Publications: Max Planck Institute of Molecular Cell Biology and Genetics

^* joint first author ^# joint corresponding author

2025

Stefan Stoldt^*, Frederike Maass^*, Michael Weber, Sven Dennerlein, Peter Ilgen, Jutta Gärtner, Aysenur Canfes, Sarah V Schweighofer, Daniel C Jans, Peter Rehling, Stefan Jakobs
Super-resolution microscopy of mitochondrial mRNAs.
Nat Commun, 16(1) Art. No. 6391 (2025)
Open Access DOI

Mitochondria contain their own DNA (mtDNA) and a dedicated gene expression machinery. As the mitochondrial dimensions are close to the diffraction limit of classical light microscopy, the spatial distribution of mitochondrial proteins and in particular of mitochondrial mRNAs remains underexplored. Here, we establish single-molecule fluorescence in situ hybridization (smFISH) combined with STED and MINFLUX super-resolution microscopy (nanoscopy) to visualize individual mitochondrial mRNA molecules and associated proteins. STED nanoscopy reveals the spatial relationships between distinct mRNA species and proteins such as the RNA granule marker GRSF1, demonstrating adaptive changes in mRNA distribution and quantity in challenged mammalian cells and patient-derived cell lines. Notably, STED-smFISH shows the release of mRNAs during apoptosis, while MINFLUX reveals the folding of the mRNAs into variable shapes, as well as their spatial proximity to mitochondrial ribosomes. These protocols are transferable to various cell types and open new avenues for understanding mitochondrial gene regulation in health and disease.

2024

Direct optical measurement of intramolecular distances with angstrom precision
SJ Sahl et al.
Science 386, 180-187 (2024)
DOI

Bleaching protection and axial sectioning in fluorescence nanoscopy through two-photon activation at 515 nm
JE Bredfeldt, J Oracz, KA Kiszka, et al.
Nature Communications 15 (1), 7472 (2024)
DOI

MINSTED tracking of single biomolecules
L Scheiderer, H von der Emde, M Hesselink, M Weber, SW Hell
Nature Methods 21 (4), 569-573 (2024)
DOI

2023

Near index matching enables solid diffractive optical element fabrication via additive manufacturing
R Orange kedem, N Opatovski, D Xiao, et al.
Light: Science & Applications 12 (1), 222 (2023)
DOI

A Bright Surprise: Live‐Cell Labeling with Negatively Charged Fluorescent Probes based on Disulfonated Rhodamines and HaloTag
D Kim, S Stoldt, M Weber, S Jakobs, VN Belov, SW Hell
Chemistry‐Methods 3 (9), e202200076 (2023)
DOI

MINSTED nanoscopy enters the Ångström localization range
M Weber, H von der Emde, M Leutenegger, et al.
Nature Biotechnology 41 (4), 569-576 (2023)
DOI

2021

Compensating the delayed electro-optical deflector response
M Leutenegger, M Weber, H von der Emde, SW Hell
arXiv preprint arXiv:2112.01621 (2021)

Photoactivatable fluorescent dyes with hydrophilic caging groups and their use in multicolor nanoscopy
Alexey N. Butkevich, Michael Weber, Angel R. Cereceda Delgado, Lynn M. Ostersehlt, Elisa D’Este, and Stefan W. Hell
Journal of the American Chemical Society 143 (44), 18388-18393 (2021)
DOI

Least-squares fitting of Gaussian spots on graphics processing units
M Leutenegger, M Weber
arXiv preprint arXiv:2106.02045 (2021)

The Positive Switching Fluorescent Protein Padron2 Enables Live-Cell Reversible Saturable Optical Linear Fluorescence Transitions (RESOLFT) Nanoscopy without Sequential Illumination Steps
Timo Konen, Daniel Stumpf, Tim Grotjohann, Isabelle Jansen, Mariano Bossi, Michael Weber, Nickels Jensen, Stefan W. Hell, and Stefan Jakobs
ACS nano 15 (6), 9509-9521 (2021)
DOI

MINSTED fluorescence localization and nanoscopy
Weber, M., Leutenegger, M., Stoldt, S. et al.
Nature photonics 15 (5), 361-366 (2021)
DOI

Photoactivatable fluorophore for stimulated emission depletion (STED) microscopy and bioconjugation technique for hydrophobic labels
M Weber, TA Khan, LJ Patalag, M Bossi, M Leutenegger, VN Belov, SW Hell
Chemistry–A European Journal 27 (1), 451-458 (2021)

2017

Fluorescent photoswitchable diarylethenes for biolabeling and single-molecule localization microscopies with optical superresolution
B Roubinet, M Weber, H Shojaei, M Bates, ML Bossi, VN Belov, M Irie, and SW Hell
Journal of the American Chemical Society 139 (19), 6611-6620 (2017)
DOI

2016

High surface area graphene foams by chemical vapor deposition
S Drieschner, M Weber, J Wohlketzetter, J Vieten, E Makrygiannis, ...
2D Materials 3 (4), 045013 (2016)

2014

Hydrophobic actuation of a DNA origami bilayer structure
J List, M Weber, FC Simmel
Angewandte Chemie International Edition 53 (16), 4236-4239