Optical Spectroscopy and Chemical Imaging
In our group we study the interaction of radiation with nanostructures. More specifically, our research encompasses the following topics: Nanophotonics, Nanoplasmonics, Nanoparticles (preparation, characterization and photochemistry) and DNA radiation damage probed by DNA nanotechnology.
Highly-selective FRET based sensing
DNA origami nanostructures are a versatile tool that can be used to arrange functionalities with high local control to study molecular processes at a single-molecule level. They can be used to suppress the formation of specific guanine (G) quadruplex structures from telomeric DNA. The folding of telomeres into G-quadruplex structures in the presence of monovalent cations (e.g. Na+ and K+) is currently used for the detection of K+ ions, however, with insufficient selectivity towards Na+. By means of FRET between two suitable dyes attached to the 3'- and 5'-ends of telomeric DNA we demonstrate that the formation of G-quadruplexes on DNA origami templates in the presence of sodium ions is suppressed due to steric hindrance. Hence, telomeric DNA attached to DNA origami structures represents a highly sensitive and selective detection tool for potassium ions even in the presence of high concentrations of sodium ions.
L. Olejko, P. Cywinski, I. Bald, Angew. Chem. Int. Ed. 2015, 54, 673.
Switchable photonic wires
The folding of single-stranded telomeric DNA into guanine (G) quadruplexes is a conformational change that plays a major role in sensing and drug targeting. The telomeric DNA can be placed on DNA origami nanostructures to make the folding process extremely selective for K+ ions even in the presence of high Na+ concentrations. Here, we demonstrate that the K+-selective G-quadruplex formation is reversible when using a cryptand to remove K+ from the G-quadruplex. We present a full characterization of the reversible switching between single-stranded telomeric DNA and G-quadruplex structures using Förster resonance energy transfer (FRET) between the dyes fluorescein (FAM) and cyanine3 (Cy3). When attached to the DNA origami platform, the G-quadruplex switch can be incorporated into more complex photonic networks, which is demonstrated for a three-color and a four-color FRET cascade from FAM over Cy3 and Cy5 to IRDye700 with G-quadruplex-Cy3 acting as a switchable transmitter.
L. Olejko, P. J. Cywiński, I. Bald, Nanoscale 2016, 8, 10339.
Surface-enhanced Raman scattering
DNA origami is a fascinating technique that allows for the precise arrangement of nanoparticles, fluorescent dyes, specific DNA structures (such as aptamers) and proteins into well-defined arrays. Consequently, DNA origami nanostructures have been used to fabricate a variety of plasmonic nanostructures by the controlled arrangement of metallic nanoparticles. Surface-enhanced Raman scattering (SERS) is one of the most promising analytical techniques for bioanalytics, capable of single-molecule detection and true multiplexing. However, the fabrication of efficient SERS substrates remains one of the most difficult challenges in SERS, since SERS relies on the formation of hot spots within Au or Ag nanoparticle aggregates and the placement of analyte molecules specifically into the hot spots.
We use DNA origami nanostructures to fabricate intense Raman scattering hot spots between two Au nanoparticles and to place target molecules precisely into these hot spots to enable highly sensitive detection of analyte molecules down to the single-molecule level.
J. Prinz, B. Schreiber, L. Olejko, J. Oertel, J. Rackwitz, A. Keller, I. Bald, J. Phys. Chem. Lett. 2013, 4, 4140-4145.
J. Prinz, C. Heck, L. Ellerik, V. Merk, I. Bald, Nanoscale 2016, 8, 5612.
Hybrid structures of gold nanoparticles and graphene
The unique electronic, mechanical, and thermal properties of graphene are combined with the plasmonic properties of gold nanoparticle (AuNP) dimers, which are assembled using DNA origami nanostructures. This novel hybrid structure is characterized by means of correlated atomic force microscopy and surface-enhanced Raman scattering (SERS). It is demonstrated that strong interactions between graphene and AuNPs result in superior SERS performance of the hybrid structure compared to their individual components. This is particularly evident in effi cient fl uorescence quenching, reduced background, and a decrease of the photobleaching rate up to one order of magnitude. The versatility of DNA origami structures to serve as interface for complex and precise arrangements of nanoparticles and other functional entities provides the basis to further exploit the potential of the here presented DNA origami–AuNP dimer–graphene hybrid structures.
J. Prinz, A. Matković, J. Pešić, R. Gajić, I. Bald, Small 2016, 12, 5458.
Nanoparticles – preparation, characterization and photochemistry
Luminescent carbon nanoparticles
A new reliable, economic, and environmentally-friendly one-step synthesis is established to obtain carbon nanodots (CNDs) with well-defined and reproducible photoluminescence (PL) properties via the microwave-assisted hydrothermal treatment of starch and Tris-acetate-EDTA (TAE) buffer as carbon sources. Three kinds of CNDs are prepared using different sets of above mentioned starting materials. The as-synthesized CNDs: C-CND (starch only), N-CND 1 (starch in TAE) and N-CND 2 (TAE only) exhibit highly homogenous PL and are ready to use without need for further purification. The CNDs are stable over a long period of time (>1 year) either in solution or as freeze-dried powder. Depending on starting material, CNDs with PL quantum yield (PLQY) ranging from less than 1% up to
28% are obtained. The influence of the precursor concentration, reaction time and type of additives on the optical properties (UV-Vis absorption, PL emission spectrum and PLQY) is carefully investigated, providing insight into the chemical processes that occur during CND formation. Remarkably, upon freeze-drying the initially brown CND-solution turns into a non-fluorescent white/slightly brown powder which recovers PL in aqueous solution and can potentially be applied as fluorescent marker in bio-imaging, as a reduction agent or as a photocatalyst.
T. T. Meiling, P. J. Cywiński, I. Bald, Scientific Reports 2016, 6, 28557.
Electron-transfer induced chemical reactions
Different approaches have been proposed to treat cancer cells using gold nanoparticles (AuNPs) in combination with radiation ranging from infrared
lasers to high-energy ion beams. Here we study the decomposition of the DNA/RNA nucleobases thymine (T) and uracil (U) and the well-known radiosensitizer
5-bromouracil (BrU) in close vicinity to AuNPs, which are irradiated with a nanosecond pulsed laser (532 nm) matching the surface plasmon resonance of the
AuNPs. The induced damage of nucleobases is analyzed by UV−vis absorption spectroscopy and surface-enhanced Raman scattering (SERS). A clear DNA
damage is observed upon laser irradiation. SERS spectra indicate the fragmentation of the aromatic ring system of T and U as the dominant form of damage, whereas with BrU mainly the cleavage of the Br−C bond and formation of Br− ions is observed. This is accompanied by a partial transformation of BrU into U. The
observed damage is at least partly ascribed to the intermediate formation of low energy electrons from the laser-excited AuNPs and subsequent dissociative
electron attachment to T, U, and BrU. These reactions represent basic DNA damage pathways occurring on the one hand in plasmon-assisted cancer therapy and on the other hand in conventional cancer radiation therapy using AuNPs as sensitizing agents.
R. Schürmann, I. Bald, J. Phys. Chem. C 2016, 120, 3001.
DNA radiation damage probed by DNA nanotechnology
Low-energy electron induced reactions
In cancer radiation therapy predetermined doses of high-energy radiation are administered to reduce tumours. More than 60 % of the patients diagnosed with cancer are treated with radiation therapy. A detailed understanding of the fundamental mechanisms of DNA radiation damage is of utmost importance with respect to the question of how the damage can be increased by therapeutics used in radiation therapy. On a molecular level a large extent of the cell damage is ascribed to the production of secondary low-energy electrons along the high-energy radiation track that induce DNA single and double strand breaks. The physico-chemical mechanisms of DNA radiation damage can currently only be described for idealized small model systems (such as individual nucleobases) and it is not known, which DNA nucleotide sequences and higher-order DNA structures are most susceptible to damage. Very recent ground-breaking advances in DNA nanotechnology allow for the first time the detailed study of the interaction of radiation with complex DNA structures. With an innovative DNA origami technique it is possible to map the radiation damage of different DNA target structures with unprecedented efficiency and accuracy. A two-dimensional DNA origami template functionalized with protruding well-defined DNA structures will be exposed to a beam of low-energy electrons. The strand break yield of different nucleotide sequences will then be determined as a function of the electron energy using atomic force microscopy. The final goal is to identify the DNA target structures that can be most efficiently sensitized to low-energy electrons by radiosensitizers.
J. Rackwitz, J. Kopyra, I. Dabkowska, K. Ebel, M. Lj. Rankovic, A. R. Milosavljevic, I. Bald, Angew. Chem. Int. Ed. 2016, 55, 10248.
A. Keller, J. Rackwitz, E. Cauët, J. Liévin, T. Körzdörfer, A. Rotaru, K.V. Gothelf, F. Besenbacher, I. Bald, Sci. Rep. 2014, 4, 7391.
A. Keller, I. Bald, A. Rotaru, E. Cauet, K.V. Gothelf, F. Besenbacher, ACS Nano 2012, 6, 4392-4399.
VUV induced reactions
We have characterized ultraviolet (UV) photon-induced DNA strand break processes by determination of absolute cross sections for
photoabsorption and for sequence-specific DNA single strand breakage induced by photons in an energy range from 6.50 to 8.94 eV. These represent the lowestenergy photons able to induce DNA strand breaks. Oligonucleotide targets are immobilized on a UV transparent substrate in controlled quantities through
attachment to DNA origami templates. Photon-induced dissociation of single DNA strands is visualized and quantified using atomic force microscopy. The
obtained quantum yields for strand breakage vary between 0.06 and 0.5, indicating highly efficient DNA strand breakage by UV photons, which is clearly
dependent on the photon energy. Above the ionization threshold strand breakage becomes clearly the dominant form of DNA radiation damage, which is then also
dependent on the nucleotide sequence.
S. Vogel, J. Rackwitz, R. Schürman, J. Prinz, A. R. Milosavljević, M. Réfrégiers, A. Giuliani, I. Bald, J. Phys. Chem. Lett. 2015, 6, 4589.
Funded by the German Research Foundation and the Marie-Curie program of the European Commission.