Super-resolved FRET imaging by confocal fluorescence-lifetime single-molecule localization microscopy

FRET-based approaches are a unique tool for sensing the immediate surroundings and interactions of (bio)molecules. FRET imaging and FLIM (Fluorescence Lifetime Imaging Microscopy) enable the visualization of the spatial distribution of molecular interactions and functional states. However, conventional FLIM and FRET imaging provide average information over an ensemble of molecules within a diffraction-limited volume, which limits the spatial information, accuracy, and dynamic range of the observed signals. Here, we demonstrate an approach to obtain super-resolved FRET imaging based on single-molecule localization microscopy using an early prototype of a commercial time-resolved confocal microscope. DNA Points Accumulation for Imaging in Nanoscale Topography (DNA-PAINT) with fluorogenic probes provides a suitable combination of background reduction and blinking kinetics compatible with the scanning speed of usual confocal microscopes. A single laser is used to excite the donor, a broad detection band is employed to retrieve both donor and acceptor emission, and FRET events are detected from lifetime information

Axonemal Lumen Dominates Cytosolic Protein Diffusion inside the Primary Cilium

Transport of membrane and cytosolic proteins in primary cilia is thought to depend on intraflagellar transport (IFT) and diffusion. However, the relative contribution and spatial routes of each transport mechanism are largely unknown. Although challenging to decipher, the details of these routes are essential for our understanding of protein transport in primary cilia, a critically affected process in many genetic diseases. By using a high-speed virtual 3D super-resolution microscopy, we have mapped the 3D spatial locations of transport routes for various cytosolic proteins in the 250-nm-wide shaft of live primary cilia with a spatiotemporal resolution of 2 ms and <16 nm. Our data reveal two spatially distinguishable transport routes for cytosolic proteins: an IFT-dependent path along the axoneme, and a passive-diffusion route in the axonemal lumen that escaped previous studies. While all cytosolic proteins tested primarily utilize the IFT path in the anterograde direction, differences are observed in the retrograde direction where IFT20 only utilizes IFT, and approximately half of KIF17 and one third of α–tubulin utilizes diffusion besides IFT

Organelle-specific targeting of polymersomes into the cell nucleus

Synthetic nanomaterials are being sought to shuttle therapeutic payloads directly into the cell nucleus as a major target for chemo- and gene-based therapies. However, it remains uncertain whether and how synthetic entities are able to bypass the nuclear pore complexes (NPCs) that regulate transport into and out of the nucleus. We have constructed biocompatible polymer vesicles that infiltrate NPCs and resolved their nuclear uptake mechanism in vitro and in vivo. Their ability to deliver payloads directly into cell nuclei is further validated by transmission electron microscopy.Organelle-specific nanocarriers (NCs) are highly sought after for delivering therapeutic agents into the cell nucleus. This necessitates nucleocytoplasmic transport (NCT) to bypass nuclear pore complexes (NPCs). However, little is known as to how comparably large NCs infiltrate this vital intracellular barrier to enter the nuclear interior. Here, we developed nuclear localization signal (NLS)-conjugated polymersome nanocarriers (NLS-NCs) and studied the NCT mechanism underlying their selective nuclear uptake. Detailed chemical, biophysical, and cellular analyses show that karyopherin receptors are required to authenticate, bind, and escort NLS-NCs through NPCs while Ran guanosine triphosphate (RanGTP) promotes their release from NPCs into the nuclear interior. Ultrastructural analysis by regressive staining transmission electron microscopy further resolves the NLS-NCs on transit in NPCs and inside the nucleus. By elucidating their ability to utilize NCT, these findings demonstrate the efficacy of polymersomes to deliver encapsulated payloads directly into cell nuclei

Helium scanning transmission ion microscopy and electrical characterization of glass nanocapillaries with reproducible tip geometries

Nanopores fabricated from glass microcapillaries are used in applications ranging from scanning ion conductance microscopy to single molecule detection. Still, evaluating the nanocapillary tip by a non-invasive means remains challenging. For instance, electron microscopy characterization techniques can charge, heat and contaminate the glass surface, and typically require conductive coatings that influence the final tip geometry. Per contra, electrical characterization by the means of ion current through the capillary lumen provides only indirect geometrical details of the tips. Here, we show that Helium scanning transmission ion microscopy provides a non-destructive and precise determination of glass nanocapillary tip geometries. This enables the reproducible fabrication of axially asymmetric blunt, bullet and hourglass-shaped tips with opening diameters from 20 nm to 400 nm by laser-assisted pulling. Accordingly, this allows for an evaluation of how tip shape, pore diameter and opening angle impacts on ionic current rectification behavior and the translocation of single molecules. Our analysis shows that current drops and translocation dwell times are dominated by the pore diameter and opening angles regardless of nanocapillary tip shape

Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers

The functional state of the genome is determined by its interactions with proteins that bind, modify, and move along the DNA. To determine the positions and binding strength of proteins localized on DNA we have developed a combined magnetic and optical tweezers apparatus that allows for both sensitive and label-free detection. A DNA loop, that acts as a scanning probe, is created by looping an optically trapped DNA tether around a DNA molecule that is held with magnetic tweezers. Upon scanning the loop along the ?-DNA molecule, EcoRI proteins were detected with ?17 nm spatial resolution. An offset of 33±5 nm for the detected protein positions was found between back and forwards scans, corresponding to the size of the DNA loop and in agreement with theoretical estimates. At higher applied stretching forces, the scanning loop was able to remove bound proteins from the DNA, showing that the method is in principle also capable of measuring the binding strength of proteins to DNA with a force resolution of 0.1 pN/[Formula: see text]. The use of magnetic tweezers in this assay allows the facile preparation of many single-molecule tethers, which can be scanned one after the other, while it also allows for direct control of the supercoiling state of the DNA molecule, making it uniquely suitable to address the effects of torque on protein-DNA interactions.BN/BionanoscienceApplied Science

Vertical "III-V" V-Shaped Nanomembranes Epitaxially Grown on a Patterned Si[001] Substrate and Their Enhanced Light Scattering

We report on a new form of III-IV compound semiconductor nanostructures growing epitaxially as vertical V-shaped nanomembranes on Si(001) and study their light-scattering properties. Precise position control of the InAs nanostructures in regular arrays is demonstrated by bottom-up synthesis using molecular beam epitaxy in nanoscale apertures on a SiO2 mask. The InAs V-shaped nanomembranes are found to originate from the two opposite facets of a rectangular pyramidal island nucleus and extend along two opposite B directions, forming flat {110} walls. Dark-field scattering experiments, in combination with light-scattering theory, show the presence of distinctive shape-dependent optical resonances significantly enhancing the local intensity of incident electromagnetic fields over tunable spectral regions. These new nanostructures could have interesting potential in nanosensors, infrared light emitters, and nonlinear optical elements