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The field of epigenetics describes the relationship between genotype and phenotype, by regulating gene expression without changing the canonical base sequence of DNA. It deals with molecular genomic information that is encoded by a rich repertoire of chemical modifications and molecular interactions. This regulation involves DNA, RNA and proteins that are enzymatically tagged with small molecular groups that alter their physical and chemical properties. It is now clear that epigenetic alterations are involved in development and disease, and thus, are the focus of intensive research. The ability to record epigenetic changes and quantify them in rare medical samples is critical for next generation diagnostics. Optical detection offers the ultimate single-molecule sensitivity and the potential for spectral multiplexing. Here we review recent progress in ultrasensitive optical detection of DNA and histone modifications.
One of the major challenges in chemical synthesis is to trigger and control a specific reaction route leading to a specific final product, while side products are avoided. Methodologies based on resonant processes at the molecular level, for example, photochemistry, offer the possibility of inducing selective reactions. Electrons at energies below the molecular ionization potential (<10 eV) are known to dissociate molecules via resonant processes with higher cross sections and specificity than photons. Here we show that even subexcitation electrons with energies as low as 1 eV produce ethylene and acetylene from dimethyl sulfide in competing reactions. However, the production of ethylene can specifically be targeted by controlling the energy of electrons (∼3 to 4 eV). Finally, pure ethylene is selectively desorbed by heating the substrate from 90 to 105 K. Beyond the synthesis of these versatile hydrocarbons for various industrial applications from a biogenic sulfur compound, our findings demonstrate the feasibility of electron-induced selective chemistry applicable on the nanoscale.
The DNA origami technique has great potential for the development of brighter and more sensitive reporters for fluorescence based detection schemes such as a microbead-based assay in diagnostic applications. The nanostructures can be programmed to include multiple dye molecules to enhance the measured signal as well as multiple probe strands to increase the binding strength of the target oligonucleotide to these nanostructures. Here we present a proof-of-concept study to quantify short oligonucleotides by developing a novel DNA origami based reporter system, combined with planar microbead assays. Analysis of the assays using the VideoScan digital imaging platform showed DNA origami to be a more suitable reporter candidate for quantification of the target oligonucleotides at lower concentrations than a conventional reporter that consists of one dye molecule attached to a single stranded DNA. Efforts have been made to conduct multiplexed analysis of different targets as well as to enhance fluorescence signals obtained from the reporters. We therefore believe that the quantification of short oligonucleotides that exist in low copy numbers is achieved in a better way with the DNA origami nanostructures as reporters.
3-Bromopyruvic acid (3BP) is a potential anticancer drug, the action of which on cellular metabolism is not yet entirely clear. The presence of a bromine atom suggests that it is also reactive towards low-energy electrons, which are produced in large quantities during tumour Radiation therapy. Detailed knowledge of the interaction of 3BP with secondary electrons is a prerequisite to gain a complete picture of the effects of 3BP in different forms of Cancer therapy. Herein, dissociative electron attachment (DEA) to 3BP in the gas phase has been studied both experimentally by using a crossed-beam setup and theoretically through scattering and quantum chemical calculations. These results are complemented by a vacuum ultraviolet absorption spectrum.
The main fragmentation channel is the formation of Br@ close to 0 eV and within several resonant features at 1.9 and 3–8 eV. At low electron energies, Br@ formation proceeds through s* and p* shape resonances, and at higher energies through core-excited resonances. It is found that the electron-capture cross-section is clearly increased compared with that of non-brominated pyruvic acid, but, at the same time, fragmentation reactions through DEA are significantly altered as well. The 3BP transient negative ion is subject to a lower number of fragmentation reactions than those of pyruvic acid, which indicates that 3BP could indeed act by modifying the electron-transport chains within oxidative phosphorylation. It could also act as a radio-sensitiser.
Photodynamic therapy (PDT) used for treating cancer relies on the generation of highly reactive oxygen species, for example, singlet oxygen 1O2, by light-induced excitation of a photosensitizer (PS) in the presence of molecular oxygen, inducing DNA damage in close proximity of the PS. Although many precious metal complexes have been explored as PS for PDT and received clinical approval, only recently, the potential of photoactive complexes of nonnoble metals as PS has been discovered. Using the DNA origami technology that can absolutely quantify DNA strand break cross sections, we assessed the potential of the luminescent transition metal complex [Cr(ddpd)2]3+ (ddpd=N,N’-dimethyl-N,N’-dipyridine-2-ylpyridine-2,6-diamine) to damage DNA in an air-saturated aqueous environment upon UV/Vis illumination. The quantum yield for strand breakage, that is, the ratio of DNA strand breaks to the number of absorbed photons, was determined to 1–4%, indicating efficient transformation of photons into DNA strand breaks by [Cr(ddpd)2]3+.
Equipping ZIF particles with a polyelectrolyte membrane provides functional groups at their interface, enabling further conjugations necessary for applications such as targeted drug delivery. Previous approaches to coat ZIF particles with polyelectrolytes led to surface corrosion of the template material. This work overcomes previous limitations by performing a Layer-by-Layer (LbL) polyelectrolyte coating onto ZIF-8 and ZIF-67 particles in nonaqueous environment. Using the 2-methylimidazolium salt of polystyrensulfonic acid instead of the acid itself and polyethyleneimine in methanol led to intact ZIF particles after polyelectrolyte coating. This was verified by electron microscopy. Further, zetapotential and atomic force microscopy measurements confirmed a continuous polyelectrolyte multilayer built up. The here reported adaption to the well-studied (LbL) polyelectrolyte selfassembly process provides a facile method to equip ZIF particles with a nanometer thin polyelectrolyte multilayer membrane.