Refine
Year of publication
Document Type
- Article (65)
- Postprint (14)
- Monograph/Edited Volume (2)
- Review (2)
- Other (1)
Is part of the Bibliography
- yes (84)
Keywords
- DNA origami (13)
- DNA radiation damage (7)
- SERS (6)
- dissociative electron attachment (6)
- low-energy electrons (6)
- DNA strand breaks (4)
- atomic force microscopy (3)
- erosion (3)
- nanolenses (3)
- nanoparticle dimers (3)
Institute
DNA nanotechnology holds great promise for the fabrication of novel plasmonic nanostructures and the potential to carry out single-molecule measurements using optical spectroscopy. Here, we demonstrate for the first time that DNA origami nanostructures can be exploited as substrates for surface-enhanced Raman scattering (SERS). Gold nanoparticles (AuNPs) have been arranged into dimers to create intense Raman scattering hot spots in the interparticle gaps. AuNPs (15 nm) covered with TAMRA-modified DNA have been placed at a nominal distance of 25 nm to demonstrate the formation of Raman hot spots. To control the plasmonic coupling between the nanoparticles and thus the field enhancement in the hot spot, the size of AuNPs has been varied from 5 to 28 nm by electroless Au deposition. By the precise positioning of a specific number of TAMRA molecules in these hot spots, SERS with the highest sensitivity down to the few-molecule level is obtained.
Biotin is an essential vitamin that is, on the one hand, relevant for the metabolism, gene expression and in the cellular response to DNA damage and, on the other hand, finds numerous applications in biotechnology. The functionality of biotin is due to two particular sub-structures, the ring structure and the side chain with carboxyl group. The heterocyclic ring structure results in the capability of biotin to form strong intermolecular hydrogen and van der Waals bonds with proteins such as streptavidin, whereas the carboxyl group can be employed to covalently bind biotin to other complex molecules. Dissociative electron attachment (DEA) to biotin results in a decomposition of the ring structure and the carboxyl group, respectively, within resonant features in the energy range 0-12 eV, thereby preventing the capability of biotin for intermolecular binding and covalent coupling to other molecules. Specifically, the fragment anions (M-H)(-), (M-O)(-), C3N2O-, CH2O2-, OCN-, CN-, OH- and O- are observed, and exemplarily the DEA cross section of OCN- formation is determined to be 3 x 10(-19) cm(2). To study the response of biotin to electrons within a complex condensed environment, we use the DNA origami technique and determine a dissociation yield of (1.1 +/- 0.2) x 10(-14) cm(2) at 18 eV electron energy, which represents the most relevant energy for biomolecular damage induced by secondary electrons. The present results thus have important implications for the use of biotin as a label in radiation experiments.
Here, we study the metastable decay of 5'-d(TTGCTT) in the presence of 0-6 alkaline metal ions (Li+, Na+, K+, Rb+) and 0-3 alkaline earth metal ions (Mg2+ and Ca2+), which replace the corresponding number of protons in the oligonucleotide. We find that all ions studied here stabilize the oligonucleotide with respect to simple 3'-C-O backbone cleavage, but at the same time these metal ions promote a central oligonucleotide deletion accompanied by a concomitant recombination of the terminal d(TT) groups. We find that the quenching of the 3'-C-O backbone cleavage is not ion specific, since it is due to the removal of the phosphate protons upon replacement with the respective metal ions. The central nucleotide deletion competes with the 3'-C-O backbone cleavage channels and is thus promoted through the replacement of the exchangeable protons against metal ions. However, with increasing positive charge density of the metal ions the yield of the central nucleotide deletion further increases. We attribute this effect to the necessity of sufficient proximity of the terminal d(TT) group to allow for their recombination on this reaction path. Hence, the formation of a reactive conformer is mediated by the metal ions.
DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.
On the role of fluoro-substituted nucleosides in DNA radiosensitization for tumor radiation therapy
(2014)
DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.
On the role of fluoro-substituted nucleosides in DNA radiosensitization for tumor radiation therapy
(2014)
Gemcitabine (2′,2′-difluorocytidine) is a well-known radiosensitizer routinely applied in concomitant chemoradiotherapy. During irradiation of biological media with high-energy radiation secondary low-energy (<10 eV) electrons are produced that can directly induce chemical bond breakage in DNA by dissociative electron attachment (DEA). Here, we investigate and compare DEA to the three molecules 2′-deoxycytidine, 2′-deoxy-5-fluorocytidine, and gemcitabine. Fluorination at specific molecular sites, i.e., nucleobase or sugar moiety, is found to control electron attachment and subsequent dissociation pathways. The presence of two fluorine atoms at the sugar ring results in more efficient electron attachment to the sugar moiety and subsequent bond cleavage. For the formation of the dehydrogenated nucleobase anion, we obtain an enhancement factor of 2.8 upon fluorination of the sugar, whereas the enhancement factor is 5.5 when the nucleobase is fluorinated. The observed fragmentation reactions suggest enhanced DNA strand breakage induced by secondary electrons when gemcitabine is incorporated into DNA.
On the role of fluoro-substituted nucleosides in DNA radiosensitization for tumor radiation therapy
(2014)
Gemcitabine (2′,2′-difluorocytidine) is a well-known radiosensitizer routinely applied in concomitant chemoradiotherapy. During irradiation of biological media with high-energy radiation secondary low-energy (<10 eV) electrons are produced that can directly induce chemical bond breakage in DNA by dissociative electron attachment (DEA). Here, we investigate and compare DEA to the three molecules 2′-deoxycytidine, 2′-deoxy-5-fluorocytidine, and gemcitabine. Fluorination at specific molecular sites, i.e., nucleobase or sugar moiety, is found to control electron attachment and subsequent dissociation pathways. The presence of two fluorine atoms at the sugar ring results in more efficient electron attachment to the sugar moiety and subsequent bond cleavage. For the formation of the dehydrogenated nucleobase anion, we obtain an enhancement factor of 2.8 upon fluorination of the sugar, whereas the enhancement factor is 5.5 when the nucleobase is fluorinated. The observed fragmentation reactions suggest enhanced DNA strand breakage induced by secondary electrons when gemcitabine is incorporated into DNA.
New V-shaped non-centrosymmetric dyes, possessing a strongly electron-deficient azacyanine core, have been synthesized based on a straightforward two-step approach. The key step in this synthesis involves palladium-catalysed cross-coupling of dibromo-N,N′-methylene-2,2′-azapyridinocyanines with arylacetylenes. The resulting strongly polarized π-expanded heterocycles exhibit green to orange fluorescence and they strongly respond to changes in solvent polarity. We demonstrate that differently electron-donating peripheral groups have a significant influence on the internal charge transfer, hence on the solvent effect and fluorescence quantum yield. TD-DFT calculations confirm that, in contrast to the previously studied bis(styryl)azacyanines, the proximity of S1 and T2 states calculated for compounds bearing two 4-N,N-dimethylaminophenylethynyl moieties establishes good conditions for efficient intersystem crossing and is responsible for its low fluorescence quantum yield. Non-linear properties have also been determined for new azacyanines and the results show that depending on peripheral groups, the synthesized dyes exhibit small to large two-photon absorption cross sections reaching 4000 GM.
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. Here, we demonstrate that DNA origami substrates 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.
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 lowest-energy photons able to induce DNA strand breaks. Oligonudeotide 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.
In this study, 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.
DNA origami nanostructures are a versatile tool to arrange metal nanostructures and other chemical entities with nanometer precision. In this way gold nanoparticle dimers with defined distance can be constructed, which can be exploited as novel substrates for surface enhanced Raman scattering (SERS). We have optimized the size, composition and arrangement of Au/Ag nanoparticles to create intense SERS hot spots, with Raman enhancement up to 1010, which is sufficient to detect single molecules by Raman scattering. This is demonstrated using single dye molecules (TAMRA and Cy3) placed into the center of the nanoparticle dimers. In conjunction with the DNA origami nanostructures novel SERS substrates are created, which can in the future be applied to the SERS analysis of more complex biomolecular targets, whose position and conformation within the SERS hot spot can be precisely controlled.
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.
The excitation of localized surface plasmons in noble metal nanoparticles (NPs) results in different nanoscale effects such as electric field enhancement, the generation of hot electrons and a temperature increase close to the NP surface. These effects are typically exploited in diverse fields such as surface-enhanced Raman scattering (SERS), NP catalysis and photothermal therapy (PTT). Halogenated nucleobases are applied as radiosensitizers in conventional radiation cancer therapy due to their high reactivity towards secondary electrons. Here, we use SERS to study the transformation of 8-bromoadenine (8BrA) into adenine on the surface of Au and AgNPs upon irradiation with a low-power continuous wave laser at 532, 633 and 785 nm, respectively. The dissociation of 8BrA is ascribed to a hot-electron transfer reaction and the underlying kinetics are carefully explored. The reaction proceeds within seconds or even milliseconds. Similar dissociation reactions might also occur with other electrophilic molecules, which must be considered in the interpretation of respective SERS spectra. Furthermore, we suggest that hot-electron transfer induced dissociation of radiosensitizers such as 8BrA can be applied in the future in PTT to enhance the damage of tumor tissue upon irradiation.
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.
In this study, 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.
A combination of three innovative materials within one hybrid structure to explore the synergistic interaction of their individual properties is presented. 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 efficient fluorescence 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.