From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently attached Cy3 dye undergoes strong enhancement of fluorescence intensity and lifetime when stacked in a nick, gap or overhang region in duplex DNA. This is used to probe hybridization dynamics of a DNA hairpin down to the single-molecule level. We also show that varying the position of a single abasic site up to 20 base pairs away modulates the dye–DNA interaction, indicative of through-backbone allosteric interactions. The phenomenon of stacking-induced fluorescence increase (SIFI) should find widespread use in the study of the structure, dynamics and reactivity of nucleic acids.

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Rhodamine 6G (R6G) was adsorbed on cellulose microparticles and fluorescence quantum yields and decays were measured as a function of dye loading. Though no spectroscopic evidence of dye aggregation was found, a noticeable decrease of quantum yield--after correction for reabsorption and reemission of fluorescence--and shortening of decays were observed at the highest loadings. These effects were attributed to the dissipation of the excitation energy by traps constituted by R6G pairs, leading to static and dynamic quenching produced by direct absorption of traps and non-radiative energy transfer from monomers, respectively. Regarding the nature of traps, two extreme approaches were considered: (a) equilibrium between monomers slightly interacting in the ground state and (b) randomly distributed monomers located below a critical distance (statistical traps). Both approaches accounted quantitatively for the observed facts. The effect of energy migration was evaluated through computational simulations. As the concentration of traps could only be indirectly inferred, in some experiments an external energy transfer quencher, Methylene Blue, was coadsorbed and the results were compared with those obtained with pure R6G.

The impact of the processing method in controlling the polymorphism and field-effect charge mobility of 2,3-thienoimide-based oligothiophenes semiconductors was investigated.

Platelet integrin αIIbβ3 is a key mediator of platelet activation and thrombosis. Upon activation αIIbβ3 undergoes significant conformational rearrangement, inducing complex bidirectional signalling and protein recruitment leading to platelet activation. Reconstituted lipid models of the integrin can enhance our understanding of the structural and mechanistic details of αIIbβ3 behaviour away from the complexity of the platelet machinery. Here, a novel method of αIIbβ3 insertion into Giant Unilamellar Vesicles (GUVs) is described that allows for effective integrin reconstitution unrestricted by lipid composition. αIIbβ3 was inserted into two GUV lipid compositions that seek to better mimic the platelet membrane. First, "nature's own", comprising 32% DOPC, 25% DOPE, 20% CH, 15% SM and 8% DOPS, intended to mimic the platelet cell membrane. Fluorescence Lifetime Correlation Spectroscopy (FLCS) reveals that exposure of the integrin to the activators Mn(2+) or DTT does not influence the diffusion coefficient of αIIbβ3. Similarly, exposure to αIIbβ3's primary ligand fibrinogen (Fg) alone does not affect αIIbβ3's diffusion coefficient. However, addition of Fg with either activator reduces the integrin diffusion coefficient from 2.52 ± 0.29 to μm(2) s(-1) to 1.56 ± 0.26 (Mn(2+)) or 1.49 ± 0.41 μm(2) s(-1) (DTT) which is consistent with aggregation of activated αIIbβ3 induced by fibrinogen binding. The Multichannel Scaler (MCS) trace shows that the integrin-Fg complex diffuses through the confocal volume in clusters. Using the Saffman-Delbrück model as a first approximation, the diffusion coefficient of the complex suggests at least a 20-fold increase in the radius of membrane bound protein, consistent with integrin clustering. Second, αIIbβ3 was also reconstituted into a "raft forming" GUV with well defined liquid disordered (Ld) and liquid ordered (Lo) phases. Using confocal microscopy and lipid partitioning dyes, αIIbβ3 showed an affinity for the DOPC rich Ld phase of the raft forming GUVs, and was effectively excluded from the cholesterol and sphingomyelin rich Lo phase. Activation and Fg binding of the integrin did not alter the distribution of αIIbβ3 between the lipid phases. This observation suggests partitioning of the activated fibrinogen bound αIIbβ3 into cholesterol rich domains is not responsible for the integrin clustering observed.

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We report a thorough photophysical characterization of the interactions between double-stranded DNA (dsDNA) and the trimethine cyanine homodimer dye YOYO-3. The fluorescence emission of this dye is enhanced by intercalation within the DNA double helix. We have explored the saturation of the dsDNA by bound YOYO-3 at the single-molecule level by studying the single-pair Förster resonance energy transfer (FRET) from an energy donor, Alexa Fluor 488, tagged at the 5' end of the double helix and the energy acceptor, YOYO-3, bound to the same DNA molecule. The spontaneous binding of YOYO-3 gives rise to an effective distribution of different FRET efficiencies and, therefore, donor-acceptor (D-A) distances. These distributions reveal the existence of multiple states of YOYO-3. Steady-state and time-resolved fluorescence and circular dichroism confirmed the presence of a DNA-bound aggregate of YOYO-3, conspicuous at high dye/base pair ratios. The spectral features of the aggregate suggest that it may have the structure of a parallel H-aggregate.

We examine here a series of meso-phenyl porphyrin micro- and nanostructures. Optical absorption and emission spectroscopy imaging and atomic force microscopy are used to investigate the effect of peripheral groups in nano- and microstructures of 5,10,15,20-tetraphenylporphyrin (H2TPP) compared to three other phenylporphyrins, i.e. 5,10,15-triphenylporphyrin (H2-Tri-PP), 5,10-diphenylporphyrin (H25,10-BPP) and 5,15-diphenylporphyrin (H25,15-BPP) molecules. We show that nanospheres and nanorods are formed, the occurrence and properties of which are influenced by the number and position of the phenyl substituents.