Fluorogenic and bioorthogonal modification of rna using photoclick chemistry

A bromoaryltetrazole-modified uridine was synthesized as a new RNA building block for bioorthogonal, light-activated and postsynthetic modification with commercially available fluorescent dyes. It allows “photoclick”-type modifications by irradiation with light (300 nm LED) at internal and terminal positions of presynthesized RNA with maleimide-conjugated fluorophores in good yields. The reaction was evidenced for three different dyes. During irradiation, the emission increases due to the formation of an intrinsically fluorescent pyrazoline moiety as photoclick product. The fluorogenecity of the photoclick reaction was significantly enhanced by energy transfer between the pyrazoline as the reaction product (poor emitter) and the photoclicked dye as the strong emitter. The RNA-dye conjugates show remarkable fluorescent properties, in particular an up to 9.4 fold increase of fluorescence, which are important for chemical biology and fluorescent imaging of RNA in cells

Diarylethene-modified nucleotides for switching optical properties in DNA

Diarylethenes were attached to the 5-position of 2’-deoxyuridine in order to yield three different photochromic nucleosides. All nucleosides were characterized with respect to their absorption and photochromic properties. Based on these results, the most promising photochromic DNA base modification was incorporated into representative oligonucleotides by using automated phosphoramidite chemistry. The switching of optical properties in DNA can be achieved selectively at 310 nm (forward) and 450 nm (backward); both wavelengths are outside the normal nucleic acid absorption range. Moreover, this nucleoside was proven to be photochemically stable and allows switching back and forth several times. These results open the way for the use of diarylethenes as photochromic compounds in DNA-based architectures

The Concept of Photozymes: Short Peptides with Photoredox Catalytic Activity for Nucleophilic Additions to α-Phenyl Styrenes

Conventional photoredox catalytic additions of alcohols to olefins require additives, like thiophenol, to promote back electron transfer. The concept of “photozymes” assumes that forward and backward electron transfer steps in a photoredox catalytic cycle are controllable by substrate binding to photocatalytically active peptides. Accordingly, we synthesized a short tripeptide modified with 1,7-dicyano-perylene-3,4 : 9,10-tetracarboxylic acid bisimide as photoredox catalyst. This peptide undergoes an unconventional photoredox catalytic cycle with the radical anion and dianion of the perylene bisimide-peptide as intermediates. The photoredox catalytic reactions with α-phenyl styrenes as substrates require remarkably low catalyst loadings (0.5 mol%) and give the methoxylation products in high yields. The concept of “photozymes” for photoredox catalysis has significant potential for other photocatalytic reactions, in particular with respect to enantioselective photocatalysis

Laser microscopy of tunneling magnetoresistance in manganite grain-boundary junctions

Using low-temperature scanning laser microscopy we directly image electric transport in a magnetoresistive element, a manganite thin film intersected by a grain boundary (GB). Imaging at variable temperature allows reconstruction and comparison of the local resistance vs temperature for both, the manganite film and the GB. Imaging at low temperature also shows that the GB switches between different resistive states due to the formation and growth of magnetic domains along the GB. We observe different types of domain wall growth; in most cases a domain wall nucleates at one edge of the bridge and then proceeds towards the other edge.Comment: 5 pages, 4 figures; submitted to Phys. Rev. Let

Complementary Photocatalytic Toolbox: Control of Intramolecular endo-versus exo-trig Cyclizations of α-Phenyl Olefins to Oxaheterocyclic Products

The regioselectivity of the intramolecular cyclization of bifunctional α-phenyl alkenes can be controlled simply by the choice of the organic chromophore as the photocatalyst. The central photoredox catalytic reaction in both cases is a nucleophilic addition of the hydroxy function to the olefin function of the substrates. N,N-(4-Diisobutylaminophenyl)phenothiazine catalyzes exo-trig cyclizations, whereas 1,7-dicyanoperylene-3,4,9,10-tetracarboxylic acid bisimides catalyze endo-trig additions to products with anti-Markovnikov regioselectivity. We preliminarily report the photoredox catalytic conversions of 11 representative substrates into 20 oxaheterocycles in order to demonstrate the similarity, but also the complementarity, of these two variants in this photoredox catalytic toolbox

Three-Dimensional Visualization of FKBP12.6 Binding to an Open Conformation of Cardiac Ryanodine Receptor

AbstractThe cardiac isoform of the ryanodine receptor (RyR2) from dog binds predominantly a 12.6-kDa isoform of the FK506-binding protein (FKBP12.6), whereas RyR2 from other species binds both FKBP12.6 and the closely related isoform FKBP12. The role played by FKBP12.6 in modulating calcium release by RyR2 is unclear at present. We have used cryoelectron microscopy and three-dimensional (3D) reconstruction techniques to determine the binding position of FKBP12.6 on the surface of canine RyR2. Buffer conditions that should favor the “open” state of RyR2 were used. Quantitative comparison of 3D reconstructions of RyR2 in the presence and absence of FKBP12.6 reveals that FKBP12.6 binds along the sides of the square-shaped cytoplasmic region of the receptor, adjacent to domain 9, which forms part of the four clamp (corner-forming) structures. The location of the FKBP12.6 binding site on “open” RyR2 appears similar, but slightly displaced (by 1–2nm) from that found previously for FKBP12 binding to the skeletal muscle ryanodine receptor that was in the buffer that favors the “closed” state. The conformation of RyR2 containing bound FKBP12.6 differs considerably from that depleted of FKBP12.6, particularly in the transmembrane region and in the clamp structures. The x-ray structure of FKBP12.6 was docked into the region of the 3D reconstruction that is attributable to bound FKBP12.6, to show the relative orientations of amino acid residues (Gln-31, Asn-32, Phe-59) that have been implicated as being critical in interactions with RyR2. A thorough understanding of the structural basis of RyR2-FKBP12.6 interaction should aid in understanding the roles that have been proposed for FKBP12.6 in heart failure and in certain forms of sudden cardiac death

Naphthalene diimides with improved solubility for visible light photoredox catalysis

Five core-substituted naphthalene diimides bearing two dialkylamino groups were synthesized as potential visible light photoredox catalysts and characterized by methods of optical spectroscopy and electrochemistry in comparison with one unsubstituted naphthalene diimide as reference. The core-substituted naphthalene diimides differ by the alkyl groups at the imide nitrogens and at the nitrogens of the two substituents at the core in order to enhance their solubility in DMF and thereby enhance their photoredox catalytic potential. The 1-ethylpropyl group as rather short and branched alkyl substituent at the imide nitrogen and the n-propyl group as short and unbranched one at the core amines yielded the best solubilities. The electron-donating diaminoalkyl substituents together with the electron-deficient aromatic core of the naphthalene diimides increase the charge-transfer character of their photoexcited states and thus shift their absorption into the visible light (500–650 nm). The excited state reduction potential was estimated to be approximately +1.0 V (vs SCE) which is sufficient to photocatalyze typical organic reactions. The photoredox catalytic activity in the visible light range was tested by the α-alkylation of 1-octanal as benchmark reaction. Irradiations were performed with LEDs in the visible light range between 520 nm and 640 nm. The irradiation by visible light together with the use of an organic dye instead of a transition metal complex as photoredox catalyst improve the sustainability and make photoredox catalysis “greener”

Gap solitons in Bragg gratings with a harmonic superlattice

Solitons are studied in a model of a fiber Bragg grating (BG) whose local reflectivity is subjected to periodic modulation. The superlattice opens an infinite number of new bandgaps in the model's spectrum. Averaging and numerical continuation methods show that each gap gives rise to gap solitons (GSs), including asymmetric and double-humped ones, which are not present without the superlattice.Computation of stability eigenvalues and direct simulation reveal the existence of completely stable families of fundamental GSs filling the new gaps - also at negative frequencies, where the ordinary GSs are unstable. Moving stable GSs with positive and negative effective mass are found too.Comment: 7 pages, 3 figures, submitted to EP

Strand displacement and duplex invasion into double-stranded DNA by pyrrolidinyl peptide nucleic acids

The so-called acpcPNA system bears a peptide backbone consisting of 4′-substituted proline units with (2′R,4′R) configuration in an alternating combination with (2S)-amino-cyclopentane-(1S)-carboxylic acids. acpcPNA forms exceptionally stable hybrids with complementary DNA. We demonstrate herein (i) strand displacements by single-stranded DNA from acpcPNA-DNA hybrids, and by acpcPNA strands from DNA duplexes, and (ii) strand invasions by acpcPNA into double-stranded DNA. These processes were studied in vitro using synthetic oligonucleotides and by means of our concept of wavelength-shifting fluorescent nucleic acid probes, including fluorescence lifetime measurements that allow quantifying energy transfer efficiencies. The strand displacements of preannealed 14mer acpcPNA-7mer DNA hybrids consecutively by 10mer and 14mer DNA strands occur with rather slow kinetics but yield high fluorescence color ratios (blue:yellow or blue:red), fluorescence intensity enhancements, and energy transfer efficiencies. Furthermore, 14mer acpcPNA strands are able to invade into 30mer double-stranded DNA, remarkably with quantitative efficiency in all studied cases. These processes can also be quantified by means of fluorescence. This remarkable behavior corroborates the extraordinary versatile properties of acpcPNA. In contrast to conventional PNA systems which require 3 or more equivalents PNA, only 1.5 equivalents acpcPNA are sufficient to get efficient double duplex invasion. Invasions also take place even in the presence of 250 mM NaCl which represents an ionic strength nearly twice as high as the physiological ion concentration. These remarkable results corroborate the extraordinary properties of acpcPNA, and thus acpcPNA represents an eligible tool for biological analytics and antigene applications. © The Royal Society of Chemistry 2015