| Office | 089/2180-77547 (Frau Steger) |
| Telephone | 089/2180-77563 |
| Room | E1.064 |
| Viktorija.Glembockyte”at”cup.lmu.de |
Publications
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.},
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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.
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.},
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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.
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}
}
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},
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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}
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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},
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pubstate = {published},
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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},
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}
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},
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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},
number = {11},
pages = {4462--4480},
publisher = {American Chemical Society (ACS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
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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},
date = {2020-04-01},
journal = {The Journal of Organic Chemistry},
volume = {85},
number = {9},
pages = {5907--5915},
publisher = {American Chemical Society (ACS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
@inbook{book_nanoscience,
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},
isbn = {9780429351594},
year = {2020},
date = {2020-04-01},
urldate = {2020-04-01},
booktitle = {21st Century Nanoscience -- A Handbook},
pages = {8-1-8-14},
publisher = {CRC Press},
address = {Boca Raton, Florida},
edition = {1},
chapter = {8},
series = {21st Century Nanoscience -- A Handbook},
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.
@article{Grabenhorst2020,
title = {Fluorophore photostability and saturation in the hotspot of DNA origami nanoantennas},
author = {Lennart Grabenhorst and Kateryna Trofymchuk and Florian Steiner and Viktorija Glembockyte and Philip Tinnefeld},
doi = {10.1088/2050-6120/ab6ac8},
year = {2020},
date = {2020-02-01},
journal = {Methods and Applications in Fluorescence},
volume = {8},
number = {2},
pages = {024003},
publisher = {IOP Publishing},
keywords = {},
pubstate = {published},
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}