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End date: 2024 × Start date: 2020 × End date: 2014 × DDC: 540 × Type: Article × Version: publishedVersion × Subject: Article × Subject: chemistry ×

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    Femtosecond 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).
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    Magnetofluidic platform for multidimensional magnetic and optical barcoding of droplets
    (Cambridge : RSC, 2014) Lin, Gungun; Makarov, Denys; Medina-Sánchez, Mariana; Guix, Maria; Baraban, Larysa; Cuniberti, Gianaurelio; Schmidt, Oliver G.
    We present a concept of multidimensional magnetic and optical barcoding of droplets based on a magnetofluidic platform. The platform comprises multiple functional areas, such as an encoding area, an encoded droplet pool and a magnetic decoding area with integrated giant magnetoresistive (GMR) sensors. To prove this concept, penicillin functionalized with fluorescent dyes is coencapsulated with magnetic nanoparticles into droplets. While fluorescent dyes are used as conventional optical barcodes which are decoded with an optical decoding setup, an additional dimensionality of barcodes is created by using magnetic nanoparticles as magnetic barcodes for individual droplets and integrated micro-patterned GMR sensors as the corresponding magnetic decoding devices. The strategy of incorporating a magnetic encoding scheme provides a dynamic range of ~40 dB in addition to that of the optical method. When combined with magnetic barcodes, the encoding capacity can be increased by more than 1 order of magnitude compared with using only optical barcodes, that is, the magnetic platform provides more than 10 unique magnetic codes in addition to each optical barcode. Besides being a unique magnetic functional element for droplet microfluidics, the platform is capable of on-demand facile magnetic encoding and real-time decoding of droplets which paves the way for the development of novel non-optical encoding schemes for highly multiplexed droplet-based biological assays.