Publications
§ = shared first; * = corresponding
Srijayee Ghosh, Sonja Schmid
The potential of fluorogenicity for single molecule FRET and DyeCycling
(2024) submitted
David Fuentenebro Navas, Jurre A. Steens, Carlos de Lannoy, Ben Noordijk, Michael Pfeffer, Dick de Ridder, Raymond H.J. Staals, and Sonja Schmid*
Nanopores Reveal the Stoichiometry of Single Oligoadenylates Produced by Type III CRISPR-Cas
ACS Nano 2024, 18 (26), 16505-16515
Taekjip Ha*, Jingyi Fei, Sonja Schmid, Nam Ki Lee, Ruben L. Gonzalez Jr, Sneha Paul, Sanghun Yeou
Fluorescence resonance energy transfer at the single-molecule level
Nature Reviews Methods Primers 4, 21 (2024)
Chenyu Wen, Sonja Schmid*, Cees Dekker*
Understanding Electrophoresis and Electroosmosis in Nanopore Sensing with the Help of the Nanopore Electro-Osmotoc Trap
ACS Nano Article ASAP (2024)
L. Silbermann§, B. Vermeer§, S. Schmid*, K. Tych*.
The known unknowns of the Hsp90 chaperone.
arxiv (2023) Submitted.
Sonja Schmid
An external speed control for nanopore reads
Nature Nanotechnology 18,1261–1262 (2023). [News & Views on Leitao et al.]
Benjamin Vermeer, Jannick van Ossenbruggen, Sonja Schmid*
Single-molecule FRET-resolved protein dynamics – from plasmid to data in 6 steps
In: Heller, I., Dulin, D., Peterman, E.J. (eds) Single Molecule Analysis . Methods in Molecular Biology, vol 2694 Single Molecule Analysis. (2023). Humana, New York, NY.
Chenyu Wen, Eva Bertosin, Xin Shi, Cees Dekker*, Sonja Schmid*
Orientation-locked DNA origami for stable trapping of small proteins in the NEOtrap
Nano Letters, 23, 3, 788–794 (2022)
Markus Götz*, Anders Barth, Søren S.-R. Bohr, Richard Börner, Jixin Chen, Thorben Cordes, Dorothy A. Erie, Christian Gebhardt, Mélodie C.A.S. Hadzic, George L. Hamilton, Nikos S. Hatzakis, Thorsten Hugel, Lydia Kisley, Don C. Lamb, Carlos de Lannoy, Chelsea Mahn, Dushani Dunukara, Dick de Ridder, Hugo Sanabria, Julia Schimpf, Claus A.M. Seidel, Roland K.O. Sigel, Magnus Berg Sletfjerding, Johannes Thomsen, Leonie Vollmar, Simon Wanninger, Keith R. Weninger, Pengning Xu, Sonja Schmid*
A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories
Nature Communications 13, 5402 (2022)
Benjamin Vermeer, Sonja Schmid*
Can DyeCycling break the photobleaching limit in single-molecule FRET?
Nano Research 15, 9818–9830 (2022).
S. Schmid, P. Stömmer, H. Dietz, C. Dekker
Nanopore electro-osmotic trap for the label-free study of single proteins and their conformations.
Nature Nanotechnology (2021). [News & Views by A. Aksimentiev] [preprint] [Nature Portfolio 'behind the paper' blogpost]
J. Alfaro§, P. Bohländer§ ,Filius§, C.J. Howard§, X. van Kooten§, S. Ohayon§, A. Pomorski§, S. Schmid§, S.H. Kim, P. Samaras, B. Kuster, G. Bedran, M. Wilhelm, L. Sepiashvili, U. Kalathiya1, S. Kumar, A. Aksimentiev, D. Stein, N. Drachman, D. Goodlett, C. Masselon, S. Hentz, M. Chinappi, C. Chan, M. Mayer, S. Lindsey, D. Rodriguez Larrea, E.M. Marcotte, G. Maglia, G. Dittmar, J. Marino, Z. Kelman, M. Wanunu, N.L. Kelleher, R. Eelkema, P. Yin, E.V. Anslyn, C. Dekker, A. Meller, C. Joo.
The emerging landscape of single-molecule protein sequencing technologies.
Nature Methods, 18, 604–617 (2021).
S. Schmid*, C. Dekker*.
Nanopores: a versatile tool to study protein dynamics.
Essays in Biochemistry, EBC20200020, (2021). [preprint]
S. Schmid* & T. Hugel*.
Controlling protein function by fine-tuning conformational flexibility
eLife , e57180 (2020).
A. Fragasso, S. Schmid & C. Dekker.
Comparing current noise in solid-state and biological nanopores.
ACS Nano 14, 1338-1349 (2020).
Björn Hellenkamp§, Sonja Schmid§, Olga Doroshenko, Oleg Opanasyuk, Ralf Kühnemuth, Soheila Rezaei Adariani, Benjamin Ambrose, Mikayel Aznauryan, Anders Barth, Victoria Birkedal, Mark E. Bowen, Hongtao Chen, Thorben Cordes, Tobias Eilert, Carel Fijen, Christian Gebhardt, Markus Götz, Giorgos Gouridis, Enrico Gratton, Taekjip Ha, Pengyu Hao, Christian A. Hanke, Andreas Hartmann, Jelle Hendrix, Lasse L. Hildebrandt, Verena Hirschfeld, Johannes Hohlbein, Boyang Hua, Christian G. Hübner, Eleni Kallis, Achillefs N. Kapanidis, Jae-Yeol Kim, Georg Krainer, Don C. Lamb, Nam Ki Lee, Edward A. Lemke, Brié Levesque, Marcia Levitus, James J. McCann, Nikolaus Naredi-Rainer, Daniel Nettels, Thuy Ngo, Ruoyi Qiu, Nicole C. Robb, Carlheinz Röcker, Hugo Sanabria, Michael Schlierf, Tim Schröder, Benjamin Schuler, Henning Seidel, Lisa Streit, Johann Thurn, Philip Tinnefeld, Swati Tyagi, Niels Vandenberk, Andrés Manuel Vera, Keith R. Weninger, Bettina Wünsch, Inna S. Yanez-Orozco, Jens Michaelis, Claus A. M. Seidel, Timothy D. Craggs & Thorsten Hugel.
Precision and accuracy of single-molecule FRET– a multi-laboratory benchmark study.
Nature Methods 15, 669–676 (2018).
S. Schmid*, M. Götz & T. Hugel*.
Effects of Inhibitors on Hsp90’s Conformational Dynamics, Cochaperone and Client Interactions.
ChemPhysChem 19, 1716–1721(2018).
S. Schmid* & T. Hugel*.
Efficient use of single molecule time traces to resolve kinetic rates, models and uncertainties.
Journal of Chemical Physics 148, 123312 (2018).
M. Götz, P. Wortmann, S. Schmid & T. Hugel.
A three-color single-molecule FRET approach to studying correlated interactions in the heat shock protein 90.
Journal of visualized experiments (JoVe) 131:e56896 (2018).
M. Götz, P. Wortmann, S. Schmid & T. Hugel.
A Multicolor Single-Molecule FRET Approach to Study Protein Dynamics and Interactions Simultaneously.
Methods in Enzymology. Ed. by Spies M, & Chemla YR. Vol. 581. Academic Press 487–516 (2016).
S. Schmid, M. Götz & T. Hugel.
Single-Molecule Analysis beyond Dwell Times: Demonstration and Assessment in and out of Equilibrium.
Biophysical Journal 111, 7:1375–1384 (2016).
S. Schmid & M. Götz. SMACKS Manual & Software.
Online: [GitHub]www.singlemolecule.uni-freiburg.de/SMACKS (2016).
S. Schmid & T. Hugel.
Regulatory posttranslational modifications in Hsp90 can be compensated by cochaperone Aha1.
Molecular Cell 41, 6:619–620 (2010).