TY  - JOUR
A1  - Kogikoski Junior, Sergio
A1  - Tapio, Kosti
A1  - Edler von Zander, Robert
A1  - Saalfrank, Peter
A1  - Bald, Ilko
T1  - Raman enhancement of nanoparticle dimers self-assembled using DNA origami nanotriangles
JF  - Molecules : a journal of synthetic chemistry and natural product chemistry / Molecular Diversity Preservation International
N2  - Surface-enhanced Raman scattering is a powerful approach to detect molecules at very low concentrations, even up to the single-molecule level. One important aspect of the materials used in such a technique is how much the signal is intensified, quantified by the enhancement factor (EF). Herein we obtained the EFs for gold nanoparticle dimers of 60 and 80 nm diameter, respectively, self-assembled using DNA origami nanotriangles. Cy5 and TAMRA were used as surface-enhanced Raman scattering (SERS) probes, which enable the observation of individual nanoparticles and dimers. EF distributions are determined at four distinct wavelengths based on the measurements of around 1000 individual dimer structures. The obtained results show that the EFs for the dimeric assemblies follow a log-normal distribution and are in the range of 10(6) at 633 nm and that the contribution of the molecular resonance effect to the EF is around 2, also showing that the plasmonic resonance is the main source of the observed signal. To support our studies, FDTD simulations of the nanoparticle's electromagnetic field enhancement has been carried out, as well as calculations of the resonance Raman spectra of the dyes using DFT. We observe a very close agreement between the experimental EF distribution and the simulated values.
KW  - surface-enhanced Raman scattering
KW  - DNA origami
KW  - resonance Raman
KW  - scattering
KW  - nanoparticle dimers
Y1  - 2021
U6  - https://doi.org/10.3390/molecules26061684
SN  - 1420-3049
VL  - 26
IS  - 6
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Heck, Christian
A1  - Prinz, Julia
A1  - Dathe, Andre
A1  - Merk, Virginia
A1  - Stranik, Ondrej
A1  - Fritzsche, Wolfgang
A1  - Kneipp, Janina
A1  - Bald, Ilko
T1  - Gold Nanolenses Self-Assembled by DNA Origami
JF  - ACS Photonics
N2  - Nanolenses are self-similar chains of metal nanoparticles, which can theoretically provide extremely high field enhancements. Yet, the complex structure renders their synthesis challenging and has hampered closer analyses so far. Here, DNA origami is used to self-assemble 10, 20, and 60 nm gold nanoparticles as plasmonic gold nanolenses (AuNLs) in solution and in billions of copies. Three different geometrical arrangements are assembled, and for each of the three designs, surface-enhanced Raman scattering (SERS) capabilities of single AuNLs are assessed. For the design which shows the best properties, SERS signals from the two different internal gaps are compared by selectively placing probe dyes. The highest Raman enhancement is found for the gap between the small and medium nanoparticle, which is indicative of a cascaded field enhancement.
KW  - plasmonics
KW  - DNA origami
KW  - SERS
KW  - nanolenses
KW  - gold nanoparticles
Y1  - 2017
U6  - https://doi.org/10.1021/acsphotonics.6b00946
SN  - 2330-4022
VL  - 4
SP  - 1123
EP  - 1130
PB  - American Chemical Society
CY  - Washington
ER  - 
TY  - JOUR
A1  - Heck, Christian
A1  - Kanehira, Yuya
A1  - Kneipp, Janina
A1  - Bald, Ilko
T1  - Placement of Single Proteins within the SERS Hot Spots of Self-Assembled Silver Nanolenses
JF  - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition
N2  - This study demonstrates the bottom-up synthesis of silver nanolenses. A robust coating protocol enabled the functionalization of differently sized silver nanoparticles with DNA single strands of orthogonal sequence. Coated particles 10nm, 20nm, and 60nm in diameter were self-assembled by DNA origami scaffolds to form silver nanolenses. Single molecules of the protein streptavidin were selectively placed in the gap of highest electric field enhancement. Streptavidin labelled with alkyne groups served as model analyte in surface-enhanced Raman scattering (SERS) experiments. By correlated Raman mapping and atomic force microscopy, SERS signals of the alkyne labels of a single streptavidin molecule, from a single silver nanolens, were detected. The discrete, self-similar aggregates of solid silver nanoparticles are promising for plasmonic applications.
KW  - DNA origami
KW  - protein analysis
KW  - SERS
KW  - silver nanoparticles
KW  - streptavidin
Y1  - 2018
U6  - https://doi.org/10.1002/anie.201801748
SN  - 1433-7851
SN  - 1521-3773
VL  - 57
IS  - 25
SP  - 7444
EP  - 7447
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Choi, Youngeun
A1  - Kotthoff, Lisa
A1  - Olejko, Lydia
A1  - Resch-Genger, Ute
A1  - Bald, Ilko
T1  - DNA origami-based forster resonance energy-transfer Nanoarrays and their application as ratiometric sensors
JF  - ACS applied materials & interfaces
N2  - DNA origami nanostructures provide a platform where dye molecules can be arranged with nanoscale accuracy allowing to assemble multiple fluorophores without dye-dye aggregation. Aiming to develop a bright and sensitive ratiometric sensor system, we systematically studied the optical properties of nanoarrays of dyes built on DNA origami platforms using a DNA template that provides a high versatility of label choice at minimum cost. The dyes are arranged at distances, at which they efficiently interact by Forster resonance energy transfer (FRET). To optimize array brightness, the FRET efficiencies between the donor fluorescein (FAM) and the acceptor cyanine 3 were determined for different sizes of the array and for different arrangements of the dye molecules within the array. By utilizing nanoarrays providing optimum FRET efficiency and brightness, we subsequently designed a ratiometric pH nanosensor using coumarin 343 as a pH-inert FRET donor and FAM as a pH responsive acceptor. Our results indicate that the sensitivity of a ratiometric sensor can be improved simply by arranging the dyes into a well-defined array. The dyes used here can be easily replaced by other analyte-responsive dyes, demonstrating the huge potential of DNA nanotechnology for light harvesting, signal enhancement, and sensing schemes in life sciences.
KW  - DNA origami
KW  - nanoarray
KW  - FRET
KW  - ratiometric sensing
KW  - pH sensing
Y1  - 2018
U6  - https://doi.org/10.1021/acsami.8b03585
SN  - 1944-8244
SN  - 1944-8252
VL  - 10
IS  - 27
SP  - 23295
EP  - 23302
PB  - American Chemical Society
CY  - Washington
ER  - 
TY  - JOUR
A1  - Vogel, Stefanie
A1  - Ebel, Kenny
A1  - Schürmann, Robin Mathis
A1  - Heck, Christian
A1  - Meiling, Till
A1  - Milosavljevic, Aleksandar R.
A1  - Giuliani, Alexandre
A1  - Bald, Ilko
T1  - Vacuum-UV and Low-Energy Electron-Induced DNA Strand Breaks
BT  - Influence of the DNA Sequence and Substrate
JF  - ChemPhysChem : a European journal of chemical physics and physical chemistry
N2  - DNA is effectively damaged by radiation, which can on the one hand lead to cancer and is on the other hand directly exploited in the treatment of tumor tissue. DNA strand breaks are already induced by photons having an energy below the ionization energy of DNA. At high photon energies, most of the DNA strand breaks are induced by low-energy secondary electrons. In the present study we quantified photon and electron induced DNA strand breaks in four different 12mer oligonucleotides. They are irradiated directly with 8.44 eV vacuum ultraviolet (VUV) photons and 8.8 eV low energy electrons (LEE). By using Si instead of VUV transparent CaF2 as a substrate the VUV exposure leads to an additional release of LEEs, which have a maximum energy of 3.6 eV and can significantly enhance strand break cross sections. Atomic force microscopy is used to visualize strand breaks on DNA origami platforms and to determine absolute values for the strand break cross sections. Upon irradiation with 8.44 eV photons all the investigated sequences show very similar strand break cross sections in the range of 1.7-2.3x10(-16) cm(2). The strand break cross sections for LEE irradiation at 8.8 eV are one to two orders of magnitude larger than the ones for VUV photons, and a slight sequence dependence is observed. The sequence dependence is even more pronounced for LEEs with energies <3.6 eV. The present results help to assess DNA damage by photons and electrons close to the ionization threshold.
KW  - DNA origami
KW  - DNA radiation damage
KW  - DNA strand breaks
KW  - low-energy electrons
KW  - vacuum-UV radiation
Y1  - 2019
U6  - https://doi.org/10.1002/cphc.201801152
SN  - 1439-4235
SN  - 1439-7641
VL  - 20
IS  - 6
SP  - 823
EP  - 830
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Schürmann, Robin Mathis
A1  - Tsering, Thupten
A1  - Tanzer, Katrin
A1  - Denifl, Stephan
A1  - Kumar, S. V. K.
A1  - Bald, Ilko
T1  - Resonant Formation of Strand Breaks in Sensitized Oligonucleotides Induced by Low-Energy Electrons (0.5-9 eV)
JF  - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition
N2  - Halogenated nucleobases are used as radiosensitizers in cancer radiation therapy, enhancing the reactivity of DNA to secondary low-energy electrons (LEEs). LEEs induce DNA strand breaks at specific energies (resonances) by dissociative electron attachment (DEA). Although halogenated nucleobases show intense DEA resonances at various electron energies in the gas phase, it is inherently difficult to investigate the influence of halogenated nucleobases on the actual DNA strand breakage over the broad range of electron energies at which DEA can take place (<12 eV). By using DNA origami nanostructures, we determined the energy dependence of the strand break cross-section for oligonucleotides modified with 8-bromoadenine ((8Br)A). These results were evaluated against DEA measurements with isolated (8Br)A in the gas phase. Contrary to expectations, the major contribution to strand breaks is from resonances at around 7 eV while resonances at very low energy (<2 eV) have little influence on strand breaks.
KW  - cancer radiation therapy
KW  - dissociative electron attachment
KW  - DNA origami
KW  - DNA radiation damage
KW  - radiosensitizers
Y1  - 2017
U6  - https://doi.org/10.1002/anie.201705504
SN  - 1433-7851
SN  - 1521-3773
VL  - 56
SP  - 10952
EP  - 10955
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Rackwitz, Jenny
A1  - Kopyra, Janina
A1  - Dabkowska, Iwona
A1  - Ebel, Kenny
A1  - Rankovic, MiloS Lj.
A1  - Milosavljevic, Aleksandar R.
A1  - Bald, Ilko
T1  - Sensitizing DNA Towards Low-Energy Electrons with 2-Fluoroadenine
JF  - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition
N2  - 2-Fluoroadenine ((2F)A) is a therapeutic agent, which is suggested for application in cancer radiotherapy. The molecular mechanism of DNA radiation damage can be ascribed to a significant extent to the action of low-energy (<20 eV) electrons (LEEs), which damage DNA by dissociative electron attachment. LEE induced reactions in (2F)A are characterized both isolated in the gas phase and in the condensed phase when it is incorporated into DNA. Information about negative ion resonances and anion-mediated fragmentation reactions is combined with an absolute quantification of DNA strand breaks in (2F)A-containing oligonucleotides upon irradiation with LEEs. The incorporation of (2F)A into DNA results in an enhanced strand breakage. The strand-break cross sections are clearly energy dependent, whereas the strand-break enhancements by (2F)A at 5.5, 10, and 15 eV are very similar. Thus, (2F)A can be considered an effective radiosensitizer operative at a wide range of electron energies.
KW  - ab initio calculations
KW  - dissociative electron attachment
KW  - DNA origami
KW  - DNA radiation damage
KW  - fludarabine
Y1  - 2016
U6  - https://doi.org/10.1002/anie.201603464
SN  - 1433-7851
SN  - 1521-3773
VL  - 55
SP  - 10248
EP  - 10252
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Ebel, Kenny
A1  - Bald, Ilko
T1  - Length and Energy Dependence of Low-Energy Electron-Induced Strand Breaks in Poly(A) DNA
JF  - International Journal of Molecular Sciences
N2  - The DNA in living cells can be effectively damaged by high-energy radiation, which can lead to cell death. Through the ionization of water molecules, highly reactive secondary species such as low-energy electrons (LEEs) with the most probable energy around 10 eV are generated, which are able to induce DNA strand breaks via dissociative electron attachment. Absolute DNA strand break cross sections of specific DNA sequences can be efficiently determined using DNA origami nanostructures as platforms exposing the target sequences towards LEEs. In this paper, we systematically study the effect of the oligonucleotide length on the strand break cross section at various irradiation energies. The present work focuses on poly-adenine sequences (d(A₄), d(A₈), d(A₁₂), d(A₁₆), and d(A₂₀)) irradiated with 5.0, 7.0, 8.4, and 10 eV electrons. Independent of the DNA length, the strand break cross section shows a maximum around 7.0 eV electron energy for all investigated oligonucleotides confirming that strand breakage occurs through the initial formation of negative ion resonances. When going from d(A₄) to d(A₁₆), the strand break cross section increases with oligonucleotide length, but only at 7.0 and 8.4 eV, i.e., close to the maximum of the negative ion resonance, the increase in the strand break cross section with the length is similar to the increase of an estimated geometrical cross section. For d(A₂₀), a markedly lower DNA strand break cross section is observed for all electron energies, which is tentatively ascribed to a conformational change of the dA₂₀ sequence. The results indicate that, although there is a general length dependence of strand break cross sections, individual nucleotides do not contribute independently of the absolute strand break cross section of the whole DNA strand. The absolute quantification of sequence specific strand breaks will help develop a more accurate molecular level understanding of radiation induced DNA damage, which can then be used for optimized risk estimates in cancer radiation therapy.
KW  - DNA origami
KW  - DNA radiation damage
KW  - DNA strand breaks
KW  - low-energy electrons
KW  - sequence dependence
Y1  - 2019
U6  - https://doi.org/10.3390/ijms21010111
SN  - 1422-0067
VL  - 21
IS  - 1
PB  - Molecular Diversity Preservation International
CY  - Basel
ER  - 
TY  - JOUR
A1  - Heck, Christian
A1  - Kanehira, Yuya
A1  - Kneipp, Janina
A1  - Bald, Ilko
T1  - Amorphous Carbon Generation as a Photocatalytic Reaction on DNA-Assembled Gold and Silver Nanostructures
JF  - Molecules
N2  - Background signals from in situ-formed amorphous carbon, despite not being fully understood, are known to be a common issue in few-molecule surface-enhanced Raman scattering (SERS). Here, discrete gold and silver nanoparticle aggregates assembled by DNA origami were used to study the conditions for the formation of amorphous carbon during SERS measurements. Gold and silver dimers were exposed to laser light of varied power densities and wavelengths. Amorphous carbon prevalently formed on silver aggregates and at high power densities. Time-resolved measurements enabled us to follow the formation of amorphous carbon. Silver nanolenses consisting of three differently-sized silver nanoparticles were used to follow the generation of amorphous carbon at the single-nanostructure level. This allowed observation of the many sharp peaks that constitute the broad amorphous carbon signal found in ensemble measurements. In conclusion, we highlight strategies to prevent amorphous carbon formation, especially for DNA-assembled SERS substrates.
KW  - amorphous carbon
KW  - DNA origami
KW  - SERS
KW  - nanoparticle dimers
KW  - nanolenses
Y1  - 2019
U6  - https://doi.org/10.3390/molecules24122324
SN  - 1420-3049
VL  - 24
IS  - 12
PB  - MDPI
CY  - Basel
ER  -