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Netropsin binding in five duplex-dimer DNA constructs as a function of size and distance between binding sites: circular dichroism and absorption spectroscopy

International audienceThe optical activity induced on binding the drug netrospin (NET) in the minor groove of DNA is studied in five oligonucleotides (OGNs) as a function of (1) the size of the binding site in (5'-(GC)(2)AATT(GC)(2)-3')(2) (OGN 1a) versus (5'-(GC)(2)AAATTT(GC)(2)-3')(2) (OGN 1b) and (2) the distance between two AATT binding sites in (5'-(GC)(2)AATT(GC) (x) AATT(GC)(2)-3')(2), with x = 1, 2, or 3 (OGNs 2a, b, c, respectively). NET binding is monitored via the induced circular dichroism (CD) at similar to 315 nm, where the nucleic acids are optically inactive. The CD titrations, fit to a tight binding model, yield lower limits for the binding constant, K-a, a parts per thousand yen8 x 10(7) M-1 for OGN 1a and a parts per thousand yen2 x 10(8) M-1 for OGNs 2a, b, c in 1 mM buffer. In 100 mM buffer, tight binding occurs in all five OGNs with K-a a parts per thousand yen 8 x 10(7) M-1 for OGN 1a and a parts per thousand yen1 x 10(8) M-1 for OGNs 1b and 2a, b, c. In contrast, the elongated AAATTT binding site of OGN 1b results in weak binding of NET in 1 mM buffer, where competing electrostatic interactions with the solvent environment are lower. In the constructs with two binding sites, the increase in flexibility introduced by intervening GC base pairs does not induce co-operative binding, although differences in the number of binding sites, n (2.05-2.65), indicate that there may be differences in the way NET is bound in OGNs 2a, b, c. In addition, the large shifts in the absorption spectra induced in bound versus free NET, and effects on the CD spectral bands at higher energy, are discussed in terms of electrostatic and excitonic interactions

Pigment Organization Effects on Energy Transfer and <i>Chl a</i> Emission Imaged in the Diatoms <i>C. meneghiniana</i> and <i>P. tricornutum</i> In Vivo: A Confocal Laser Scanning Fluorescence (CLSF) Microscopy and Spectroscopy Study

The (auto)­fluorescence from three diatom strains, Cyclotella meneghiniana (<i>Cm</i>), Phaeodactylum tricornutum 1a (<i>Pt1a</i>), and Phaeodactylum UTex (<i>PtUTex</i>), has been imaged in vivo to submicrometer resolution using confocal laser scanning fluorescence (CLSF) microscopy. The diatoms are excited at 473 and 532 nm, energy primarily absorbed by the carotenoid fucoxanthin (<i>Fx</i>) found within the fucoxanthin chlorophyll <i>a</i>/<i>c</i> proteins (FCPs). On the basis of the fluorescence spectra measured in each image voxel, we obtain information about the spatial and energetic distribution of the terminal <i>Chl a</i> emitters, localized in the FCPs and the reaction centers of the PSII protein complexes, and the nature and location of the primary absorbers that are linked to these emitters; 532 nm excites the highly efficient <i>Fx</i>_red light harvesters, and lesser amounts of <i>Fx</i>_greens, that are enriched in some FCPs and preferentially transfer energy to PSII, compared to 473 nm, which excites almost equal amounts of all three previously identified sets of <i>Fx</i> – <i>Fx</i>_red, <i>Fx</i>_green and <i>Fx</i>_blue – as well as <i>Chl c</i>. The heterogeneous <i>Chl a</i> emission observed from the (C)­LSF images indicates that the different <i>Fx</i>’s serve different final emitters in P. tricornutum and suggest, at least in C. meneghiniana, a localization of FCPs with relatively greater <i>Fx</i>_red content at the chloroplast edges, but with overall higher FCP concentration in the interior of the plastid. To better understand our results, the concentration-dependent ensemble-averaged diatom solution spectra are compared to the (auto)­fluorescence spectra of individual diatoms, which indicate that pigment packing effects at an intracellular level do affect the diatoms’ spectral properties, in particular, concerning a 710 nm emission band apparent under stress conditions. A species-specific response of the spectral signature to the incident light is also discussed in terms of the presence of a silica shell in <i>Cm</i> but not in <i>Pt1a</i> nor <i>PtUTex</i>