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- ItemFemtosecond stimulated Raman spectroscopy of the cyclobutane thymine dimer repair mechanism: A computational study(Washington, DC : American Chemical Society, 2014) Ando, H.; Fingerhut, B.P.; Dorfman, K.E.; Biggs, J.D.; Mukamel, S.Cyclobutane thymine dimer, one of the major lesions in DNA formed by exposure to UV sunlight, is repaired in a photoreactivation process, which is essential to maintain life. The molecular mechanism of the central step, i.e., intradimer C-C bond splitting, still remains an open question. In a simulation study, we demonstrate how the time evolution of characteristic marker bands (C=O and C=C/C-C stretch vibrations) of cyclobutane thymine dimer and thymine dinucleotide radical anion, thymidylyl(3′→5′)-thymidine, can be directly probed with femtosecond stimulated Raman spectroscopy (FSRS). We construct a DFT(M05-2X) potential energy surface with two minor barriers for the intradimer C5-C′5 splitting and a main barrier for the C6-C′6 splitting, and identify the appearance of two C5=C6 stretch vibrations due to the C6-C′6 splitting as a spectroscopic signature of the underlying bond splitting mechanism. The sequential mechanism shows only absorptive features in the simulated FSRS signals, whereas the fast concerted mechanism shows characteristic dispersive line shapes. (Figure Presented).
- ItemTime-resolved photoelectron spectroscopy of adenine and adenosine in aqueous solution(London [u.a.] : Royal Society of Chemistry, 2013) Buchner, F.; Ritze, H.-H.; Lahl, J.; Lübcke, A.Time-resolved photoelectron spectroscopy is applied to study the excited state dynamics of the DNA base adenine and its ribonucleoside adenosine in aqueous solution for pump and probe photon energies in the range between 4.66 eV and 5.21 eV. We follow the evolution of the prepared excited state on the potential energy surface and retrieve lifetimes of the S1 state under different excitation conditions.
- ItemNon-instrumented DNA isolation, amplification and microarray-based hybridization for a rapid on-site detection of devastating Phytophthora kernoviae(Cambridge : Soc., 2015) Schwenkbier, Lydia; Pollok, Sibyll; Rudloff, Anne; Sailer, Sebastian; Cialla-May, Dana; Weber, Karina; Popp, JürgenA rapid and simple instrument-free detection system was developed for the identification of the plant pathogen Phytophthora kernoviae (P. kernoviae). The on-site operable analysis steps include magnetic particle based DNA isolation, helicase-dependent amplification (HDA) and chip-based DNA hybridization. The isothermal approach enabled the convenient amplification of the yeast GTP-binding protein (Ypt1) target gene in a miniaturized HDA-zeolite-heater (HZH) by an exothermic reaction. The amplicon detection on the chip was performed under room temperature conditions – either by successive hybridization and enzyme binding or by a combined step. A positive signal is displayed by enzymatically generated silver nanoparticle deposits, which serve as robust endpoint signals allowing an immediate visual readout. The hybridization assay enabled the reliable detection of 10 pg μL−1 target DNA. This is the first report of an entirely electricity-free, field applicable detection approach for devastating Phytophthora species, exemplarily shown for P. kernoviae.
- ItemAll-in-one: a versatile gas sensor based on fiber enhanced Raman spectroscopy for monitoring postharvest fruit conservation and ripening(Cambridge : Soc., 2016) Jochum, Tobias; Rahal, Leila; Suckert, Renè J.; Popp, Jürgen; Frosch, TorstenIn today's fruit conservation rooms the ripening of harvested fruit is delayed by precise management of the interior oxygen (O2) and carbon dioxide (CO2) levels. Ethylene (C2H4), a natural plant hormone, is commonly used to trigger fruit ripening shortly before entering the market. Monitoring of these critical process gases, also of the increasingly favored cooling agent ammonia (NH3), is a crucial task in modern postharvest fruit management. The goal of this work was to develop and characterize a gas sensor setup based on fiber enhanced Raman spectroscopy for fast (time resolution of a few minutes) and non-destructive process gas monitoring throughout the complete postharvest production chain encompassing storage and transport in fruit conservation chambers as well as commercial fruit ripening in industrial ripening rooms. Exploiting a micro-structured hollow-core photonic crystal fiber for analyte gas confinement and sensitivity enhancement, the sensor features simultaneous quantification of O2, CO2, NH3 and C2H4 without cross-sensitivity in just one single measurement. Laboratory measurements of typical fruit conservation gas mixtures showed that the sensor is capable of quantifying O2 and CO2 concentration levels with accuracy of 3% or less with respect to reference concentrations. The sensor detected ammonia concentrations, relevant for chemical alarm purposes. Due to the high spectral resolution of the gas sensor, ethylene could be quantified simultaneously with O2 and CO2 in a multi-component mixture. These results indicate that fiber enhanced Raman sensors have a potential to become universally usable on-site gas sensors for controlled atmosphere applications in postharvest fruit management.