---
_id: '65490'
abstract:
- lang: eng
text: In recent years, nanostructures assembled by DNA have found promising
applications in optics, medicine, and sensing. DNA origami in particular provides
unique self‐assembly properties, not only enabling a vast variety of functionalization
schemes but also presenting a promising route to fabricate large‐scale, bottom‐up
nanostructured arrays. This approach has comparable precision to electron beam
lithography but avoids slow and expensive patterning steps. However, self‐assembly
of lattices with high order and well‐defined periodicity requires careful tuning
of the deposition parameters and interactions involved, which has been done mostly
on mica so far. As mica is not compatible with standard microfabrication processes,
we investigate here the assembly of DNA origami lattices on the most general microfabrication
material, that is, silicon wafers, which has turned out to be rather challenging.
We study how the forming of polycrystalline 2D‐fishnet‐type lattices is influenced
by different incubation conditions and strengths of the origami–origami and origami‐surface
interactions, with the aim to create large‐scale single‐crystalline lattices.
The lattices are characterized by atomic force microscopy and analyzed for precision
of formation, achievable domain size, and surface coverage of well‐formed lattices.
Thanks to the silicon substrate, these DNA origami lattices can be further combined
with traditional microfabrication processes to turn them, for example, into metamaterials
with novel optical properties.
article_number: e202500813
author:
- first_name: Heini
full_name: Järvinen, Heini
last_name: Järvinen
- first_name: Johannes M.
full_name: Parikka, Johannes M.
last_name: Parikka
- first_name: R. P. Thiwangi N.
full_name: Rajapaksha, R. P. Thiwangi N.
last_name: Rajapaksha
- first_name: Adrian Clemens
full_name: Keller, Adrian Clemens
id: '48864'
last_name: Keller
orcid: 0000-0001-7139-3110
- first_name: J. Jussi
full_name: Toppari, J. Jussi
last_name: Toppari
citation:
ama: Järvinen H, Parikka JM, Rajapaksha RPTN, Keller AC, Toppari JJ. Towards Single‐Crystalline
DNA Origami Lattices on Silicon Wafers for Bottom‐Up Nanofabrication. Small
Structures. 2026;7(4). doi:10.1002/sstr.202500813
apa: Järvinen, H., Parikka, J. M., Rajapaksha, R. P. T. N., Keller, A. C., &
Toppari, J. J. (2026). Towards Single‐Crystalline DNA Origami Lattices on Silicon
Wafers for Bottom‐Up Nanofabrication. Small Structures, 7(4), Article
e202500813. https://doi.org/10.1002/sstr.202500813
bibtex: '@article{Järvinen_Parikka_Rajapaksha_Keller_Toppari_2026, title={Towards
Single‐Crystalline DNA Origami Lattices on Silicon Wafers for Bottom‐Up Nanofabrication},
volume={7}, DOI={10.1002/sstr.202500813},
number={4e202500813}, journal={Small Structures}, publisher={Wiley}, author={Järvinen,
Heini and Parikka, Johannes M. and Rajapaksha, R. P. Thiwangi N. and Keller, Adrian
Clemens and Toppari, J. Jussi}, year={2026} }'
chicago: Järvinen, Heini, Johannes M. Parikka, R. P. Thiwangi N. Rajapaksha, Adrian
Clemens Keller, and J. Jussi Toppari. “Towards Single‐Crystalline DNA Origami
Lattices on Silicon Wafers for Bottom‐Up Nanofabrication.” Small Structures
7, no. 4 (2026). https://doi.org/10.1002/sstr.202500813.
ieee: 'H. Järvinen, J. M. Parikka, R. P. T. N. Rajapaksha, A. C. Keller, and J.
J. Toppari, “Towards Single‐Crystalline DNA Origami Lattices on Silicon Wafers
for Bottom‐Up Nanofabrication,” Small Structures, vol. 7, no. 4, Art. no.
e202500813, 2026, doi: 10.1002/sstr.202500813.'
mla: Järvinen, Heini, et al. “Towards Single‐Crystalline DNA Origami Lattices on
Silicon Wafers for Bottom‐Up Nanofabrication.” Small Structures, vol. 7,
no. 4, e202500813, Wiley, 2026, doi:10.1002/sstr.202500813.
short: H. Järvinen, J.M. Parikka, R.P.T.N. Rajapaksha, A.C. Keller, J.J. Toppari,
Small Structures 7 (2026).
date_created: 2026-04-22T16:17:08Z
date_updated: 2026-04-22T16:17:22Z
department:
- _id: '302'
doi: 10.1002/sstr.202500813
intvolume: ' 7'
issue: '4'
language:
- iso: eng
publication: Small Structures
publication_identifier:
issn:
- 2688-4062
- 2688-4062
publication_status: published
publisher: Wiley
status: public
title: Towards Single‐Crystalline DNA Origami Lattices on Silicon Wafers for Bottom‐Up
Nanofabrication
type: journal_article
user_id: '48864'
volume: 7
year: '2026'
...
---
_id: '60973'
abstract:
- lang: eng
text: The specific binding of DNA origami nanostructures (DONs) to bacteria
is an important prerequisite for their application in pathogen targeting and antimicrobial
drug delivery. So far, targeting bacteria with DONs has been achieved exclusively
via aptamers, which suffer from drawbacks such as sensitivity toward environmental
conditions and reduced binding after immobilization or conjugation. Here, an alternative
approach is presented based on the modification of DONs with the cell wall‐binding
glycopeptide antibiotic vancomycin. Using strain‐promoted azide‐alkyne cycloaddition,
azide‐modified vancomycin is conjugated to selected staple strands and subsequently
incorporated into 2D DON triangles. The resulting constructs show specific binding
to the Gram‐positive species Bacillus subtilis (B.
subtilis) and Staphylococcus capitis
(S. capitis), and remarkably, to Gram‐negative Escherichia
coli (E. coli), but no antimicrobial
activity at vancomycin concentrations up to at least 2.91 μM. For B.
subtilis and E. coli, DONs with vancomycin
modifications on both sides exhibit better binding than DONs modified on only
one side. However, both variants bind equally well to S. capitis.
These results demonstrate the great potential of small molecule drug compounds
for the robust, broad‐spectrum targeting of bacteria with DONs. Targeting a ubiquitous
cell wall component of most pathogenic bacteria, vancomycin‐modified DONs have
many potential applications in the prevention and treatment of nosocomial infections.
article_number: '2500246'
author:
- first_name: Özge
full_name: Coşkuner Leineweber, Özge
last_name: Coşkuner Leineweber
- first_name: Bhanu K.
full_name: Pothineni, Bhanu K.
last_name: Pothineni
- first_name: Nils
full_name: Schumann, Nils
last_name: Schumann
- first_name: Ulrike
full_name: Hofmann, Ulrike
last_name: Hofmann
- first_name: Christin
full_name: Möser, Christin
last_name: Möser
- first_name: David M.
full_name: Smith, David M.
last_name: Smith
- first_name: Guido
full_name: Grundmeier, Guido
id: '194'
last_name: Grundmeier
- first_name: Yixin
full_name: Zhang, Yixin
last_name: Zhang
- first_name: Adrian
full_name: Keller, Adrian
id: '48864'
last_name: Keller
orcid: 0000-0001-7139-3110
citation:
ama: Coşkuner Leineweber Ö, Pothineni BK, Schumann N, et al. Vancomycin‐Modified
DNA Origami Nanostructures for Targeting Bacterial Pathogens. Small Structures.
Published online 2025. doi:10.1002/sstr.202500246
apa: Coşkuner Leineweber, Ö., Pothineni, B. K., Schumann, N., Hofmann, U., Möser,
C., Smith, D. M., Grundmeier, G., Zhang, Y., & Keller, A. (2025). Vancomycin‐Modified
DNA Origami Nanostructures for Targeting Bacterial Pathogens. Small Structures,
Article 2500246. https://doi.org/10.1002/sstr.202500246
bibtex: '@article{Coşkuner Leineweber_Pothineni_Schumann_Hofmann_Möser_Smith_Grundmeier_Zhang_Keller_2025,
title={Vancomycin‐Modified DNA Origami Nanostructures for Targeting Bacterial
Pathogens}, DOI={10.1002/sstr.202500246},
number={2500246}, journal={Small Structures}, publisher={Wiley}, author={Coşkuner
Leineweber, Özge and Pothineni, Bhanu K. and Schumann, Nils and Hofmann, Ulrike
and Möser, Christin and Smith, David M. and Grundmeier, Guido and Zhang, Yixin
and Keller, Adrian}, year={2025} }'
chicago: Coşkuner Leineweber, Özge, Bhanu K. Pothineni, Nils Schumann, Ulrike Hofmann,
Christin Möser, David M. Smith, Guido Grundmeier, Yixin Zhang, and Adrian Keller.
“Vancomycin‐Modified DNA Origami Nanostructures for Targeting Bacterial Pathogens.”
Small Structures, 2025. https://doi.org/10.1002/sstr.202500246.
ieee: 'Ö. Coşkuner Leineweber et al., “Vancomycin‐Modified DNA Origami Nanostructures
for Targeting Bacterial Pathogens,” Small Structures, Art. no. 2500246,
2025, doi: 10.1002/sstr.202500246.'
mla: Coşkuner Leineweber, Özge, et al. “Vancomycin‐Modified DNA Origami Nanostructures
for Targeting Bacterial Pathogens.” Small Structures, 2500246, Wiley, 2025,
doi:10.1002/sstr.202500246.
short: Ö. Coşkuner Leineweber, B.K. Pothineni, N. Schumann, U. Hofmann, C. Möser,
D.M. Smith, G. Grundmeier, Y. Zhang, A. Keller, Small Structures (2025).
date_created: 2025-08-22T06:02:45Z
date_updated: 2025-08-22T06:04:06Z
department:
- _id: '302'
doi: 10.1002/sstr.202500246
language:
- iso: eng
publication: Small Structures
publication_identifier:
issn:
- 2688-4062
- 2688-4062
publication_status: published
publisher: Wiley
status: public
title: Vancomycin‐Modified DNA Origami Nanostructures for Targeting Bacterial Pathogens
type: journal_article
user_id: '48864'
year: '2025'
...
---
_id: '55310'
abstract:
- lang: eng
text: DNA origami nanostructures are promising carries for drug delivery
applications. However, their limited stability under relevant conditions often
presents a challenge. Herein, the structural stability of DNA origami nanostructures
is investigated in a setting compatible with their application in photodynamic
therapy (PDT). To this end, DNA origami triangles and six‐helix bundles (6HBs)
are loaded with the clinically tested photosensitizer methylene blue, which upon
irradiation with red light generates reactive oxygen species (ROS) that attack
the DNA origami nanostructures. ROS‐induced structural damage is observed to depend
on the ionic composition of the surrounding medium and becomes more severe at
low ionic strength. Mg2+ ions can efficiently protect the
DNA origami nanostructures from ROS‐induced damage and may even heal some of the
damage obtained under Mg2+‐free conditions when added after
irradiation. Finally, the employed DNA origami 6HBs are more resistant toward
ROS‐induced structural damage than the triangles, which is attributed to their
markedly different mechanical properties. These results thus provide some fundamental
insights into the stabilizing role of DNA origami superstructure that may guide
the selection or design of DNA origami nanocarriers with optimized stability for
their application in PDT.
author:
- first_name: Lukas
full_name: Rabbe, Lukas
last_name: Rabbe
- first_name: Jaime Andres
full_name: Garcia‐Diosa, Jaime Andres
last_name: Garcia‐Diosa
- first_name: Guido
full_name: Grundmeier, Guido
id: '194'
last_name: Grundmeier
- first_name: Adrian
full_name: Keller, Adrian
id: '48864'
last_name: Keller
orcid: 0000-0001-7139-3110
citation:
ama: Rabbe L, Garcia‐Diosa JA, Grundmeier G, Keller A. Ion‐Dependent Stability of
DNA Origami Nanostructures in the Presence of Photo‐Generated Reactive Oxygen
Species. Small Structures. Published online 2024. doi:10.1002/sstr.202400094
apa: Rabbe, L., Garcia‐Diosa, J. A., Grundmeier, G., & Keller, A. (2024). Ion‐Dependent
Stability of DNA Origami Nanostructures in the Presence of Photo‐Generated Reactive
Oxygen Species. Small Structures. https://doi.org/10.1002/sstr.202400094
bibtex: '@article{Rabbe_Garcia‐Diosa_Grundmeier_Keller_2024, title={Ion‐Dependent
Stability of DNA Origami Nanostructures in the Presence of Photo‐Generated Reactive
Oxygen Species}, DOI={10.1002/sstr.202400094},
journal={Small Structures}, publisher={Wiley}, author={Rabbe, Lukas and Garcia‐Diosa,
Jaime Andres and Grundmeier, Guido and Keller, Adrian}, year={2024} }'
chicago: Rabbe, Lukas, Jaime Andres Garcia‐Diosa, Guido Grundmeier, and Adrian Keller.
“Ion‐Dependent Stability of DNA Origami Nanostructures in the Presence of Photo‐Generated
Reactive Oxygen Species.” Small Structures, 2024. https://doi.org/10.1002/sstr.202400094.
ieee: 'L. Rabbe, J. A. Garcia‐Diosa, G. Grundmeier, and A. Keller, “Ion‐Dependent
Stability of DNA Origami Nanostructures in the Presence of Photo‐Generated Reactive
Oxygen Species,” Small Structures, 2024, doi: 10.1002/sstr.202400094.'
mla: Rabbe, Lukas, et al. “Ion‐Dependent Stability of DNA Origami Nanostructures
in the Presence of Photo‐Generated Reactive Oxygen Species.” Small Structures,
Wiley, 2024, doi:10.1002/sstr.202400094.
short: L. Rabbe, J.A. Garcia‐Diosa, G. Grundmeier, A. Keller, Small Structures (2024).
date_created: 2024-07-18T09:03:17Z
date_updated: 2024-07-18T09:03:49Z
department:
- _id: '302'
doi: 10.1002/sstr.202400094
language:
- iso: eng
publication: Small Structures
publication_identifier:
issn:
- 2688-4062
- 2688-4062
publication_status: published
publisher: Wiley
status: public
title: Ion‐Dependent Stability of DNA Origami Nanostructures in the Presence of Photo‐Generated
Reactive Oxygen Species
type: journal_article
user_id: '48864'
year: '2024'
...
---
_id: '22684'
author:
- first_name: Jingyuan
full_name: Huang, Jingyuan
last_name: Huang
- first_name: Antonio
full_name: Suma, Antonio
last_name: Suma
- first_name: Meiying
full_name: Cui, Meiying
last_name: Cui
- first_name: Guido
full_name: Grundmeier, Guido
id: '194'
last_name: Grundmeier
- first_name: Vincenzo
full_name: Carnevale, Vincenzo
last_name: Carnevale
- first_name: Yixin
full_name: Zhang, Yixin
last_name: Zhang
- first_name: Charlotte
full_name: Kielar, Charlotte
last_name: Kielar
- first_name: Adrian
full_name: Keller, Adrian
id: '48864'
last_name: Keller
orcid: 0000-0001-7139-3110
citation:
ama: Huang J, Suma A, Cui M, et al. Arranging Small Molecules with Subnanometer
Precision on DNA Origami Substrates for the Single‐Molecule Investigation of Protein–Ligand
Interactions. Small Structures. 2020;1:2000038. doi:10.1002/sstr.202000038
apa: Huang, J., Suma, A., Cui, M., Grundmeier, G., Carnevale, V., Zhang, Y., … Keller,
A. (2020). Arranging Small Molecules with Subnanometer Precision on DNA Origami
Substrates for the Single‐Molecule Investigation of Protein–Ligand Interactions.
Small Structures, 1, 2000038. https://doi.org/10.1002/sstr.202000038
bibtex: '@article{Huang_Suma_Cui_Grundmeier_Carnevale_Zhang_Kielar_Keller_2020,
title={Arranging Small Molecules with Subnanometer Precision on DNA Origami Substrates
for the Single‐Molecule Investigation of Protein–Ligand Interactions}, volume={1},
DOI={10.1002/sstr.202000038},
journal={Small Structures}, author={Huang, Jingyuan and Suma, Antonio and Cui,
Meiying and Grundmeier, Guido and Carnevale, Vincenzo and Zhang, Yixin and Kielar,
Charlotte and Keller, Adrian}, year={2020}, pages={2000038} }'
chicago: 'Huang, Jingyuan, Antonio Suma, Meiying Cui, Guido Grundmeier, Vincenzo
Carnevale, Yixin Zhang, Charlotte Kielar, and Adrian Keller. “Arranging Small
Molecules with Subnanometer Precision on DNA Origami Substrates for the Single‐Molecule
Investigation of Protein–Ligand Interactions.” Small Structures 1 (2020):
2000038. https://doi.org/10.1002/sstr.202000038.'
ieee: J. Huang et al., “Arranging Small Molecules with Subnanometer Precision
on DNA Origami Substrates for the Single‐Molecule Investigation of Protein–Ligand
Interactions,” Small Structures, vol. 1, p. 2000038, 2020.
mla: Huang, Jingyuan, et al. “Arranging Small Molecules with Subnanometer Precision
on DNA Origami Substrates for the Single‐Molecule Investigation of Protein–Ligand
Interactions.” Small Structures, vol. 1, 2020, p. 2000038, doi:10.1002/sstr.202000038.
short: J. Huang, A. Suma, M. Cui, G. Grundmeier, V. Carnevale, Y. Zhang, C. Kielar,
A. Keller, Small Structures 1 (2020) 2000038.
date_created: 2021-07-09T07:45:38Z
date_updated: 2022-01-06T06:55:38Z
department:
- _id: '302'
doi: 10.1002/sstr.202000038
intvolume: ' 1'
language:
- iso: eng
page: '2000038'
publication: Small Structures
publication_identifier:
issn:
- 2688-4062
- 2688-4062
publication_status: published
status: public
title: Arranging Small Molecules with Subnanometer Precision on DNA Origami Substrates
for the Single‐Molecule Investigation of Protein–Ligand Interactions
type: journal_article
user_id: '48864'
volume: 1
year: '2020'
...