tuned across the entire visible spectrum.

Efficient excitation of channel plasmons in tailored, UV-lithography-defined V-grooves

We demonstrate the highly efficient (>50%) conversion of freely propagating light to channel plasmon-polaritons (CPPs) in gold V-groove waveguides using compact 1.6 μm long waveguide-termination coupling mirrors. Our straightforward fabrication process, involving UV-lithography and crystallographic silicon etching, forms the coupling mirrors innately and ensures exceptional-quality, wafer-scale device production. We tailor the V-shaped profiles by thermal silicon oxidation in order to shift initially wedge-located modes downward into the V-grooves, resulting in well-confined CPPs suitable for nanophotonic applications.