@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 = {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.
@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.
Niederauer, C., Wang-Henderson, M., Stein, J., Stehr, F., Bauer, J., Jungmann, R., et al. (2021). Single-molecule studies of membrane protein interactions via continuous DNA-mediated fluorophore exchange. European Biophysics Journal with Biophysics Letters,50 (Suppl. 1), 54-54.
Stehr, F., Stein, J., Bauer, J. et al. Tracking single particles for hours via continuous DNA-mediated fluorophore exchange. Nat Commun12, 4432 (2021). https://doi.org/10.1038/s41467-021-24223-4
Blumhardt, P., Stein, J., Mücksch, J., Stehr, F., Bauer, J., Jungmann, R., & Schwille, P. (2018). Photo-Induced Depletion of Binding Sites in DNA-PAINT Microscopy. Molecules (Basel, Switzerland), 23 (12), 3165. https://doi.org/10.3390/molecules23123165
