Dr. Tim Schröder

@article{nokey,

title = {2D Titanium Carbide MXene and Single-Molecule Fluorescence: Distance-Dependent Nonradiative Energy Transfer and Leaflet-Resolved Dye Sensing in Lipid Bilayers},

author = {Lorena Manzanares and Dahnan Spurling and Alan M. Szalai and Tim Schröder and Ece Büber and Giovanni Ferrari and Martin R. J. Dagleish and Valeria Nicolosi and Philip Tinnefeld},

url = {https://doi.org/10.1002/adma.202411724},

doi = {10.1002/adma.202411724},

year  = {2024},

date = {2024-10-24},

urldate = {2024-10-24},

journal = {Advanced Materials},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Controlled mechanochemical coupling of anti-junctions in DNA origami arrays},

author = {Fiona Cole and Martina Pfeiffer and Dongfang Wang and Tim Schröder and Yonggang Ke and Philip Tinnefeld},

url = {https://www.nature.com/articles/s41467-024-51721-y#citeas},

doi = {10.1038/s41467-024-51721-y},

year  = {2024},

date = {2024-09-10},

urldate = {2024-09-10},

journal = {Nature Communications},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {DNA Origami Vesicle Sensors with Triggered Single-Molecule Cargo Transfer},

author = {Ece Büber and Renukka Yaadav and Tim Schröder and Henri G. Franquelim and Philip Tinnefeld},

url = {https://onlinelibrary.wiley.com/doi/10.1002/anie.202408295},

doi = {10.1002/anie.202408295},

year  = {2024},

date = {2024-09-09},

urldate = {2024-09-09},

journal = {Angewandte Chemie International Edition},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Ultra-specific detection of nucleic acids by intramolecular referencing},

author = {Julian Bauer and Fiona Cole and Renukka Yaadav and Jonas Zähringer and Tim Schröder and Philip Tinnefeld},

url = {https://doi.org/10.1117/12.3010119},

doi = {10.1117/12.3010119},

year  = {2024},

date = {2024-03-12},

urldate = {2024-03-12},

journal = {Single Molecule Spectroscopy and Superresolution Imaging XVII},

volume = {12849},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Super-resolved FRET and co-tracking in pMINFLUX},

author = {Fiona Cole and Jonas Zähringer and Johann Bohlen and Tim Schröder and Florian Steiner and Martina Pfeiffer and Patrick Schüler and Fernando D. Stefani and Philip Tinnefeld},

url = {https://doi.org/10.1038/s41566-024-01384-4},

doi = {10.1038/s41566-024-01384-4},

year  = {2024},

date = {2024-02-09},

urldate = {2024-02-09},

journal = {Nature Photonics},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36973549,

title = {Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins},

author = {Ganesh Agam and Christian Gebhardt and Milana Popara and Rebecca Mächtel and Julian Folz and Benjamin Ambrose and Neharika Chamachi and Sang Yoon Chung and Timothy D Craggs and Marijn de Boer and Dina Grohmann and Taekjip Ha and Andreas Hartmann and Jelle Hendrix and Verena Hirschfeld and Christian G Hübner and Thorsten Hugel and Dominik Kammerer and Hyun-Seo Kang and Achillefs N Kapanidis and Georg Krainer and Kevin Kramm and Edward A Lemke and Eitan Lerner and Emmanuel Margeat and Kirsten Martens and Jens Michaelis and Jaba Mitra and Gabriel G Moya Muñoz and Robert B Quast and Nicole C Robb and Michael Sattler and Michael Schlierf and Jonathan Schneider and Tim Schröder and Anna Sefer and Piau Siong Tan and Johann Thurn and Philip Tinnefeld and John van Noort and Shimon Weiss and Nicolas Wendler and Niels Zijlstra and Anders Barth and Claus A M Seidel and Don C Lamb and Thorben Cordes},

doi = {10.1038/s41592-023-01807-0},

issn = {1548-7105},

year  = {2023},

date = {2023-03-01},

urldate = {2023-03-01},

journal = {Nat Methods},

abstract = {Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro and in vivo. We performed an international blind study involving 19 laboratories to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems with distinct conformational changes and dynamics, we obtained an uncertainty of the FRET efficiency ≤0.06, corresponding to an interdye distance precision of ≤2 Å and accuracy of ≤5 Å. We further discuss the limits for detecting fluctuations in this distance range and how to identify dye perturbations. Our work demonstrates the ability of smFRET experiments to simultaneously measure distances and avoid the averaging of conformational dynamics for realistic protein systems, highlighting its importance in the expanding toolbox of integrative structural biology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36735241,

title = {DNA Origami Curvature Sensors for Nanoparticle and Vesicle Size Determination with Single-Molecule FRET Readout},

author = {Ece Büber and Tim Schröder and Michael Scheckenbach and Mihir Dass and Henri G Franquelim and Philip Tinnefeld},

doi = {10.1021/acsnano.2c11981},

issn = {1936-086X},

year  = {2023},

date = {2023-02-01},

urldate = {2023-02-01},

journal = {ACS Nano},

abstract = {Particle size is an important characteristic of materials with a direct effect on their physicochemical features. Besides nanoparticles, particle size and surface curvature are particularly important in the world of lipids and cellular membranes as the cell membrane undergoes conformational changes in many biological processes which leads to diverging local curvature values. On account of that, it is important to develop cost-effective, rapid and sufficiently precise systems that can measure the surface curvature on the nanoscale that can be translated to size for spherical particles. As an alternative approach for particle characterization, we present flexible DNA nanodevices that can adapt to the curvature of the structure they are bound to. The curvature sensors use Fluorescence Resonance Energy Transfer (FRET) as the transduction mechanism on the single-molecule level. The curvature sensors consist of segmented DNA origami structures connected via flexible DNA linkers incorporating a FRET pair. The activity of the sensors was first demonstrated with defined binding to different DNA origami geometries used as templates. Then the DNA origami curvature sensors were applied to measure spherical silica beads having different size, and subsequently on lipid vesicles. With the designed sensors, we could reliably distinguish different sized nanoparticles within a size range of 50-300 nm as well as the bending angle range of 50-180°. This study helps with the development of more advanced modular-curvature sensing devices that are capable of determining the sizes of nanoparticles and biological complexes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36652471,

title = {Shrinking gate fluorescence correlation spectroscopy yields equilibrium constants and separates photophysics from structural dynamics},

author = {Tim Schröder and Johann Bohlen and Sarah E Ochmann and Patrick Schüler and Stefan Krause and Don C Lamb and Philip Tinnefeld},

doi = {10.1073/pnas.2211896120},

issn = {1091-6490},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {120},

number = {4},

pages = {e2211896120},

abstract = {Fluorescence correlation spectroscopy is a versatile tool for studying fast conformational changes of biomolecules especially when combined with Förster resonance energy transfer (FRET). Despite the many methods available for identifying structural dynamics in FRET experiments, the determination of the forward and backward transition rate constants and thereby also the equilibrium constant is difficult when two intensity levels are involved. Here, we combine intensity correlation analysis with fluorescence lifetime information by including only a subset of photons in the autocorrelation analysis based on their arrival time with respect to the excitation pulse (microtime). By fitting the correlation amplitude as a function of microtime gate, the transition rate constants from two fluorescence-intensity level systems and the corresponding equilibrium constants are obtained. This shrinking-gate fluorescence correlation spectroscopy (sg-FCS) approach is demonstrated using simulations and with a DNA origami-based model system in experiments on immobilized and freely diffusing molecules. We further show that sg-FCS can distinguish photophysics from dynamic intensity changes even if a dark quencher, in this case graphene, is involved. Finally, we unravel the mechanism of a FRET-based membrane charge sensor indicating the broad potential of the method. With sg-FCS, we present an algorithm that does not require prior knowledge and is therefore easily implemented when an autocorrelation analysis is carried out on time-correlated single-photon data.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid35089694,

title = {Quantitative Single-Molecule Measurements of Membrane Charges with DNA Origami Sensors},

author = {Sarah E Ochmann and Tim Schröder and Clara M Schulz and Philip Tinnefeld},

doi = {10.1021/acs.analchem.1c05092},

issn = {1520-6882},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Anal Chem},

abstract = {Charges in lipid head groups generate electrical surface potentials at cell membranes, and changes in their composition are involved in various signaling pathways, such as T-cell activation or apoptosis. Here, we present a DNA origami-based sensor for membrane surface charges with a quantitative fluorescence read-out of single molecules. A DNA origami plate is equipped with modifications for specific membrane targeting, surface immobilization, and an anionic sensing unit consisting of single-stranded DNA and the dye ATTO542. This unit is anchored to a lipid membrane by the dye ATTO647N, and conformational changes of the sensing unit in response to surface charges are read out by fluorescence resonance energy transfer between the two dyes. We test the performance of our sensor with single-molecule fluorescence microscopy by exposing it to differently charged large unilamellar vesicles. We achieve a change in energy transfer of ∼10% points between uncharged and highly charged membranes and demonstrate a quantitative relation between the surface charge and the energy transfer. Further, with autocorrelation analyses of confocal data, we unravel the working principle of our sensor that is switching dynamically between a membrane-bound state and an unbound state on the timescale of 1-10 ms. Our study introduces a complementary sensing system for membrane surface charges to previously published genetically encoded sensors. Additionally, the single-molecule read-out enables investigations of lipid membranes on the nanoscale with a high spatial resolution circumventing ensemble averaging.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid34735135,

title = {How Blinking Affects Photon Correlations in Multichromophoric Nanoparticles},

author = {Tim Schröder and Sebastian Bange and Jakob Schedlbauer and Florian Steiner and John M Lupton and Philip Tinnefeld and Jan Vogelsang},

doi = {10.1021/acsnano.1c06649},

issn = {1936-086X},

year  = {2021},

date = {2021-11-01},

urldate = {2021-11-01},

journal = {ACS Nano},

abstract = {A single chromophore can only emit a maximum of one single photon per excitation cycle. This limitation results in a phenomenon commonly referred to as photon antibunching (pAB). When multiple chromophores contribute to the fluorescence measured, the degree of pAB has been used as a metric to "count" the number of chromophores. But the fact that chromophores can switch randomly between bright and dark states also impacts pAB and can lead to incorrect chromophore numbers being determined from pAB measurements. By both simulations and experiment, we demonstrate how pAB is affected by independent and collective chromophore blinking, enabling us to formulate universal guidelines for correct interpretation of pAB measurements. We use DNA-origami nanostructures to design multichromophoric model systems that exhibit either independent or collective chromophore blinking. Two approaches are presented that can distinguish experimentally between these two blinking mechanisms. The first one utilizes the different excitation intensity dependence on the blinking mechanisms. The second approach exploits the fact that collective blinking implies energy transfer to a quenching moiety, which is a time-dependent process. In pulsed-excitation experiments, the degree of collective blinking can therefore be altered by time gating the fluorescence photon stream, enabling us to extract the energy-transfer rate to a quencher. The ability to distinguish between different blinking mechanisms is valuable in materials science, such as for multichromophoric nanoparticles like conjugated-polymer chains as well as in biophysics, for example, for quantitative analysis of protein assemblies by counting chromophores.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kaminska2021,

title = {Graphene Energy Transfer for Single-Molecule Biophysics, Biosensing, and Super-Resolution Microscopy},

author = {Izabela Kamińska and Johann Bohlen and Renukka Yaadav and Patrick Schüler and Mario Raab and Tim Schröder and Jonas Zähringer and Karolina Zielonka and Stefan Krause and Philip Tinnefeld},

doi = {10.1002/adma.202101099},

year  = {2021},

date = {2021-05-01},

urldate = {2021-05-01},

journal = {Advanced Materials},

volume = {33},

number = {24},

pages = {2101099},

publisher = {Wiley},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hedley2021,

title = {Picosecond time-resolved photon antibunching measures nanoscale exciton motion and the true number of chromophores},

author = {Gordon J. Hedley and Tim Schröder and Florian Steiner and Theresa Eder and Felix J. Hofmann and Sebastian Bange and Dirk Laux and Sigurd Höger and Philip Tinnefeld and John M. Lupton and Jan Vogelsang},

url = {https://www.cup.uni-muenchen.de/de/aktuelles/archiv/2021/energieuebertragung-in-organischen-leuchtdioden-oled/

https://www.e-conversion.de/the-secret-of-the-missing-excitons/},

doi = {10.1038/s41467-021-21474-z},

year  = {2021},

date = {2021-02-01},

urldate = {2021-02-01},

journal = {Nature Communications},

volume = {12},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kramm2020,

title = {DNA origami-based single-molecule force spectroscopy elucidates RNA Polymerase III pre-initiation complex stability},

author = {Kevin Kramm and Tim Schröder and Jerome Gouge and Andrés Manuel Vera and Kapil Gupta and Florian B. Heiss and Tim Liedl and Christoph Engel and Imre Berger and Alessandro Vannini and Philip Tinnefeld and Dina Grohmann},

doi = {10.1038/s41467-020-16702-x},

year  = {2020},

date = {2020-06-01},

journal = {Nature Communications},

volume = {11},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Schroeder2019,

title = {Interchromophoric Interactions Determine the Maximum Brightness Density in DNA Origami Structures},

author = {Tim Schröder and Max B. Scheible and Florian Steiner and Jan Vogelsang and Philip Tinnefeld},

doi = {10.1021/acs.nanolett.8b04845},

year  = {2019},

date = {2019-01-01},

journal = {Nano Letters},

volume = {19},

number = {2},

pages = {1275--1281},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hellenkamp2018,

title = {Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study},

author = {Björn Hellenkamp and Sonja Schmid and Olga Doroshenko and Oleg Opanasyuk and Ralf Kühnemuth and Soheila Rezaei Adariani and Benjamin Ambrose and Mikayel Aznauryan and Anders Barth and Victoria Birkedal and Mark E. Bowen and Hongtao Chen and Thorben Cordes and Tobias Eilert and Carel Fijen and Christian Gebhardt and Markus Götz and Giorgos Gouridis and Enrico Gratton and Taekjip Ha and Pengyu Hao and Christian A. Hanke and Andreas Hartmann and Jelle Hendrix and Lasse L. Hildebrandt and Verena Hirschfeld and Johannes Hohlbein and Boyang Hua and Christian G. Hübner and Eleni Kallis and Achillefs N. Kapanidis and Jae-Yeol Kim and Georg Krainer and Don C. Lamb and Nam Ki Lee and Edward A. Lemke and Brié Levesque and Marcia Levitus and James J. McCann and Nikolaus Naredi-Rainer and Daniel Nettels and Thuy Ngo and Ruoyi Qiu and Nicole C. Robb and Carlheinz Röcker and Hugo Sanabria and Michael Schlierf and Tim Schröder and Benjamin Schuler and Henning Seidel and Lisa Streit and Johann Thurn and Philip Tinnefeld and Swati Tyagi and Niels Vandenberk and Andrés Manuel Vera and Keith R. Weninger and Bettina Wünsch and Inna S. Yanez-Orozco and Jens Michaelis and Claus A. M. Seidel and Timothy D. Craggs and Thorsten Hugel},

doi = {10.1038/s41592-018-0085-0},

year  = {2018},

date = {2018-08-01},

journal = {Nature Methods},

volume = {15},

number = {9},

pages = {669--676},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wang2017,

title = {A DNA Walker as a Fluorescence Signal Amplifier},

author = {Dongfang Wang and Carolin Vietz and Tim Schröder and Guillermo Acuna and Birka Lalkens and Philip Tinnefeld},

doi = {10.1021/acs.nanolett.7b01829},

year  = {2017},

date = {2017-08-01},

journal = {Nano Letters},

volume = {17},

number = {9},

pages = {5368--5374},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}