Gold nanoparticles and nearby fluorophores interact via electromagnetic coupling upon light excitation. We determine the distance and wavelength dependence of this coupling theoretically and experimentally via steady-state and time-resolved fluorescence spectroscopy. For the first time, the fluorescence quenching of four different dye molecules, which absorb light at different wavelengths across the visible spectrum and into the near-infrared, is studied using a rigid silica shell as a spacer. A comprehensive experimental determination of the distance dependence from complete quenching to no coupling is carried out by a systematic variation of the silica shell thickness. Electrodynamic theory predicts the observed quenching quantitatively in terms of energy transfer from the molecular emitter to the gold nanoparticle. The plasmonic field enhancement in the vicinity of the 13 nm gold nanoparticles is calculated as a function of distance and excitation wavelength and is included in all calculations. Relative radiative and energy transfer rates are determined experimentally and are in good agreement with calculated rates. We demonstrate and quantify the severe effect of dye-dye interactions on the fluorescence properties of dyes attached to the surface of a silica nanoparticle in control experiments. This allows us to determine the experimental conditions, under which dye-dye interactions do not affect the experimental results.

The blinking behavior of single Atto565 molecules on a glass surface is studied under air or nitrogen atmospheres using confocal microscopy. The broad distributions for both on- and off-time durations obey power law kinetics that are rationalized using a charge tunneling model. In this case, a charge is transferred from the Atto565 molecule to localized states found on the glass surface. Subsequent charge recombination by back charge tunneling from trap to Atto565 cation (i.e., dark state) restores the fluorescence. The off-time distribution is independent of excitation intensity (I), whereas the on-time distribution exhibits a power law exponent that varies with I. Two pathways have been identified to lead to the formation of the radical dark state. The first involves direct charge tunneling from the excited singlet S1 state to charge traps in the surrounding matrix, and the second requires charge ejection from the triplet T1 state after intersystem crossing from S1. Monte Carlo simulation studies complement the two-pathway model. Photobleaching curves of both single and ensemble molecules do not exhibit monoexponential decays suggesting complex bleaching dynamics arising from triplet and radical states.

Single molecule localization microscopy (SMLM) techniques allow for sub-diffraction imaging with spatial resolutions better than 10 nm reported. Much has been discussed relating to different variations of SMLM and all-inclusive microscopes can now be purchased, removing the need for in-house software or hardware development. However, little discussion has occurred examining the reliability and quality of the images being produced, as well as the potential for overlooked preparative artifacts. As a result of the up to an order-of-magnitude improvement in spatial resolution, substantially more detail is observed, including changes in distribution and ultrastructure caused by the many steps required to fix, permeabilize, and stain a sample. Here we systematically investigate many of these steps including different fixatives, fixative concentration, permeabilization concentration and timing, antibody concentration, and buffering. We present three well-optimized fixation protocols for staining microtubules, mitochondria and actin in a mammalian cell line and then discuss various artifacts in relation to images obtained from samples prepared using the protocols. The potential for such errors to go undetected in SMLM images and the complications in defining a ‘good’ image using previous parameters applied to confocal microscopy are also discussed.

Expansion microscopy (ExM) enables super-resolution fluorescence imaging of physically expanded biological samples with conventional microscopes. By combining ExM with singlemolecule localization microscopy (SMLM) it is potentially possible to approach the resolution of electron microscopy. However, current attempts to combine both methods remained challenging because of protein and fluorophore loss during digestion or denaturation, gelation, and the incompatibility of expanded polyelectrolyte hydrogels with photoswitching buffers. Here we show that re-embedding of expanded hydrogels enables dSTORM imaging of expanded samples and demonstrate that post-labeling ExM resolves the current limitations of super-resolution microscopy. Using microtubules as a reference structure and centrioles, we demonstrate that post-labeling Ex-SMLM preserves ultrastructural details, improves the labeling efficiency and reduces the positional error arising from linking fluorophores into the gel thus paving the way for super-resolution imaging of immunolabeled endogenous proteins with true molecular resolution.

Background Pathological forms of TAR DNA-binding protein 43 (TDP-43) are present in motor neurons of almost all amyotrophic lateral sclerosis (ALS) patients, and mutations in TDP-43 are also present in ALS. Loss and gain of TDP-43 functions are implicated in pathogenesis, but the mechanisms are unclear. While the RNA functions of TDP-43 have been widely investigated, its DNA binding roles remain unclear. However, recent studies have implicated a role for TDP-43 in the DNA damage response. Methods We used NSC-34 motor neuron-like cells and primary cortical neurons expressing wildtype TDP-43 or TDP-43 ALS associated mutants (A315T, Q331K), in which DNA damage was induced by etoposide or H2O2 treatment. We investigated the consequences of depletion of TDP-43 on DNA repair using small interfering RNAs. Specific non homologous end joining (NHEJ) reporters (EJ5GFP and EJ2GFP) and cells lacking DNA-dependent serine/threonine protein kinase (DNA-PK) were used to investigate the role of TDP-43 in DNA repair. To investigate the recruitment of TDP-43 to sites of DNA damage we used single molecule super-resolution microscopy and a co-immunoprecipitation assay. We also investigated DNA damage in an ALS transgenic mouse model, in which TDP-43 accumulates pathologically in the cytoplasm. We also examined fibroblasts derived from ALS patients bearing the TDP-43 M337V mutation for evidence of DNA damage. Results We demonstrate that wildtype TDP-43 is recruited to sites of DNA damage where it participates in classical NHEJ DNA repair. However, ALS-associated TDP-43 mutants lose this activity, which induces DNA damage. Furthermore, DNA damage is present in mice displaying TDP-43 pathology, implying an active role in neurodegeneration. Additionally, DNA damage triggers features typical of TDP-43 pathology; cytoplasmic mis-localisation and stress granule formation. Similarly, inhibition of NHEJ induces TDP-43 mis-localisation to the cytoplasm. Conclusions This study reveals that TDP-43 functions in DNA repair, but loss of this function triggers DNA damage and is associated with key pathological features of ALS.