@article {70297, title = {Nanoscale imaging of expanded cells and proteins with spontaneously blinking dyes}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 23}, abstract = {

Expansion microscopy (ExM) enables nanoscale imaging on standard microscopes, but combining ExM with single-molecule localization microscopy (SMLM) remains difficult, owing to the incompatibility of expanded hydrogels with photoswitching buffers. Here, we introduce a single-step expansion microscopy method that allows SMLM with spontaneously blinking dyes in 6-14{\texttimes} expanded samples, without re-embedding. We demonstrate nanometer-resolution imaging by resolving the organization of the nuclear pore complex (NPC) and the molecular structure of recombinant homotrimeric proliferating cell nuclear antigen (PCNA).

}, doi = {10.64898/2026.02.23.707413}, url = {https://www.biorxiv.org/content/early/2026/02/23/2026.02.23.707413}, author = {Taban, Danush and Jungblut, Marvin and Budiarta, Made and Helmerich, Dominic A. and Kiesel, Cerridwen and Plutkis, Sarah E. and Lavis, Luke D. and Krah, Donatus and Shaib, Ali H. and Doose, S{\"o}ren and Kollmannsberger, Philip and Rizzoli, Silvio O. and Beliu, Gerti and Sauer, Markus} } @article {70304, title = {Nanoscale imaging of expanded cells and proteins with spontaneously blinking dyes}, journal = {bioRxiv}, year = {2026}, month = {2026 Feb 23}, abstract = {

Expansion microscopy (ExM) enables nanoscale imaging on standard microscopes, but combining ExM with single-molecule localization microscopy (SMLM) remains difficult, owing to the incompatibility of expanded hydrogels with photoswitching buffers. Here, we introduce a single-step expansion microscopy method that allows SMLM with spontaneously blinking dyes in 6-14{\texttimes} expanded samples, without re-embedding. We demonstrate nanometer-resolution imaging by resolving the organization of the nuclear pore complex (NPC) and the molecular structure of recombinant homotrimeric proliferating cell nuclear antigen (PCNA).

}, doi = {10.64898/2026.02.23.707413}, url = {https://www.biorxiv.org/content/early/2026/02/23/2026.02.23.707413}, author = {Taban, Danush and Jungblut, Marvin and Budiarta, Made and Helmerich, Dominic A. and Kiesel, Cerridwen and Plutkis, Sarah E. and Lavis, Luke D. and Krah, Donatus and Shaib, Ali H. and Doose, S{\"o}ren and Kollmannsberger, Philip and Rizzoli, Silvio O. and Beliu, Gerti and Sauer, Markus} } @article {47242, title = {Synthesis of a far-red photoactivatable silicon-containing rhodamine for super-resolution microscopy.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {55}, year = {2015}, month = {2015 Dec 11}, pages = {1723-7}, abstract = {

The rhodamine system is a flexible framework for building small-molecule fluorescent probes. Changing N-substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si-containing analogue of Q-rhodamine. This probe is the first example of a "caged" Si-rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red-shifted to allow multicolor imaging. The dye is a useful label for super-resolution imaging and constitutes a new scaffold for far-red fluorogenic molecules.

}, issn = {1521-3773}, doi = {10.1002/anie.201509649}, author = {Grimm, Jonathan B and Klein, Teresa and Kopek, Benjamin G and Shtengel, Gleb and Hess, Harald F and Sauer, Markus and Lavis, Luke D} }