Refine
Year of publication
Document Type
- Preprint (638)
- Article (374)
- Conference Proceeding (1)
Language
- English (1013) (remove)
Has Fulltext
- yes (1013)
Is part of the Bibliography
- no (1013)
Keywords
- Heavy Ion Experiments (20)
- Hadron-Hadron Scattering (11)
- Hadron-Hadron scattering (experiments) (11)
- Heavy-ion collision (6)
- LHC (6)
- photochemistry (6)
- ALICE experiment (4)
- Collective Flow (4)
- Jets (4)
- Quark-Gluon Plasma (4)
- oligonucleotides (4)
- photolabile protecting groups (4)
- DNA (3)
- Heavy Ions (3)
- Jets and Jet Substructure (3)
- pp collisions (3)
- Baird's rule (2)
- Beauty production (2)
- Charm physics (2)
- Experimental nuclear physics (2)
- Experimental particle physics (2)
- Heavy Quark Production (2)
- Lepton-Nucleon Scattering (experiments) (2)
- NMR spectroscopy (2)
- Particle Correlations and Fluctuations (2)
- Particle and resonance production (2)
- Particle correlations and fluctuations (2)
- Pb–Pb collisions (2)
- QCD (2)
- Single electrons (2)
- azo compounds (2)
- click chemistry (2)
- computational chemistry (2)
- excited state aromaticity (2)
- substituent effects (2)
- ALICE (1)
- ALICE detector (1)
- ATTO 390 (1)
- Anti-nuclei (1)
- Boosted Jets (1)
- Centrality Class (1)
- Centrality Selection (1)
- Collective Flow, (1)
- Comparison with QCD (1)
- DgkA (1)
- EPR (1)
- Electron-pion identification (1)
- Electroweak interaction (1)
- Elliptic flow (1)
- Fibre/foam sandwich radiator (1)
- Hadron production (1)
- Hadron-Hadron Scattering Heavy (1)
- Hadron-hadron interactions (1)
- Hard Scattering (1)
- Heavy Ion Experiment (1)
- Heavy flavor production (1)
- Heavy flavour production (1)
- Heavy ions (1)
- Heavy-flavour decay muons (1)
- Heavy-flavour production (1)
- Inclusive spectra (1)
- Invariant Mass Distribution (1)
- Ionisation energy loss (1)
- Jet Physics (1)
- Jet Substructure (1)
- Kinases (1)
- Material budget (1)
- Mid-rapidity (1)
- Minimum Bias (1)
- Molecular conformation (1)
- Monte Carlo (1)
- Multi-Parton Interactions (1)
- Multi-strange baryons (1)
- Multi-wire proportional drift chamber (1)
- Neural network (1)
- PELDOR/DEER (1)
- Particle and Resonance Production (1)
- Production Cross Section (1)
- Properties of Hadrons (1)
- Proton–proton (1)
- Quark Deconfinement (1)
- Quark Gluon Plasma (1)
- Quark Production (1)
- Quark gluon plasma (1)
- Quarkonium (1)
- RNA (1)
- RNA synthesis (1)
- Rapidity Range (1)
- Relativistic heavy ion physics (1)
- Relativistic heavy-ion collisions (1)
- Resolution Parameter (1)
- Single muons (1)
- Solid-state NMR (1)
- Systematic Uncertainty (1)
- TICT (1)
- TR (1)
- Time Projection Chamber (1)
- Tracking (1)
- Transition radiation detector (1)
- Trigger (1)
- Vector Boson Production (1)
- Xenon-based gas mixture (1)
- anticoagulants (1)
- aptamer (1)
- atropisomers (1)
- bioconjugation (1)
- blood coagulation (1)
- caged ATP (1)
- caged diacylglycerol (1)
- charge transfer (1)
- chemoenzymatic synthesis (1)
- circular dichroism (1)
- coagulation process (1)
- coumarin (1)
- coumarin-4-ylmethyl (1)
- cyanines (1)
- dE/dx (1)
- detector (1)
- dsRNA (1)
- energy barriers (1)
- enzymes (1)
- experimental results (1)
- fluorescence (1)
- fluorophore (1)
- fulgide (1)
- green gap (1)
- heavy ion experiments (1)
- hotochromism (1)
- ligases (1)
- light control (1)
- nucleobases (1)
- oligonucleotide (1)
- p-hydroxyphenacyl (1)
- photo-tethering (1)
- photoacid (1)
- photoacid generator (1)
- photocage (1)
- photocaging (1)
- photolysis (1)
- photopharmacology (1)
- photoswitch (1)
- phototherapeutic window (1)
- proton transfer (1)
- quark gluon plasma (1)
- red light (1)
- solid-phase synthesis (1)
- solid-state NMR (1)
- spectra (1)
- spiro compounds (1)
- stability (1)
- stacking (1)
- thrombin (1)
- ultrafast spectroscopy (1)
- water solubility (1)
Institute
- Physik (989)
- Frankfurt Institute for Advanced Studies (FIAS) (918)
- Informatik (884)
- Biochemie und Chemie (13)
- Biochemie, Chemie und Pharmazie (11)
- Zentrum für Biomolekulare Magnetische Resonanz (BMRZ) (4)
- Biowissenschaften (3)
- Exzellenzcluster Makromolekulare Komplexe (3)
- Informatik und Mathematik (3)
- Hochschulrechenzentrum (2)
Light‐induced activation of biomolecules by uncaging of photolabile protection groups has found many applications for triggering biochemical reactions with minimal perturbations directly within cells. Such an approach might also offer unique advantages for solid‐state NMR experiments on membrane proteins for initiating reactions within or at the membrane directly within the closed MAS rotor. Herein, we demonstrate that the integral membrane protein E. coli diacylglycerol kinase (DgkA), which catalyzes the phosphorylation of diacylglycerol, can be controlled by light under MAS‐NMR conditions. Uncaging of NPE‐ATP or of lipid substrate NPE‐DOG by in situ illumination triggers its enzymatic activity, which can be monitored by real‐time 31P‐MAS NMR. This proof‐of‐concept illustrates that combining MAS‐NMR with uncaging strategies and illumination methods offers new possibilities for controlling biochemical reactions at or within lipid bilayers.
Photolabile protecting groups are widely used to trigger oligonucleotide activity. The ON/OFF‐amplitude is a critical parameter. An experimental setup has been developed to identify protecting group derivatives with superior caging properties. Bulky rests are attached to the cage moiety via Cu‐catalyzed azide–alkyne cycloaddition post‐synthetically on DNA. Interestingly, the decrease in melting temperature upon introducing o‐nitrobenzyl‐caged (NPBY‐) and diethylaminocoumarin‐cages (DEACM‐) in DNA duplexes reaches a limiting value. NMR spectroscopy was used to characterize individual base‐pair stabilities and determine experimental structures of a selected number of photocaged DNA molecules. The experimental structures agree well with structures predicted by MD simulations. Combined, the structural data indicate that once a sterically demanding group is added to generate a tri‐substituted carbon, the sterically less demanding cage moiety points towards the neighboring nucleoside and the bulkier substituents remain in the major groove.
We developed three bathochromic, green-light activatable, photolabile protecting groups based on a nitrodibenzofuran (NDBF) core with D-π-A push–pull structures. Variation of donor substituents (D) at the favored ring position enabled us to observe their impact on the photolysis quantum yields. Comparing our new azetidinyl-NDBF (Az-NDBF) photolabile protecting group with our earlier published DMA-NDBF, we obtained insight into its excitation-specific photochemistry. While the “two-photon-only” cage DMA-NDBF was inert against one-photon excitation (1PE) in the visible spectral range, we were able to efficiently release glutamic acid from azetidinyl-NDBF with irradiation at 420 and 530 nm. Thus, a minimal change (a cyclization adding only one carbon atom) resulted in a drastically changed photochemical behavior, which enables photolysis in the green part of the spectrum.
Photoactivatable compounds for example photoswitches or photolabile protecting groups (PPGs, photocages) for spatiotemporal light control, play a crucial role in different areas of research. For each application, parameters such as the absorption spectrum, solubility in the respective media and/or photochemical quantum yields for several competing processes need to be optimized. The design of new photochemical tools therefore remains an important task. In this study, we exploited the concept of excited-state-aromaticity, first described by N. Colin Baird in 1971, to investigate a new class of photocages, based on cyclic, ground-state-antiaromatic systems. Several thio- and nitrogen-functionalized compounds were synthesized, photochemically characterized and further optimized, supported by quantum chemical calculations. After choosing the optimal scaffold, which shows an excellent uncaging quantum yield of 28 %, we achieved a bathochromic shift of over 100 nm, resulting in a robust, well accessible, visible light absorbing, compact new photocage with a clean photoreaction and a high quantum product (ϵ⋅Φ) of 893 M−1 cm−1 at 405 nm.
Photoactivatable compounds for example photoswitches or photolabile protecting groups (PPGs, photocages) for spatiotemporal light control, play a crucial role in different areas of research. For each application, parameters such as the absorption spectrum, solubility in the respective media and/or photochemical quantum yields for several competing processes need to be optimized. The design of new photochemical tools therefore remains an important task. In this study, we exploited the concept of excited-state-aromaticity, first described by N. Colin Baird in 1971, to investigate a new class of photocages, based on cyclic, ground-state-antiaromatic systems. Several thio- and nitrogen-functionalized compounds were synthesized, photochemically characterized and further optimized, supported by quantum chemical calculations. After choosing the optimal scaffold, which shows an excellent uncaging quantum yield of 28 %, we achieved a bathochromic shift of over 100 nm, resulting in a robust, well accessible, visible light absorbing, compact new photocage with a clean photoreaction and a high quantum product (ϵ⋅Φ) of 893 M−1 cm−1 at 405 nm.
Recently, photochromic derivatives of nucleobases have drawn attention for regulating oligonucleotide hybridization with light for photopharmacological applications. The nucleobase moiety provides attractive interaction for hybridization, whereas the photochromic moiety can alter the interaction upon irradiation due to conformational changes. Herein we report the synthesis of 2‐phenyldiazenyl‐substituted 2’‐deoxyadenosine (dAAzo) and 2’‐deoxyguanosine (dGAzo) and investigate their influence in a DNA context by UV/Vis absorption, fluorescence and CD spectroscopies. For comparison, the literature‐known azobenzene C‐nucleoside DNAzo was used as a reference system. It could be shown that photochromic purines improve overall hybridization affinity compared to azobenzene C‐nucleosides. In particular, 2’‐deoxyadenosine analogue dAAzo increases melting temperatures by 7.5 °C in the favored trans state with 86 % of the switching efficiency of the reference system.
Herein, we present a multi-cycle chemoenzymatic synthesis of modified RNA with simplified solid-phase handling to overcome size limitations of RNA synthesis. It combines the advantages of classical chemical solid-phase synthesis and enzymatic synthesis using magnetic streptavidin beads and biotinylated RNA. Successful introduction of light-controllable RNA nucleotides into the tRNAMet sequence was confirmed by gel electrophoresis and mass spectrometry. The methods tolerate modifications in the RNA phosphodiester backbone and allow introductions of photocaged and photoswitchable nucleotides as well as photocleavable strand breaks and fluorophores.
PELDOR (pulse electron-electron double resonance) is an established method to study intramolecular distances and can give evidence for conformational changes and flexibilities. However, it can also be used to study intermolecular interactions as for example oligerimization. Here, we used PELDOR to study the ‘end-to-end’ stacking of small double stranded (ds)RNAs. For this study, the dsRNA molecules were only singly labelled with the spin label TPA to avoid multi-spin effects and to measure only the intermolecular stacking interactions. It can be shown that small dsRNAs tend to assemble to rod-like structures due to π-π-interactions between the base pairs at the end of the strands. On the one hand, these interactions can influence or complicate measurements aimed at the determining of the structure and dynamics of the dsRNA molecule itself. On the other hand, it can be interesting to study such intermolecular stacking interactions in more detail, as for example their dependence on ion concentration. We quantitatively determined the stacking probability as a function of the monovalent NaCl salt and the dsRNA concentration. From this data the dissociation constant Kd was deduced and found to depend on the ratio between the NaCl salt and dsRNA concentrations. Additionally, the distances and distance distributions obtained predict a model for the stacking geometry of dsRNAs. Introducing a nucleotide overhangs at one end of the dsRNA molecule restricts the stacking to the other end, leading only to dimer formations. Introducing such an overhang at both ends of the dsRNA molecule fully suppresses stacking, as we could demonstrate by PELDOR experiments quantitatively.
Oligonucleotide-based therapeutics have made rapid progress in clinical treatment of a variety of disease indications. Since most therapeutic oligonucleotides serve more than just one function and tend to have a prolonged lifetime, spatio-temporal control of these functions would be desirable. Photoswitches like azobenzene have proven themselves as useful tools in this matter. Upon irradiation, the photoisomerization of the azobenzene moiety causes destabilization in adjacent base pairs, leading to a decreased hybridization affinity. Since the way the azobenzene is incorporated in the oligonucleotide is of utmost importance, we synthesized locked azobenzene C-nucleosides and compared their photocontrol capabilities to established azobenzene C-nucleosides in oligonucleotide test-sequences by means of fluorescence-, UV/Vis-, and CD-spectroscopy.
Electronic circular dichroism unravels atropisomers of a broadly absorbing fulgide derivative
(2022)
We prepared and studied six atropisomers with different chiroptical properties emerging from a single, robust, broadly-absorbing fulgide photoswitch. After separation of the different atropisomers via HPLC on a chiral column, their isomerization processes at room temperature and the energy barriers of the different species were investigated in detail using spectroscopic and theoretical methods.
We synthesized two green-light activatable 5’-caps for oligonucleotides based on the BODIPY and coumarin scaffold. Both bear an alkyne functionality allowing their use in numerous biological applications. They were successfully incorporated in oligonucleotides via solid-phase synthesis. Copper-catalyzed alkyne-azide cycloaddition (CuAAC) using a bisazide photo-tether gave cyclic oligonucleotides that could be relinearized by activation with green light and were shown to exhibit high stability against exonucleases. Chemical ligation as another example for bioconjugation yielded oligonucleotides with an internal strand break site. Irradiation at 530 nm or 565 nm resulted in complete photolysis of both caging groups.
In the development of photolabile protecting groups, it is of high interest to selectively modify photochemical properties with structural changes as simple as possible. In this work, knowledge of fluorophore optimization was adopted and used to design new coumarin- based photocages. Photolysis efficiency was selectively modulated by inactivating competitive decay channels, such as twisted intramolecular charge transfer (TICT) or hydrogen-bonding, and the photolytic release of the neurotransmitter serotonin was demonstrated. Structural modifications inspired by the fluorophore ATTO 390 led to a significant increase in the uncaging cross section that can be further improved by the simple addition of a double bond. Ultrafast transient absorption spectroscopy gave insights into the underlying solvent-dependent photophysical dynamics. The chromophores presented here are excellently suited as new photocages in the visible wavelength range due to their simple synthesis and their superior photochemical properties.
Decades of work have demonstrated that messenger RNAs (mRNAs) are localized and translated within neuronal dendrites and axons to provide proteins for remodeling and maintaining growth cones or synapses. It remains unknown, however, whether specific forms of plasticity differentially regulate the dynamics and translation of individual mRNA species. To address this, we targeted three individual synaptically localized mRNAs, CamkIIa, β-actin, Psd95, and used molecular beacons to track endogenous mRNA movements. We used reporters and CRISPR/Cas9 gene editing to track mRNA translation in cultured neurons. We found alterations in mRNA dynamic properties occurred during two forms of synaptic plasticity, long-term potentiation (cLTP) and depression (mGluR-LTD). Changes in mRNA dynamics following either form of plasticity resulted in an enrichment of mRNA in the vicinity of dendritic spines. Both the reporters and tagging of endogenous proteins revealed the transcript-specific stimulation of protein synthesis following cLTP or mGluR-LTD. As such, the plasticity-induced enrichment of mRNA near synapses could be uncoupled from its translational status. The enrichment of mRNA in the proximity of spines allows for localized signaling pathways to decode plasticity milieus and stimulate a specific translational profile, resulting in a customized remodeling of the synaptic proteome.