Group theses
2024
Lennart Grabenhorst; Flurin Sturzenegger; Moa Hasler; Benjamin Schuler; Philip Tinnefeld
Single-Molecule FRET at 10 MHz Count Rates Journal Article
In: J Am Chem Soc, 2024, ISSN: 1520-5126.
@article{pmid38266173,
title = {Single-Molecule FRET at 10 MHz Count Rates},
author = {Lennart Grabenhorst and Flurin Sturzenegger and Moa Hasler and Benjamin Schuler and Philip Tinnefeld},
doi = {10.1021/jacs.3c13757},
issn = {1520-5126},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {J Am Chem Soc},
abstract = {A bottleneck in many studies utilizing single-molecule Förster resonance energy transfer is the attainable photon count rate, as it determines the temporal resolution of the experiment. As many biologically relevant processes occur on time scales that are hardly accessible with currently achievable photon count rates, there has been considerable effort to find strategies to increase the stability and brightness of fluorescent dyes. Here, we use DNA nanoantennas to drastically increase the achievable photon count rates and observe fast biomolecular dynamics in the small volume between two plasmonic nanoparticles. As a proof of concept, we observe the coupled folding and binding of two intrinsically disordered proteins, which form transient encounter complexes with lifetimes on the order of 100 μs. To test the limits of our approach, we also investigated the hybridization of a short single-stranded DNA to its complementary counterpart, revealing a transition path time of 17 μs at photon count rates of around 10 MHz, which is an order-of-magnitude improvement compared to the state of the art. Concomitantly, the photostability was increased, enabling many seconds long megahertz fluorescence time traces. Due to the modular nature of the DNA origami method, this platform can be adapted to a broad range of biomolecules, providing a promising approach to study previously unobservable ultrafast biophysical processes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
A bottleneck in many studies utilizing single-molecule Förster resonance energy transfer is the attainable photon count rate, as it determines the temporal resolution of the experiment. As many biologically relevant processes occur on time scales that are hardly accessible with currently achievable photon count rates, there has been considerable effort to find strategies to increase the stability and brightness of fluorescent dyes. Here, we use DNA nanoantennas to drastically increase the achievable photon count rates and observe fast biomolecular dynamics in the small volume between two plasmonic nanoparticles. As a proof of concept, we observe the coupled folding and binding of two intrinsically disordered proteins, which form transient encounter complexes with lifetimes on the order of 100 μs. To test the limits of our approach, we also investigated the hybridization of a short single-stranded DNA to its complementary counterpart, revealing a transition path time of 17 μs at photon count rates of around 10 MHz, which is an order-of-magnitude improvement compared to the state of the art. Concomitantly, the photostability was increased, enabling many seconds long megahertz fluorescence time traces. Due to the modular nature of the DNA origami method, this platform can be adapted to a broad range of biomolecules, providing a promising approach to study previously unobservable ultrafast biophysical processes.
2023
Julian Bauer; Andreas Reichl; Philip Tinnefeld
In: ACS Nano, 2023.
@article{nokey,
title = {Kinetic Referencing Allows Identification of Epigenetic Cytosine Modifications by Single-Molecule Hybridization Kinetics and Superresolution DNA-PAINT Microscopy},
author = {Julian Bauer and Andreas Reichl and Philip Tinnefeld},
doi = {10.1021/acsnano.3c08451},
year = {2023},
date = {2023-12-29},
urldate = {2023-12-29},
journal = {ACS Nano},
abstract = {We develop a DNA origami-based internal kinetic referencing system with a colocalized reference and target molecule to provide increased sensitivity and robustness for transient binding kinetics. To showcase this, we investigate the subtle changes in binding strength of DNA oligonucleotide hybrids induced by cytosine modifications. These cytosine modifications, especially 5-methylcytosine but also its oxidized derivatives, have been increasingly studied in the context of epigenetics. Recently revealed correlations of epigenetic modifications and disease also render them interesting biomarkers for early diagnosis. Internal kinetic referencing allows us to probe and compare the influence of the different epigenetic cytosine modifications on the strengths of 7-nucleotide long DNA hybrids with one or two modified nucleotides by single-molecule imaging of their transient binding, revealing subtle differences in binding times. Interestingly, the influence of epigenetic modifications depends on their position in the DNA strand, and in the case of two modifications, effects are additive. The sensitivity of the assay indicates its potential for the direct detection of epigenetic disease markers.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We develop a DNA origami-based internal kinetic referencing system with a colocalized reference and target molecule to provide increased sensitivity and robustness for transient binding kinetics. To showcase this, we investigate the subtle changes in binding strength of DNA oligonucleotide hybrids induced by cytosine modifications. These cytosine modifications, especially 5-methylcytosine but also its oxidized derivatives, have been increasingly studied in the context of epigenetics. Recently revealed correlations of epigenetic modifications and disease also render them interesting biomarkers for early diagnosis. Internal kinetic referencing allows us to probe and compare the influence of the different epigenetic cytosine modifications on the strengths of 7-nucleotide long DNA hybrids with one or two modified nucleotides by single-molecule imaging of their transient binding, revealing subtle differences in binding times. Interestingly, the influence of epigenetic modifications depends on their position in the DNA strand, and in the case of two modifications, effects are additive. The sensitivity of the assay indicates its potential for the direct detection of epigenetic disease markers.
Lars Richter; Alan M Szalai; C Lorena Manzanares-Palenzuela; Izabela Kamińska; Philip Tinnefeld
Exploring the Synergies of Single-Molecule Fluorescence and 2D Materials Coupled by DNA Journal Article
In: Adv Mater, pp. e2303152, 2023, ISSN: 1521-4095.
@article{pmid37670535,
title = {Exploring the Synergies of Single-Molecule Fluorescence and 2D Materials Coupled by DNA},
author = {Lars Richter and Alan M Szalai and C Lorena Manzanares-Palenzuela and Izabela Kamińska and Philip Tinnefeld},
doi = {10.1002/adma.202303152},
issn = {1521-4095},
year = {2023},
date = {2023-09-01},
urldate = {2023-09-01},
journal = {Adv Mater},
pages = {e2303152},
abstract = {The world of 2D materials is steadily growing, with numerous researchers attempting to discover, elucidate, and exploit their properties. Approaches relying on the detection of single fluorescent molecules offer a set of advantages, for instance, high sensitivity and specificity, that allow the drawing of conclusions with unprecedented precision. Herein, it is argued how the study of 2D materials benefits from fluorescence-based single-molecule modalities, and vice versa. A special focus is placed on DNA, serving as a versatile adaptor when anchoring single dye molecules to 2D materials. The existing literature on the fruitful combination of the two fields is reviewed, and an outlook on the additional synergies that can be created between them provided.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The world of 2D materials is steadily growing, with numerous researchers attempting to discover, elucidate, and exploit their properties. Approaches relying on the detection of single fluorescent molecules offer a set of advantages, for instance, high sensitivity and specificity, that allow the drawing of conclusions with unprecedented precision. Herein, it is argued how the study of 2D materials benefits from fluorescence-based single-molecule modalities, and vice versa. A special focus is placed on DNA, serving as a versatile adaptor when anchoring single dye molecules to 2D materials. The existing literature on the fruitful combination of the two fields is reviewed, and an outlook on the additional synergies that can be created between them provided.
Lea M. Wassermann; Michael Scheckenbach; Anna V. Baptist; Viktorija Glembockyte; Amelie Heuer-Jungemann
Full Site-Specific Addressability in DNA Origami-Templated Silica Nanostructures Journal Article
In: Advanced Materials, 2023.
@article{nokey,
title = {Full Site-Specific Addressability in DNA Origami-Templated Silica Nanostructures},
author = {Lea M. Wassermann and Michael Scheckenbach and Anna V. Baptist and Viktorija Glembockyte and Amelie Heuer-Jungemann},
url = {https://onlinelibrary.wiley.com/doi/10.1002/adma.202212024},
doi = {10.1002/adma.202212024},
year = {2023},
date = {2023-04-25},
urldate = {2023-04-25},
journal = {Advanced Materials},
abstract = {DNA nanotechnology allows for the fabrication of nanometer-sized objects with high precision and selective addressability as a result of the programmable hybridization of complementary DNA strands. Such structures can template the formation of other materials, including metals and complex silica nanostructures, where the silica shell simultaneously acts to protect the DNA from external detrimental factors. However, the formation of silica nanostructures with site-specific addressability has thus far not been explored. Here, it is shown that silica nanostructures templated by DNA origami remain addressable for post silicification modification with guest molecules even if the silica shell measures several nm in thickness. The conjugation of fluorescently labeled oligonucleotides is used to different silicified DNA origami structures carrying a complementary ssDNA handle as well as DNA-PAINT super-resolution imaging to show that ssDNA handles remain unsilicified and thus ensure retained addressability. It is also demonstrated that not only handles, but also ssDNA scaffold segments within a DNA origami nanostructure remain accessible, allowing for the formation of dynamic silica nanostructures. Finally, the power of this approach is demonstrated by forming 3D DNA origami crystals from silicified monomers. These results thus present a fully site-specifically addressable silica nanostructure with complete control over size and shape.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
DNA nanotechnology allows for the fabrication of nanometer-sized objects with high precision and selective addressability as a result of the programmable hybridization of complementary DNA strands. Such structures can template the formation of other materials, including metals and complex silica nanostructures, where the silica shell simultaneously acts to protect the DNA from external detrimental factors. However, the formation of silica nanostructures with site-specific addressability has thus far not been explored. Here, it is shown that silica nanostructures templated by DNA origami remain addressable for post silicification modification with guest molecules even if the silica shell measures several nm in thickness. The conjugation of fluorescently labeled oligonucleotides is used to different silicified DNA origami structures carrying a complementary ssDNA handle as well as DNA-PAINT super-resolution imaging to show that ssDNA handles remain unsilicified and thus ensure retained addressability. It is also demonstrated that not only handles, but also ssDNA scaffold segments within a DNA origami nanostructure remain accessible, allowing for the formation of dynamic silica nanostructures. Finally, the power of this approach is demonstrated by forming 3D DNA origami crystals from silicified monomers. These results thus present a fully site-specifically addressable silica nanostructure with complete control over size and shape.
Ganesh Agam; Christian Gebhardt; Milana Popara; Rebecca Mächtel; Julian Folz; Benjamin Ambrose; Neharika Chamachi; Sang Yoon Chung; Timothy D Craggs; Marijn de Boer; Dina Grohmann; Taekjip Ha; Andreas Hartmann; Jelle Hendrix; Verena Hirschfeld; Christian G Hübner; Thorsten Hugel; Dominik Kammerer; Hyun-Seo Kang; Achillefs N Kapanidis; Georg Krainer; Kevin Kramm; Edward A Lemke; Eitan Lerner; Emmanuel Margeat; Kirsten Martens; Jens Michaelis; Jaba Mitra; Gabriel G Moya Muñoz; Robert B Quast; Nicole C Robb; Michael Sattler; Michael Schlierf; Jonathan Schneider; Tim Schröder; Anna Sefer; Piau Siong Tan; Johann Thurn; Philip Tinnefeld; John van Noort; Shimon Weiss; Nicolas Wendler; Niels Zijlstra; Anders Barth; Claus A M Seidel; Don C Lamb; Thorben Cordes
Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins Journal Article
In: Nat Methods, 2023, ISSN: 1548-7105.
@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}
}
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.
Jonas Zähringer; Fiona Cole; Johann Bohlen; Florian Steiner; Izabela Kamińska; Philip Tinnefeld
Combining pMINFLUX, graphene energy transfer and DNA-PAINT for nanometer precise 3D super-resolution microscopy Journal Article
In: Light Sci Appl, vol. 12, no. 1, pp. 70, 2023, ISSN: 2047-7538.
@article{pmid36898993,
title = {Combining pMINFLUX, graphene energy transfer and DNA-PAINT for nanometer precise 3D super-resolution microscopy},
author = {Jonas Zähringer and Fiona Cole and Johann Bohlen and Florian Steiner and Izabela Kamińska and Philip Tinnefeld},
doi = {10.1038/s41377-023-01111-8},
issn = {2047-7538},
year = {2023},
date = {2023-03-01},
urldate = {2023-03-01},
journal = {Light Sci Appl},
volume = {12},
number = {1},
pages = {70},
abstract = {3D super-resolution microscopy with nanometric resolution is a key to fully complement ultrastructural techniques with fluorescence imaging. Here, we achieve 3D super-resolution by combining the 2D localization of pMINFLUX with the axial information of graphene energy transfer (GET) and the single-molecule switching by DNA-PAINT. We demonstrate <2 nm localization precision in all 3 dimension with axial precision reaching below 0.3 nm. In 3D DNA-PAINT measurements, structural features, i.e., individual docking strands at distances of 3 nm, are directly resolved on DNA origami structures. pMINFLUX and GET represent a particular synergetic combination for super-resolution imaging near the surface such as for cell adhesion and membrane complexes as the information of each photon is used for both 2D and axial localization information. Furthermore, we introduce local PAINT (L-PAINT), in which DNA-PAINT imager strands are equipped with an additional binding sequence for local upconcentration improving signal-to-background ratio and imaging speed of local clusters. L-PAINT is demonstrated by imaging a triangular structure with 6 nm side lengths within seconds.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
3D super-resolution microscopy with nanometric resolution is a key to fully complement ultrastructural techniques with fluorescence imaging. Here, we achieve 3D super-resolution by combining the 2D localization of pMINFLUX with the axial information of graphene energy transfer (GET) and the single-molecule switching by DNA-PAINT. We demonstrate <2 nm localization precision in all 3 dimension with axial precision reaching below 0.3 nm. In 3D DNA-PAINT measurements, structural features, i.e., individual docking strands at distances of 3 nm, are directly resolved on DNA origami structures. pMINFLUX and GET represent a particular synergetic combination for super-resolution imaging near the surface such as for cell adhesion and membrane complexes as the information of each photon is used for both 2D and axial localization information. Furthermore, we introduce local PAINT (L-PAINT), in which DNA-PAINT imager strands are equipped with an additional binding sequence for local upconcentration improving signal-to-background ratio and imaging speed of local clusters. L-PAINT is demonstrated by imaging a triangular structure with 6 nm side lengths within seconds.
Ece Büber; Tim Schröder; Michael Scheckenbach; Mihir Dass; Henri G Franquelim; Philip Tinnefeld
DNA Origami Curvature Sensors for Nanoparticle and Vesicle Size Determination with Single-Molecule FRET Readout Journal Article
In: ACS Nano, 2023, ISSN: 1936-086X.
@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}
}
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.
Tim Schröder; Johann Bohlen; Sarah E Ochmann; Patrick Schüler; Stefan Krause; Don C Lamb; Philip Tinnefeld
Shrinking gate fluorescence correlation spectroscopy yields equilibrium constants and separates photophysics from structural dynamics Journal Article
In: Proc Natl Acad Sci U S A, vol. 120, no. 4, pp. e2211896120, 2023, ISSN: 1091-6490.
@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}
}
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.
Kateryna Trofymchuk; Karol Kołątaj; Viktorija Glembockyte; Fangjia Zhu; Guillermo P Acuna; Tim Liedl; Philip Tinnefeld
Gold Nanorod DNA Origami Antennas for 3 Orders of Magnitude Fluorescence Enhancement in NIR Journal Article
In: ACS Nano, 2023, ISSN: 1936-086X.
@article{pmid36594816,
title = {Gold Nanorod DNA Origami Antennas for 3 Orders of Magnitude Fluorescence Enhancement in NIR},
author = {Kateryna Trofymchuk and Karol Kołątaj and Viktorija Glembockyte and Fangjia Zhu and Guillermo P Acuna and Tim Liedl and Philip Tinnefeld},
doi = {10.1021/acsnano.2c09577},
issn = {1936-086X},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {ACS Nano},
abstract = {DNA origami has taken a leading position in organizing materials at the nanoscale for various applications such as manipulation of light by exploiting plasmonic nanoparticles. We here present the arrangement of gold nanorods in a plasmonic nanoantenna dimer enabling up to 1600-fold fluorescence enhancement of a conventional near-infrared (NIR) dye positioned at the plasmonic hotspot between the nanorods. Transmission electron microscopy, dark-field spectroscopy, and fluorescence analysis together with numerical simulations give us insights on the heterogeneity of the observed enhancement values. The size of our hotspot region is ∼12 nm, granted by using the recently introduced design of NAnoantenna with Cleared HotSpot (NACHOS), which provides enough space for placing of tailored bioassays. Additionally, the possibility to synthesize nanoantennas in solution might allow for production upscaling.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
DNA origami has taken a leading position in organizing materials at the nanoscale for various applications such as manipulation of light by exploiting plasmonic nanoparticles. We here present the arrangement of gold nanorods in a plasmonic nanoantenna dimer enabling up to 1600-fold fluorescence enhancement of a conventional near-infrared (NIR) dye positioned at the plasmonic hotspot between the nanorods. Transmission electron microscopy, dark-field spectroscopy, and fluorescence analysis together with numerical simulations give us insights on the heterogeneity of the observed enhancement values. The size of our hotspot region is ∼12 nm, granted by using the recently introduced design of NAnoantenna with Cleared HotSpot (NACHOS), which provides enough space for placing of tailored bioassays. Additionally, the possibility to synthesize nanoantennas in solution might allow for production upscaling.
2022
Kevin N. Baumann, Tim Schröder , Prashanth S. Ciryam, Diana Morzy, Philip Tinnefeld, Tuomas P. J. Knowles, Silvia Hernández-Ainsa
DNA–Liposome Hybrid Carriers for Triggered Cargo Release Journal Article
In: ACS Applied Bio Materials, vol. 5, iss. 8, 2022.
@article{nokey,
title = {DNA–Liposome Hybrid Carriers for Triggered Cargo Release},
author = {Kevin N. Baumann, Tim Schröder
, Prashanth S. Ciryam, Diana Morzy, Philip Tinnefeld,
Tuomas P. J. Knowles, Silvia Hernández-Ainsa},
doi = {doi: 10.1021/acsabm.2c00225},
year = {2022},
date = {2022-07-15},
urldate = {2022-07-15},
journal = {ACS Applied Bio Materials},
volume = {5},
issue = {8},
publisher = {American Chemical Society},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cindy Close; Kateryna Trofymchuk; Lennart Grabenhorst; Birka Lalkens; Viktorija Glembockyte; Philip Tinnefeld
Maximizing the Accessibility in DNA Origami Nanoantenna Plasmonic Hotspots Journal Article
In: Advanced Materials Interfaces, vol. 9, iss. 24, pp. 2200255, 2022.
@article{Close2022,
title = {Maximizing the Accessibility in DNA Origami Nanoantenna Plasmonic Hotspots},
author = {Cindy Close and Kateryna Trofymchuk and Lennart Grabenhorst and Birka Lalkens and Viktorija Glembockyte and Philip Tinnefeld},
url = {https://doi.org/10.1002/admi.202200255},
doi = {10.1002/admi.202200255},
year = {2022},
date = {2022-07-01},
urldate = {2022-07-01},
journal = {Advanced Materials Interfaces},
volume = {9},
issue = {24},
pages = {2200255},
publisher = {Wiley},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kristina Hübner; Mario Raab; Johann Bohlen; Julian Bauer; Philip Tinnefeld
Salt-Induced Conformational Switching of a Flat Rectangular DNA Origami Structure Journal Article
In: Nanoscale, vol. 14, pp. 7898 - 7905, 2022.
@article{nokey,
title = {Salt-Induced Conformational Switching of a Flat Rectangular DNA Origami Structure},
author = {Kristina Hübner and Mario Raab and Johann Bohlen and Julian Bauer and Philip Tinnefeld },
url = {https://doi.org/10.1039/D1NR07793G},
doi = {10.1039/D1NR07793G},
year = {2022},
date = {2022-05-11},
urldate = {2022-05-11},
journal = {Nanoscale},
volume = {14},
pages = { 7898 - 7905},
abstract = {A rectangular DNA origami structure is one of the most studied and often used motif for
applications in DNA nanotechnology. Here, we present two assays to study structural
changes in DNA nanostructures and reveal a reversible rolling-up of the rectangular DNA
origami structure induced by bivalent cations such as magnesium or calcium. First, we
applied one-color and two-color superresolution DNA-PAINT with protruding strands
along the long edges of the DNA origami rectangle. At increasing salt concentration, a
single line instead of two lines is observed as a first indicator of rolling-up. Two-color
measurements also revealed different conformations with parallel and angled edges.
Second, we placed a gold nanoparticle and a dye molecule at different positions on the
DNA origami structure. Distance dependent fluorescence quenching by the nanoparticle
reports on dynamic transitions as well as it provides evidence that the rolling-up occurs
preferentially along the diagonal of the DNA origami rectangle. The results will be helpful
to test DNA structural models and the assays presented will be useful to study further
structural transitions in DNA nanotechnology. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
A rectangular DNA origami structure is one of the most studied and often used motif for
applications in DNA nanotechnology. Here, we present two assays to study structural
changes in DNA nanostructures and reveal a reversible rolling-up of the rectangular DNA
origami structure induced by bivalent cations such as magnesium or calcium. First, we
applied one-color and two-color superresolution DNA-PAINT with protruding strands
along the long edges of the DNA origami rectangle. At increasing salt concentration, a
single line instead of two lines is observed as a first indicator of rolling-up. Two-color
measurements also revealed different conformations with parallel and angled edges.
Second, we placed a gold nanoparticle and a dye molecule at different positions on the
DNA origami structure. Distance dependent fluorescence quenching by the nanoparticle
reports on dynamic transitions as well as it provides evidence that the rolling-up occurs
preferentially along the diagonal of the DNA origami rectangle. The results will be helpful
to test DNA structural models and the assays presented will be useful to study further
structural transitions in DNA nanotechnology.
applications in DNA nanotechnology. Here, we present two assays to study structural
changes in DNA nanostructures and reveal a reversible rolling-up of the rectangular DNA
origami structure induced by bivalent cations such as magnesium or calcium. First, we
applied one-color and two-color superresolution DNA-PAINT with protruding strands
along the long edges of the DNA origami rectangle. At increasing salt concentration, a
single line instead of two lines is observed as a first indicator of rolling-up. Two-color
measurements also revealed different conformations with parallel and angled edges.
Second, we placed a gold nanoparticle and a dye molecule at different positions on the
DNA origami structure. Distance dependent fluorescence quenching by the nanoparticle
reports on dynamic transitions as well as it provides evidence that the rolling-up occurs
preferentially along the diagonal of the DNA origami rectangle. The results will be helpful
to test DNA structural models and the assays presented will be useful to study further
structural transitions in DNA nanotechnology.
Sarah E Ochmann; Tim Schröder; Clara M Schulz; Philip Tinnefeld
Quantitative Single-Molecule Measurements of Membrane Charges with DNA Origami Sensors Journal Article
In: Anal Chem, 2022, ISSN: 1520-6882.
@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}
}
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.
2021
Merve-Zeynep Kesici; Philip Tinnefeld; Andrés Manuel Vera
A simple and general approach to generate photoactivatable DNA processing enzymes Journal Article
In: Nucleic Acids Res, 2021, ISSN: 1362-4962.
@article{pmid34904657,
title = {A simple and general approach to generate photoactivatable DNA processing enzymes},
author = {Merve-Zeynep Kesici and Philip Tinnefeld and Andrés Manuel Vera},
doi = {10.1093/nar/gkab1212},
issn = {1362-4962},
year = {2021},
date = {2021-12-01},
urldate = {2021-12-01},
journal = {Nucleic Acids Res},
abstract = {DNA processing enzymes, such as DNA polymerases and endonucleases, have found many applications in biotechnology, molecular diagnostics, and synthetic biology, among others. The development of enzymes with controllable activity, such as hot-start or light-activatable versions, has boosted their applications and improved the sensitivity and specificity of the existing ones. However, current approaches to produce controllable enzymes are experimentally demanding to develop and case-specific. Here, we introduce a simple and general method to design light-start DNA processing enzymes. In order to prove its versatility, we applied our method to three DNA polymerases commonly used in biotechnology, including the Phi29 (mesophilic), Taq, and Pfu polymerases, and one restriction enzyme. Light-start enzymes showed suppressed polymerase, exonuclease, and endonuclease activity until they were re-activated by an UV pulse. Finally, we applied our enzymes to common molecular biology assays and showed comparable performance to commercial hot-start enzymes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
DNA processing enzymes, such as DNA polymerases and endonucleases, have found many applications in biotechnology, molecular diagnostics, and synthetic biology, among others. The development of enzymes with controllable activity, such as hot-start or light-activatable versions, has boosted their applications and improved the sensitivity and specificity of the existing ones. However, current approaches to produce controllable enzymes are experimentally demanding to develop and case-specific. Here, we introduce a simple and general method to design light-start DNA processing enzymes. In order to prove its versatility, we applied our method to three DNA polymerases commonly used in biotechnology, including the Phi29 (mesophilic), Taq, and Pfu polymerases, and one restriction enzyme. Light-start enzymes showed suppressed polymerase, exonuclease, and endonuclease activity until they were re-activated by an UV pulse. Finally, we applied our enzymes to common molecular biology assays and showed comparable performance to commercial hot-start enzymes.
Tim Schröder; Sebastian Bange; Jakob Schedlbauer; Florian Steiner; John M Lupton; Philip Tinnefeld; Jan Vogelsang
How Blinking Affects Photon Correlations in Multichromophoric Nanoparticles Journal Article
In: ACS Nano, 2021, ISSN: 1936-086X.
@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}
}
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.
Sarah E. Ochmann; Himanshu Joshi; Ece Büber; Henri G. Franquelim; Pierre Stegemann; Barbara Saccà; Ulrich F. Keyser; Aleksei Aksimentiev; Philip Tinnefeld
DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity Journal Article
In: Nano Letters, vol. 21, no. 20, pp. 8634–8641, 2021.
@article{Ochmann2021,
title = {DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity},
author = {Sarah E. Ochmann and Himanshu Joshi and Ece Büber and Henri G. Franquelim and Pierre Stegemann and Barbara Saccà and Ulrich F. Keyser and Aleksei Aksimentiev and Philip Tinnefeld},
doi = {10.1021/acs.nanolett.1c02584},
year = {2021},
date = {2021-10-01},
urldate = {2021-10-01},
journal = {Nano Letters},
volume = {21},
number = {20},
pages = {8634--8641},
publisher = {American Chemical Society (ACS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Martina Pfeiffer; Kateryna Trofymchuk; Simona Ranallo; Francesco Ricci; Florian Steiner; Fiona Cole; Viktorija Glembockyte; Philip Tinnefeld
Single antibody detection in a DNA origami nanoantenna Journal Article
In: iScience, vol. 24, no. 9, pp. 103072, 2021.
@article{Pfeiffer2021,
title = {Single antibody detection in a DNA origami nanoantenna},
author = {Martina Pfeiffer and Kateryna Trofymchuk and Simona Ranallo and Francesco Ricci and Florian Steiner and Fiona Cole and Viktorija Glembockyte and Philip Tinnefeld},
doi = {10.1016/j.isci.2021.103072},
year = {2021},
date = {2021-09-01},
urldate = {2021-09-01},
journal = {iScience},
volume = {24},
number = {9},
pages = {103072},
publisher = {Elsevier BV},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Viktorija Glembockyte; Lennart Grabenhorst; Kateryna Trofymchuk; Philip Tinnefeld
DNA Origami Nanoantennas for Fluorescence Enhancement Journal Article
In: Acc Chem Res, vol. 54, no. 17, pp. 3338–3348, 2021.
@article{Glembockyte2021,
title = {DNA Origami Nanoantennas for Fluorescence Enhancement},
author = {Viktorija Glembockyte and Lennart Grabenhorst and Kateryna Trofymchuk and Philip Tinnefeld},
doi = {10.1021/acs.accounts.1c00307},
year = {2021},
date = {2021-08-01},
urldate = {2021-08-01},
journal = {Acc Chem Res},
volume = {54},
number = {17},
pages = {3338--3348},
publisher = {American Chemical Society (ACS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Andrés Manuel Vera; Albert Galera-Prat; Michał Wojciechowski; Bartosz Różycki; Douglas V. Laurents; Mariano Carrión-Vázquez; Marek Cieplak; Philip Tinnefeld
Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization Journal Article
In: Structure, vol. 29, no. 6, pp. 587–597.e8, 2021.
@article{Vera2021,
title = {Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization},
author = {Andrés Manuel Vera and Albert Galera-Prat and Michał Wojciechowski and Bartosz Różycki and Douglas V. Laurents and Mariano Carrión-Vázquez and Marek Cieplak and Philip Tinnefeld},
doi = {10.1016/j.str.2021.01.006},
year = {2021},
date = {2021-06-01},
urldate = {2021-06-01},
journal = {Structure},
volume = {29},
number = {6},
pages = {587--597.e8},
publisher = {Elsevier BV},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Izabela Kamińska; Johann Bohlen; Renukka Yaadav; Patrick Schüler; Mario Raab; Tim Schröder; Jonas Zähringer; Karolina Zielonka; Stefan Krause; Philip Tinnefeld
Graphene Energy Transfer for Single-Molecule Biophysics, Biosensing, and Super-Resolution Microscopy Journal Article
In: Advanced Materials, vol. 33, no. 24, pp. 2101099, 2021.
@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}
}
Stefan Krause; Evelyn Ploetz; Johann Bohlen; Patrick Schüler; Renukka Yaadav; Florian Selbach; Florian Steiner; Izabela Kamińska; Philip Tinnefeld
Graphene-on-Glass Preparation and Cleaning Methods Characterized by Single-Molecule DNA Origami Fluorescent Probes and Raman Spectroscopy Journal Article
In: ACS Nano, vol. 15, no. 4, pp. 6430–6438, 2021.
@article{Krause2021,
title = {Graphene-on-Glass Preparation and Cleaning Methods Characterized by Single-Molecule DNA Origami Fluorescent Probes and Raman Spectroscopy},
author = {Stefan Krause and Evelyn Ploetz and Johann Bohlen and Patrick Schüler and Renukka Yaadav and Florian Selbach and Florian Steiner and Izabela Kamińska and Philip Tinnefeld},
doi = {10.1021/acsnano.0c08383},
year = {2021},
date = {2021-04-01},
urldate = {2021-04-01},
journal = {ACS Nano},
volume = {15},
number = {4},
pages = {6430--6438},
publisher = {American Chemical Society (ACS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kristina Hübner; Himanshu Joshi; Aleksei Aksimentiev; Fernando D. Stefani; Philip Tinnefeld; Guillermo P. Acuna
Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures Journal Article
In: ACS Nano, vol. 15, no. 3, pp. 5109–5117, 2021.
@article{Huebner2021,
title = {Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures},
author = {Kristina Hübner and Himanshu Joshi and Aleksei Aksimentiev and Fernando D. Stefani and Philip Tinnefeld and Guillermo P. Acuna},
doi = {10.1021/acsnano.0c10259},
year = {2021},
date = {2021-03-01},
urldate = {2021-03-01},
journal = {ACS Nano},
volume = {15},
number = {3},
pages = {5109--5117},
publisher = {American Chemical Society (ACS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Alan M. Szalai; Bruno Siarry; Jerónimo Lukin; Sebastián Giusti; Nicolás Unsain; Alfredo Cáceres; Florian Steiner; Philip Tinnefeld; Damián Refojo; Thomas M. Jovin; Fernando D. Stefani
Super-resolution Imaging of Energy Transfer by Intensity-Based STED-FRET Journal Article
In: Nano Letters, vol. 21, no. 5, pp. 2296–2303, 2021.
@article{Szalai2021,
title = {Super-resolution Imaging of Energy Transfer by Intensity-Based STED-FRET},
author = {Alan M. Szalai and Bruno Siarry and Jerónimo Lukin and Sebastián Giusti and Nicolás Unsain and Alfredo Cáceres and Florian Steiner and Philip Tinnefeld and Damián Refojo and Thomas M. Jovin and Fernando D. Stefani},
doi = {10.1021/acs.nanolett.1c00158},
year = {2021},
date = {2021-02-01},
urldate = {2021-02-01},
journal = {Nano Letters},
volume = {21},
number = {5},
pages = {2296--2303},
publisher = {American Chemical Society (ACS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Gordon J. Hedley; Tim Schröder; Florian Steiner; Theresa Eder; Felix J. Hofmann; Sebastian Bange; Dirk Laux; Sigurd Höger; Philip Tinnefeld; John M. Lupton; Jan Vogelsang
Picosecond time-resolved photon antibunching measures nanoscale exciton motion and the true number of chromophores Journal Article
In: Nature Communications, vol. 12, no. 1, 2021.
@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}
}
Kateryna Trofymchuk; Viktorija Glembockyte; Lennart Grabenhorst; Florian Steiner; Carolin Vietz; Cindy Close; Martina Pfeiffer; Lars Richter; Max L. Schütte; Florian Selbach; Renukka Yaadav; Jonas Zähringer; Qingshan Wei; Aydogan Ozcan; Birka Lalkens; Guillermo P. Acuna; Philip Tinnefeld
Addressable nanoantennas with cleared hotspots for single-molecule detection on a portable smartphone microscope Journal Article
In: Nature Communications, vol. 12, no. 1, 2021.
@article{Trofymchuk2021,
title = {Addressable nanoantennas with cleared hotspots for single-molecule detection on a portable smartphone microscope},
author = {Kateryna Trofymchuk and Viktorija Glembockyte and Lennart Grabenhorst and Florian Steiner and Carolin Vietz and Cindy Close and Martina Pfeiffer and Lars Richter and Max L. Schütte and Florian Selbach and Renukka Yaadav and Jonas Zähringer and Qingshan Wei and Aydogan Ozcan and Birka Lalkens and Guillermo P. Acuna and Philip Tinnefeld},
doi = {10.1038/s41467-021-21238-9},
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}
}
Patrick Eiring; Ryan McLaughlin; Siddharth S Matikonda; Zhongying Han; Lennart Grabenhorst; Dominic A Helmerich; Mara Meub; Gerti Beliu; Michael Luciano; Venu Bandi; Niels Zijlstra; Zhen-Dan Shi; Sergey G Tarasov; Rolf Swenson; Philip Tinnefeld; Viktorija Glembockyte; Thorben Cordes; Markus Sauer; Martin J Schnermann
Targetable Conformationally Restricted Cyanines Enable Photon-Count-Limited Applications* Journal Article
In: Angew Chem Int Ed Engl, vol. 60, no. 51, pp. 26685–26693, 2021, ISSN: 1521-3773.
@article{pmid34606673,
title = {Targetable Conformationally Restricted Cyanines Enable Photon-Count-Limited Applications*},
author = {Patrick Eiring and Ryan McLaughlin and Siddharth S Matikonda and Zhongying Han and Lennart Grabenhorst and Dominic A Helmerich and Mara Meub and Gerti Beliu and Michael Luciano and Venu Bandi and Niels Zijlstra and Zhen-Dan Shi and Sergey G Tarasov and Rolf Swenson and Philip Tinnefeld and Viktorija Glembockyte and Thorben Cordes and Markus Sauer and Martin J Schnermann},
doi = {10.1002/anie.202109749},
issn = {1521-3773},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Angew Chem Int Ed Engl},
volume = {60},
number = {51},
pages = {26685--26693},
abstract = {Cyanine dyes are exceptionally useful probes for a range of fluorescence-based applications, but their photon output can be limited by trans-to-cis photoisomerization. We recently demonstrated that appending a ring system to the pentamethine cyanine ring system improves the quantum yield and extends the fluorescence lifetime. Here, we report an optimized synthesis of persulfonated variants that enable efficient labeling of nucleic acids and proteins. We demonstrate that a bifunctional sulfonated tertiary amide significantly improves the optical properties of the resulting bioconjugates. These new conformationally restricted cyanines are compared to the parent cyanine derivatives in a range of contexts. These include their use in the plasmonic hotspot of a DNA-nanoantenna, in single-molecule Förster-resonance energy transfer (FRET) applications, far-red fluorescence-lifetime imaging microscopy (FLIM), and single-molecule localization microscopy (SMLM). These efforts define contexts in which eliminating cyanine isomerization provides meaningful benefits to imaging performance.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cyanine dyes are exceptionally useful probes for a range of fluorescence-based applications, but their photon output can be limited by trans-to-cis photoisomerization. We recently demonstrated that appending a ring system to the pentamethine cyanine ring system improves the quantum yield and extends the fluorescence lifetime. Here, we report an optimized synthesis of persulfonated variants that enable efficient labeling of nucleic acids and proteins. We demonstrate that a bifunctional sulfonated tertiary amide significantly improves the optical properties of the resulting bioconjugates. These new conformationally restricted cyanines are compared to the parent cyanine derivatives in a range of contexts. These include their use in the plasmonic hotspot of a DNA-nanoantenna, in single-molecule Förster-resonance energy transfer (FRET) applications, far-red fluorescence-lifetime imaging microscopy (FLIM), and single-molecule localization microscopy (SMLM). These efforts define contexts in which eliminating cyanine isomerization provides meaningful benefits to imaging performance.
Michael Scheckenbach; Tom Schubert; Carsten Forthmann; Viktorija Glembockyte; Philip Tinnefeld
Self-Regeneration and Self-Healing in DNA Origami Nanostructures Journal Article
In: Angewandte Chemie International Edition, vol. 60, no. 9, pp. 4931–4938, 2021.
@article{Scheckenbach2021,
title = {Self-Regeneration and Self-Healing in DNA Origami Nanostructures},
author = {Michael Scheckenbach and Tom Schubert and Carsten Forthmann and Viktorija Glembockyte and Philip Tinnefeld},
doi = {10.1002/anie.202012986},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Angewandte Chemie International Edition},
volume = {60},
number = {9},
pages = {4931--4938},
publisher = {Wiley},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lior Shani; Philip Tinnefeld; Yafit Fleger; Amos Sharoni; Boris Ya. Shapiro; Avner Shaulov; Oleg Gang; Yosef Yeshurun
DNA origami based superconducting nanowires Journal Article
In: AIP Advances, vol. 11, no. 1, pp. 015130, 2021.
@article{Shani2021,
title = {DNA origami based superconducting nanowires},
author = {Lior Shani and Philip Tinnefeld and Yafit Fleger and Amos Sharoni and Boris Ya. Shapiro and Avner Shaulov and Oleg Gang and Yosef Yeshurun},
doi = {10.1063/5.0029781},
year = {2021},
date = {2021-01-01},
journal = {AIP Advances},
volume = {11},
number = {1},
pages = {015130},
publisher = {AIP Publishing},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2020
Luciano A. Masullo; Florian Steiner; Jonas Zähringer; Lucía F. Lopez; Johann Bohlen; Lars Richter; Fiona Cole; Philip Tinnefeld; Fernando D. Stefani
Pulsed Interleaved MINFLUX Journal Article
In: Nano Letters, vol. 21, no. 1, pp. 840–846, 2020.
@article{Masullo2020,
title = {Pulsed Interleaved MINFLUX},
author = {Luciano A. Masullo and Florian Steiner and Jonas Zähringer and Lucía F. Lopez and Johann Bohlen and Lars Richter and Fiona Cole and Philip Tinnefeld and Fernando D. Stefani},
doi = {10.1021/acs.nanolett.0c04600},
year = {2020},
date = {2020-12-01},
journal = {Nano Letters},
volume = {21},
number = {1},
pages = {840--846},
publisher = {American Chemical Society (ACS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Andrés Manuel Vera; Philip Tinnefeld
Single-Molecule Approved Surface Passivation Journal Article
In: Structure, vol. 28, no. 12, pp. 1269–1270, 2020.
@article{Vera2020,
title = {Single-Molecule Approved Surface Passivation},
author = {Andrés Manuel Vera and Philip Tinnefeld},
doi = {10.1016/j.str.2020.11.009},
year = {2020},
date = {2020-12-01},
journal = {Structure},
volume = {28},
number = {12},
pages = {1269--1270},
publisher = {Elsevier BV},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Michael Scheckenbach; Julian Bauer; Jonas Zähringer; Florian Selbach; Philip Tinnefeld
DNA origami nanorulers and emerging reference structures Journal Article
In: APL Materials, vol. 8, no. 11, pp. 110902, 2020.
@article{Scheckenbach2020,
title = {DNA origami nanorulers and emerging reference structures},
author = {Michael Scheckenbach and Julian Bauer and Jonas Zähringer and Florian Selbach and Philip Tinnefeld},
doi = {10.1063/5.0022885},
year = {2020},
date = {2020-11-01},
journal = {APL Materials},
volume = {8},
number = {11},
pages = {110902},
publisher = {AIP Publishing},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zhaowei Liu; Haipei Liu; Andrés M. Vera; Rafael C. Bernardi; Philip Tinnefeld; Michael A. Nash
High force catch bond mechanism of bacterial adhesion in the human gut Journal Article
In: Nature Communications, vol. 11, no. 1, 2020.
@article{Liu2020,
title = {High force catch bond mechanism of bacterial adhesion in the human gut},
author = {Zhaowei Liu and Haipei Liu and Andrés M. Vera and Rafael C. Bernardi and Philip Tinnefeld and Michael A. Nash},
doi = {10.1038/s41467-020-18063-x},
year = {2020},
date = {2020-08-01},
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Kevin Kramm; Tim Schröder; Jerome Gouge; Andrés Manuel Vera; Kapil Gupta; Florian B. Heiss; Tim Liedl; Christoph Engel; Imre Berger; Alessandro Vannini; Philip Tinnefeld; Dina Grohmann
DNA origami-based single-molecule force spectroscopy elucidates RNA Polymerase III pre-initiation complex stability Journal Article
In: Nature Communications, vol. 11, no. 1, 2020.
@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},
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Michael Isselstein; Lei Zhang; Viktorija Glembockyte; Oliver Brix; Gonzalo Cosa; Philip Tinnefeld; Thorben Cordes
Self-Healing Dyes—Keeping the Promise? Journal Article
In: The Journal of Physical Chemistry Letters, vol. 11, no. 11, pp. 4462–4480, 2020.
@article{Isselstein2020,
title = {Self-Healing Dyes—Keeping the Promise?},
author = {Michael Isselstein and Lei Zhang and Viktorija Glembockyte and Oliver Brix and Gonzalo Cosa and Philip Tinnefeld and Thorben Cordes},
doi = {10.1021/acs.jpclett.9b03833},
year = {2020},
date = {2020-05-01},
journal = {The Journal of Physical Chemistry Letters},
volume = {11},
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Siddharth S. Matikonda; Gabrielle Hammersley; Nikita Kumari; Lennart Grabenhorst; Viktorija Glembockyte; Philip Tinnefeld; Joseph Ivanic; Marcia Levitus; Martin J. Schnermann
Impact of Cyanine Conformational Restraint in the Near-Infrared Range Journal Article
In: The Journal of Organic Chemistry, vol. 85, no. 9, pp. 5907–5915, 2020.
@article{Matikonda2020,
title = {Impact of Cyanine Conformational Restraint in the Near-Infrared Range},
author = {Siddharth S. Matikonda and Gabrielle Hammersley and Nikita Kumari and Lennart Grabenhorst and Viktorija Glembockyte and Philip Tinnefeld and Joseph Ivanic and Marcia Levitus and Martin J. Schnermann},
doi = {10.1021/acs.joc.0c00236},
year = {2020},
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Kateryna Trofymchuk; Guillermo P. Acuna; Viktorija Glembockyte; Philip Tinnefeld
Self-Assembled Nanoparticle Optical Antennas Book Chapter
In: Sattler, Klaus D. (Ed.): 21st Century Nanoscience -- A Handbook, Chapter 8, pp. 8-1-8-14, CRC Press, Boca Raton, Florida, 1, 2020, ISBN: 9780429351594.
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title = {Self-Assembled Nanoparticle Optical Antennas},
author = {Kateryna Trofymchuk and Guillermo P. Acuna and Viktorija Glembockyte and Philip Tinnefeld},
editor = {Klaus D. Sattler},
url = {https://www.taylorfrancis.com/chapters/edit/10.1201/9780429351594-8/self-assembled-nanoparticle-optical-antennas-kateryna-trofymchuk-guillermo-acuna-viktorija-glembockyte-philip-tinnefeld?context=ubx&refId=82b30638-67e5-4622-bd6d-91cdf0ab43e1},
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abstract = {Noble metal nanoparticles (NPs) are able to localize the electromagnetic (EM) energy of the incident light into subwavelength volumes. In addition, they can mediate the radiation from coupled emitters into the far-field. This allows to consider metal NPs as optical nanoantennas (NAs), analogous to common radio antennas.
Good optical NAs meet some requirements for their practical applications, namely, they possess a large scattering cross-section to collect maximal EM energy and display a large electric field enhancement to optimally transfer freely propagating EM energy into localized modes. To achieve this high enhancement, not only the photophysics of metal NP-emitter coupling in terms of all of the decay channels should be fully understood and controlled but also the geometry of the system should be very well defined and reproducible. Self-assembly is widely used for this purpose, as it allows to produce a large number of identical structures with defined positioning of all elements. In this chapter, we first discuss the general rules governing the decay rates of emitters in the vicinity of metal NPs. This will be followed with the discussion of general self-assembly strategies for NAs and applications of NAs for biosensing and single molecule studies. An alternative way to design NAs by using light-harvesting NPs will be briefly introduced. Finally, the challenges in the fabrication of NAs and their applications will be outlined.},
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Noble metal nanoparticles (NPs) are able to localize the electromagnetic (EM) energy of the incident light into subwavelength volumes. In addition, they can mediate the radiation from coupled emitters into the far-field. This allows to consider metal NPs as optical nanoantennas (NAs), analogous to common radio antennas.
Good optical NAs meet some requirements for their practical applications, namely, they possess a large scattering cross-section to collect maximal EM energy and display a large electric field enhancement to optimally transfer freely propagating EM energy into localized modes. To achieve this high enhancement, not only the photophysics of metal NP-emitter coupling in terms of all of the decay channels should be fully understood and controlled but also the geometry of the system should be very well defined and reproducible. Self-assembly is widely used for this purpose, as it allows to produce a large number of identical structures with defined positioning of all elements. In this chapter, we first discuss the general rules governing the decay rates of emitters in the vicinity of metal NPs. This will be followed with the discussion of general self-assembly strategies for NAs and applications of NAs for biosensing and single molecule studies. An alternative way to design NAs by using light-harvesting NPs will be briefly introduced. Finally, the challenges in the fabrication of NAs and their applications will be outlined.
Good optical NAs meet some requirements for their practical applications, namely, they possess a large scattering cross-section to collect maximal EM energy and display a large electric field enhancement to optimally transfer freely propagating EM energy into localized modes. To achieve this high enhancement, not only the photophysics of metal NP-emitter coupling in terms of all of the decay channels should be fully understood and controlled but also the geometry of the system should be very well defined and reproducible. Self-assembly is widely used for this purpose, as it allows to produce a large number of identical structures with defined positioning of all elements. In this chapter, we first discuss the general rules governing the decay rates of emitters in the vicinity of metal NPs. This will be followed with the discussion of general self-assembly strategies for NAs and applications of NAs for biosensing and single molecule studies. An alternative way to design NAs by using light-harvesting NPs will be briefly introduced. Finally, the challenges in the fabrication of NAs and their applications will be outlined.
Lennart Grabenhorst; Kateryna Trofymchuk; Florian Steiner; Viktorija Glembockyte; Philip Tinnefeld
Fluorophore photostability and saturation in the hotspot of DNA origami nanoantennas Journal Article
In: Methods and Applications in Fluorescence, vol. 8, no. 2, pp. 024003, 2020.
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2019
J. Schedlbauer; P. Wilhelm; L. Grabenhorst; M. E. Federl; B. Lalkens; F. Hinderer; U. Scherf; S. Höger; P. Tinnefeld; S. Bange; J. Vogelsang; J. M. Lupton
Ultrafast Single-Molecule Fluorescence Measured by Femtosecond Double-Pulse Excitation Photon Antibunching Journal Article
In: Nano Letters, vol. 20, no. 2, pp. 1074–1079, 2019.
@article{Schedlbauer2019,
title = {Ultrafast Single-Molecule Fluorescence Measured by Femtosecond Double-Pulse Excitation Photon Antibunching},
author = {J. Schedlbauer and P. Wilhelm and L. Grabenhorst and M. E. Federl and B. Lalkens and F. Hinderer and U. Scherf and S. Höger and P. Tinnefeld and S. Bange and J. Vogelsang and J. M. Lupton},
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Kristina Hübner; Mauricio Pilo-Pais; Florian Selbach; Tim Liedl; Philip Tinnefeld; Fernando D. Stefani; Guillermo P. Acuna
Directing Single-Molecule Emission with DNA Origami-Assembled Optical Antennas Journal Article
In: Nano Letters, vol. 19, no. 9, pp. 6629–6634, 2019.
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title = {Directing Single-Molecule Emission with DNA Origami-Assembled Optical Antennas},
author = {Kristina Hübner and Mauricio Pilo-Pais and Florian Selbach and Tim Liedl and Philip Tinnefeld and Fernando D. Stefani and Guillermo P. Acuna},
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I. Kaminska; J. Bohlen; S. Rocchetti; F. Selbach; G. P. Acuna; P. Tinnefeld
Distance Dependence of Single-Molecule Energy Transfer to Graphene Measured with DNA Origami Nanopositioners Journal Article
In: Nano Letters, vol. 19, no. 7, pp. 4257–4262, 2019.
@article{Kaminska2019,
title = {Distance Dependence of Single-Molecule Energy Transfer to Graphene Measured with DNA Origami Nanopositioners},
author = {I. Kaminska and J. Bohlen and S. Rocchetti and F. Selbach and G. P. Acuna and P. Tinnefeld},
doi = {10.1021/acs.nanolett.9b00172},
year = {2019},
date = {2019-06-01},
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Youngeun Choi; Carsten Schmidt; Philip Tinnefeld; Ilko Bald; Stefan Rödiger
A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads Journal Article
In: Scientific Reports, vol. 9, no. 1, 2019.
@article{Choi2019,
title = {A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads},
author = {Youngeun Choi and Carsten Schmidt and Philip Tinnefeld and Ilko Bald and Stefan Rödiger},
doi = {10.1038/s41598-019-41136-x},
year = {2019},
date = {2019-03-01},
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J. Bohlen; Á. Cuartero-González; E. Pibiri; D. Ruhlandt; A. I. Fernández-Domínguez; P. Tinnefeld; G. P. Acuna
Plasmon-assisted Förster resonance energy transfer at the single-molecule level in the moderate quenching regime Journal Article
In: Nanoscale, vol. 11, no. 16, pp. 7674–7681, 2019.
@article{Bohlen2019,
title = {Plasmon-assisted Förster resonance energy transfer at the single-molecule level in the moderate quenching regime},
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year = {2019},
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Tim Schröder; Max B. Scheible; Florian Steiner; Jan Vogelsang; Philip Tinnefeld
Interchromophoric Interactions Determine the Maximum Brightness Density in DNA Origami Structures Journal Article
In: Nano Letters, vol. 19, no. 2, pp. 1275–1281, 2019.
@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},
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Carolin Vietz; Max L. Schütte; Qingshan Wei; Lars Richter; Birka Lalkens; Aydogan Ozcan; Philip Tinnefeld; Guillermo P. Acuna
Benchmarking Smartphone Fluorescence-Based Microscopy with DNA Origami Nanobeads: Reducing the Gap toward Single-Molecule Sensitivity Journal Article
In: ACS Omega, vol. 4, no. 1, pp. 637–642, 2019.
@article{Vietz2019,
title = {Benchmarking Smartphone Fluorescence-Based Microscopy with DNA Origami Nanobeads: Reducing the Gap toward Single-Molecule Sensitivity},
author = {Carolin Vietz and Max L. Schütte and Qingshan Wei and Lars Richter and Birka Lalkens and Aydogan Ozcan and Philip Tinnefeld and Guillermo P. Acuna},
doi = {10.1021/acsomega.8b03136},
year = {2019},
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journal = {ACS Omega},
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2018
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 measurements—a multi-laboratory benchmark study Journal Article
In: Nature Methods, vol. 15, no. 9, pp. 669–676, 2018.
@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},
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journal = {Nature Methods},
volume = {15},
number = {9},
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Sebastian Isbaner; Narain Karedla; Izabela Kaminska; Daja Ruhlandt; Mario Raab; Johann Bohlen; Alexey Chizhik; Ingo Gregor; Philip Tinnefeld; Jörg Enderlein; Roman Tsukanov
Axial Colocalization of Single Molecules with Nanometer Accuracy Using Metal-Induced Energy Transfer Journal Article
In: Nano Letters, vol. 18, no. 4, pp. 2616–2622, 2018.
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title = {Axial Colocalization of Single Molecules with Nanometer Accuracy Using Metal-Induced Energy Transfer},
author = {Sebastian Isbaner and Narain Karedla and Izabela Kaminska and Daja Ruhlandt and Mario Raab and Johann Bohlen and Alexey Chizhik and Ingo Gregor and Philip Tinnefeld and Jörg Enderlein and Roman Tsukanov},
doi = {10.1021/acs.nanolett.8b00425},
year = {2018},
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Alexander Gust; Leonhard Jakob; Daniela M. Zeitler; Astrid Bruckmann; Kevin Kramm; Sarah Willkomm; Philip Tinnefeld; Gunter Meister; Dina Grohmann
Site-Specific Labelling of Native Mammalian Proteins for Single-Molecule FRET Measurements Journal Article
In: ChemBioChem, vol. 19, no. 8, pp. 780–783, 2018.
@article{Gust2018,
title = {Site-Specific Labelling of Native Mammalian Proteins for Single-Molecule FRET Measurements},
author = {Alexander Gust and Leonhard Jakob and Daniela M. Zeitler and Astrid Bruckmann and Kevin Kramm and Sarah Willkomm and Philip Tinnefeld and Gunter Meister and Dina Grohmann},
doi = {10.1002/cbic.201700696},
year = {2018},
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Max B. Scheible; Philip Tinnefeld
Quantifying Expansion Microscopy with DNA Origami Expansion Nanorulers Journal Article
In: 2018.
@article{Scheible2018,
title = {Quantifying Expansion Microscopy with DNA Origami Expansion Nanorulers},
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Izabela Kaminska; Carolin Vietz; Álvaro Cuartero-González; Philip Tinnefeld; Antonio I. Fernández-Domínguez; Guillermo P. Acuna
Strong plasmonic enhancement of single molecule photostability in silver dimer optical antennas Journal Article
In: Nanophotonics, vol. 7, no. 3, pp. 643–649, 2018.
@article{Kaminska2018a,
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Elisa A. Hemmig; Clare Fitzgerald; Christopher Maffeo; Lisa Hecker; Sarah E. Ochmann; Aleksei Aksimentiev; Philip Tinnefeld; Ulrich F. Keyser
Optical Voltage Sensing Using DNA Origami Journal Article
In: Nano Letters, vol. 18, no. 3, pp. 1962–1971, 2018.
@article{Hemmig2018,
title = {Optical Voltage Sensing Using DNA Origami},
author = {Elisa A. Hemmig and Clare Fitzgerald and Christopher Maffeo and Lisa Hecker and Sarah E. Ochmann and Aleksei Aksimentiev and Philip Tinnefeld and Ulrich F. Keyser},
doi = {10.1021/acs.nanolett.7b05354},
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