Abstract
Single molecule localization (SML) and tracking (SPT) techniques, such as (spt)PALM, (u/DNA)PAINT and quantum dot tracking, have given unprecedented insight into the nanoscale molecular organization and dynamics in living cells. They allow monitoring individual proteins with millisecond temporal resolution and high spatial resolution (<30 nm) by precisely localizing the point spread function (PSF) of individual emitters and tracking their position over time. While SPT methods have been extended to study the temporal dynamics and co-organization of multiple proteins, conventional experimental setups are restricted in the number of proteins they can probe simultaneously and usually have to tradeoff between the number of colors, the spatio-temporal resolution, and the field of view. Yet, localizing and tracking several proteins simultaneously at high spatial and temporal resolution within large field of views can provide important biological insights. By employing a dual-objective spectral imaging configuration compatible with live cell imaging combined with dedicated computation tools, we demonstrate simultaneous 3D single particle localization and tracking of multiple distinct species over large field of views to be feasible without compromising spatio-temporal resolution. The dispersive element introduced into the second optical path induces a spectrally dependent displacement, which we used to analytically separate up to five different fluorescent species of single emitters based on their emission spectra. We used commercially available microscope bodies aligned one on top of the other, offering biologists with a very ergonomic and flexible instrument covering a broad range of SMLM applications. Finally, we developed a powerful freely available software, called PALMTracer, which allows to quantitatively assess 3D + t + λ SMLM data. We illustrate the capacity of our approach by performing multi-color 3D DNA-PAINT of fixed samples, and demonstrate simultaneous tracking of multiple receptors in live fibroblast and neuron cultures.
Highlights
Single Molecule Localization Microscopy (SMLM) relies on the optical- (Betzig et al, 2006; Rust et al, 2006; Heilemann et al, 2008) or binding-induced (Jungmann et al, 2014) spatial isolation and computational localization of individual fluorophores attached to a protein of interest
Composed of commercially available standard equipment and software, and a freely available analysis solution, we demonstrate that optimal spectral SMLM can be performed without compromising the 2D and 3D localization and tracking performance
We described a powerful and versatile multidimensional singlemolecule localization microscopy workflow
Summary
Single Molecule Localization Microscopy (SMLM) relies on the optical- (Betzig et al, 2006; Rust et al, 2006; Heilemann et al, 2008) or binding-induced (Jungmann et al, 2014) spatial isolation and computational localization of individual fluorophores attached to a protein of interest. It provides unprecedented biological insight into the nanoscale organization and dynamics of biomolecules, and Spectral Single Molecule Localization Microscopy has allowed major discoveries in cell biology and neuroscience (Choquet et al, 2021; Lelek et al, 2021). High-density based single molecule localization approaches can be used to improve temporal resolution (Cox et al, 2012; Zhu et al, 2012; Gustafsson et al, 2016), but at the expense of losing access to single molecular coordinates and single molecule tracking capabilities
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