Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions

Recombination of genes is essential to the evolution of genetic diversity, the segregation of chromosomes during cell division, and certain DNA repair processes. The Holliday junction, a four-arm, four-strand branched DNA crossover structure, is formed as a transient intermediate during genetic recombination and repair processes in the cell. The recognition and subsequent resolution of Holliday junctions into parental or recombined products appear to be critically dependent on their three-dimensional structure. Complementary NMR and time-resolved fluorescence resonance energy transfer experiments on immobilized four-arm DNA junctions reported here indicate that the Holliday junction cannot be viewed as a static structure but rather as an equilibrium mixture of two conformational isomers. Furthermore, the distribution between the two possible crossover isomers was found to depend on the sequence in a manner that was not anticipated on the basis of previous low-resolution experiments.

Interaction between HLA-DM and HLA-DR involves regions that undergo conformational changes at lysosomal pH

Antigenic peptide loading of major histocompatibility complex class II molecules is enhanced by lysosomal pH and catalyzed by the HLA-DM molecule. The physical mechanism behind the catalytic activity of DM was investigated by using time-resolved fluorescence anisotropy (TRFA) and fluorescence binding studies with the dye 8-anilino-1-naphthalenesulfonic acid (ANS). We demonstrate that the conformations of both HLA-DM and HLA-DR3, irrespective of the composition of bound peptide, are pH sensitive. Both complexes reversibly expose more nonpolar regions upon protonation. Interaction of DM with DR shields these hydrophobic domains from the aqueous environment, leading to stabilization of the DM and DR conformations. At lysosomal pH, the uncovering of additional hydrophobic patches leads to a more extensive DM–DR association. We propose that DM catalyzes class II peptide loading by stabilizing the low-pH conformation of DR, favoring peptide exchange. The DM–DR association involves a larger hydrophobic surface area with DR/class II-associated invariant chain peptides (CLIP) than with stable DR/peptide complexes, explaining the preferred association of DM with the former. The data support a release mechanism of DM from the DM–DR complex through reduction of the interactive surface, upon binding of class II molecules with antigenic peptide or upon neutralization of the DM–DR complex at the cell surface.

Preparação, caracterização e propriedades de lipossomas contendo o ácido -ciano-4-hidroxicinâmico e o agente fotossenbilizador AICIPc: um novo sistema carreador específico com ação sinérgica aplicado a terapia fotodinâmica

Ftalocianina de alumínio-cloro (AlClPc) é um fotossensibilizador de segunda geração em terapia fotodinâmica (TFD) caracterizado por seu caráter anfifílico e tendência de auto-agregação em meio aquoso, o que prejudica seu potencial de aplicação. O aCHC é um substrato de transportadores de monocarboxilato (MCT) superexpresso em células de MCF-7. Objetivando a solubilização da AlClPc e aumento de internalização em tecidos neoplásicos nos propomos aqui o uso de DSPC e DOPC em diferentes proporções para formar vesículas lipidicas mistas (LV) na presença de aCHC como sistemas veiculadores de fármaco. Lv foi preparado pelo método de injeção etanólica e formou vesículas de dimensões nanométricas (aproximadamente 100 nm) com bom índice de polidispersão, valores negativos de potencial zeta e estáveis em meio aquoso por mais de 50 dias. AlClPc se complexou com o fosfato das LV o que conferiu uma localização interfacial às moléculas de AlClPc como demonstrado pelos resultados de supressão de fluorescência. Medidas de anisotropia, fluorescência estática e resolvida no tempo corroboram com estes resultados e demonstram que a auto-agregação da AlClPc ocorre mesmo em lipossomas. Entretanto, a veiculação da AlClPc por LV em carcinoma de células escamosas oral (OSCC) levou a um processo de desagregação demonstrado por (FLIM). Este incrível comportamento é novo e aumenta o conhecimento científico sobre o mecanismo intracelular de ação de fotossensibilizadores em TFD. Em TFD, ambos os sistemas LVIII+AlClPc e LVIII+AlClPc+aCHC não apresentaram toxicidade no escuro no período de incubação de 3 h com as concentrações de lipídios, AlClPc e aCHC iguais a 0,15 mmol/L, 0,5 umol/L e 10,0 umol/L, respectivamente. De maneira inesperada, o sistema LVIII+AlClPc foi mais eficiente em TFD que o sistema LVIII+AlClPc+aCHC, devido ao caráter antioxidante do aCHC. Estes resultados abrem uma nova perspectiva do potencial uso de LV-AlClPc para o tratamento fotodinâmico.

Electronic energy-transfer rate constants for geometrical isomers of a bichromophoric macrocyclic complex

The rate of electronic energy transfer (EET) between a naphthalene donor and an anthracene acceptor in [ZnL3]-(ClO4)(2) and [ZnL4](ClO4)(2) was determined by time-resolved fluorescence measurements, where L 3 and L 4 are the geometrical isomers of 6-[(anthracen-9-ylmethyl)amino]-trans-6,13-dimethyl-1,4,8,11-tetraazacyclotetradecane-13-amine (L-2), substituted with either a naphthalen-1-ylmethyl or naphthalen-2-ylmethyl donor, respectively. The energy transfer rate constant, k(EET), was determined to be (0.92 +/- 0.02) x 10(9) s(-1) for the naphthalen-1-ylmethyl-substituted isomer, while that for the naphthalen-2-ylmethyl-substituted isomer is somewhat faster, with k(EET) = (1.31 +/- 0.01) x 10(9) s(-1). The solid-state structure of [(ZnLCl)-Cl-3]ClO4 has been determined, and using molecular modeling calculations, the likely distributions of solution conformations in CH3CN have been evaluated for both complexes. The calculated conformational distributions in the common trans-III N-based isomeric form gave Forster EET rate constants that account for the differences observed and are in excellent agreement with the experimental values. It is shown that the full range of conformers must be considered to accurately reproduce the observed EET kinetics.

Study of NAD(P)H fluorescence in living cardiomyocytes by spectrally resolved time-correlated single photon counting

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Fluorescence spectroscopy of small peptides interacting with microheterogeneous micelles

Many peptides containing tryptophan have therapeutic uses and can be studied by their fluorescent properties. The biological activity of these peptides involves interactions with many cellular components and micelles can function as carriers inside organisms. We report results from the interaction of small peptides containing tryptophan with several microheterogeneous systems: sodium dodecyl sulphate (SDS) micelles; sodium dodecyl sulphate-poly(ethylene oxide) (SDS-PEO) aggregates; and neutral polymeric micelles. We observed that specific parameters, such as wavelength of maximum emission and fluorescence anisotropy, could be used to ascertain the occurrence of interactions. Affinity constants were determined from changes in the intensity of emission while structural modifications in rotameric conformations were verified from time-resolved measurements. Information about the location and diffusion of peptides in the microheterogeneous systems were obtained from tryptophan emission quenching experiments using N-alkylpyridinium ions. The results show the importance of electrostatic and hydrophobic effects, and of the ionization state of charged residues, in the presence of anionic and amphiphilic SDS in the microheterogeneous systems. Conformational stability of peptides is best preserved in the interaction with the neutral polymeric micelles. (C) 2009 Elsevier B.V. All rights reserved.

Interaction of adrenocorticotropin peptides with microheterogeneous systems - A fluorescence study

Adrenocorticotropin (ACM) and alpha-melanocyte stimulating hormone (alpha-MSH) are peptides which present many physiological effects related to pigmentation, motor and sexual behavior, learning and memory, analgesia, anti-inflammatory and antipyretic processes. The 13 amino acid residues of alpha-MSH are the same initial sequence of ACM and due to the presence of a tryptophan residue in position 9 of the peptide chain, fluorescence techniques could be used to investigate the conformational properties of the hormones in different environments and the mechanisms of interaction with biomimetic systems like sodium dodecyl sulphate (SDS) micelles, sodium dodecyl sulphate-poly(ethylene oxide) (SDS-PEO) aggregates and neutral polymeric micelles. In buffer solution, fluorescence parameters were typical of peptides containing tryptophan exposed to the aqueous medium and upon addition of surfactant and polymer molecules, the gradual change of those parameters demonstrated the interaction of the peptides with the microheterogeneous systems. From time-resolved experiments it was shown that the interaction proceeded with conformational changes in both peptides, and further information was obtained from quenching of Trp fluorescence by a family of N-alkylpyridinium ions, which possess affinity to the microheterogeneous systems dependent on the length of the alkyl chain. The quenching of Trp fluorescence was enhanced in the presence of charged micelles, compared to the buffer solution and the accessibility of the fluorophore to the quencher was dependent on the peptide and the alkylpyridinium: in ACTH(1-21) highest collisional constants were obtained using ethylpyridinium as quencher, indicating a location of the residue in the surface of the micelle, while in alpha-MSH the best quencher was hexylpyridinium, indicating insertion of the residue into the non-polar region of the micelles. The results had shown that the interaction between the peptides and the biomimetic systems where driven by combined electrostatic and hydrophobic effects: in ACTH(1-24) the electrostatic interaction between highly positively charged C-terminal and negatively charged surface of micelles; and aggregates predominates over hydrophobic interactions involving residues in the central region of the peptide; in alpha-MSH, which presents one residual positive charge, the hydrophobic interactions are relevant to position the Trp residue in the non-polar region of the microheterogeneous systems. (C) 2008 Elsevier B.V. All rights reserved.

Effect of surface plasmon resonance in TiO2/Au thin films on the fluorescence of self-assembled CdTe QDs structure

The exceptional properties of localised surface plasmons (LSPs), such as local field enhancement and confinement effects, resonant behavior, make them ideal candidates to control the emission of luminescent nanoparticles. In the present work, we investigated the LSP effect on the steady-state and time-resolved emission properties of quantum dots (QDs) by organizing the dots into self-assembled dendrite structures deposited on plasmonic nanostructures. Self-assembled structures consisting of water-soluble CdTe mono-size QDs, were developed on the surface of co-sputtered TiO2 thin films doped with Au nanoparticles (NPs) annealed at different temperatures. Their steady-state fluorescence properties were probed by scanning the spatially resolved emission spectra and the energy transfer processes were investigated by the fluorescence lifetime imaging (FLIM) microscopy. Our results indicate that a resonant coupling between excitons confined in QDs and LSPs in Au NPs located beneath the self-assembled structure indeed takes place and results in (i) a shift of the ground state luminescence towards higher energies and onset of emission from excited states in QDs, and (ii) a decrease of the ground state exciton lifetime (fluorescence quenching).

Femtosecond real-time probing of reactions. 12. Vectorial dynamics of transition states

Femtosecond time-resolved techniques with KETOF (kinetic energy time-of-flight) detection in a molecular beam are developed for studies of the vectorial dynamics of transition states. Application to the dissociation reaction of IHgI is presented. For this system, the complex [I---Hg---I](++)* is unstable and, through the symmetric and asymmetric stretch motions, yields different product fragments: [I---Hg---I](++)* -> HgI(X^2/sigma^+) + I(^2P_3/2) [or I*(^2P_l/2)] (1a); [I---Hg---I](++)* -> Hg(^1S_0) + I(^2P_3/2) + I(^2P_3/2) [or I* (^2P_1/2)] (1 b). These two channels, (1a) and (1b), lead to different kinetic energy distributions in the products. It is shown that the motion of the wave packet in the transition-state region can be observed by MPI mass detection; the transient time ranges from 120 to 300 fs depending on the available energy. With polarized pulses, the vectorial properties (transition moments alignment relative to recoil direction) are studied for fragment separations on the femtosecond time scale. The results indicate the nature of the structure (symmetry properties) and the correlation to final products. For 311-nm excitation, no evidence of crossing between the I and I* potentials is found at the internuclear separations studied. (Results for 287-nm excitation are also presented.) Molecular dynamics simulations and studies by laser-induced fluorescence support these findings.

Biolabeling with nanoparticles based on Y(2)O(3):Nd(3+) and luminescence detection in the near-infrared

Neodymium based fluorescence presents several advantages in comparison to conventional rare earth or enzyme-substrate based fluorescence emitting sources (e.g.Tb, HRP). Based on this fact we have herein explored a Nd-based fluoroimmunoassay. We efficiently detected the presence of an oxidized low-density lipoprotein (oxLDL) in human plasma a well-known marker for cardiovascular diseases, which causes around 30% of deaths worldwide. Conventional fluoroimmunoassay uses time-resolved luminescence techniques, with detection in the visible range, to eliminate the fluorescence background from the biological specimens. By using an immunoassay based on functionalized Y(2)O(3):Nd(3+) nanoparticles, where the excitation and emission processes in the Nd(3+) ion occur in the near-infrared (NIR) region, we have succeeded in eliminating the interferences from the biological fluorescence background, avoiding the use of time-resolved techniques. This yields higher emission intensity from the Nd(3+)-nanolabels and efficient detection of anti-oxidized low-density lipoproteins (anti-oxLDL) by Y(2)O(3):Nd(3+)-antibody-antigen conjugation, leading to a novel biolabeling method. (C) 2010 Elsevier B.V. All rights reserved.

Studies of Inorganic Layer and Framework Structures Using Time-, Temperature- and Pressure-Resolved Powder Diffraction Techniques

This thesis is concerned with in-situ time-, temperature- and pressure-resolved synchrotron X-ray powder diffraction investigations of a variety of inorganic compounds with twodimensional layer structures and three-dimensional framework structures. In particular, phase stability, reaction kinetics, thermal expansion and compressibility at non-ambient conditions has been studied for 1) Phosphates with composition MIV(HPO4)2·nH2O (MIV = Ti, Zr); 2) Pyrophosphates and pyrovanadates with composition MIVX2O7 (MIV = Ti, Zr and X = P, V); 3) Molybdates with composition ZrMo2O8. The results are compiled in seven published papers and two manuscripts. Reaction kinetics for the hydrothermal synthesis of α-Ti(HPO4)2·H2O and intercalation of alkane diamines in α-Zr(HPO4)2·H2O was studied using time-resolved experiments. In the high-temperature transformation of γ-Ti(PO4)(H2PO4)·2H2O to TiP2O7 three intermediate phases, γ'-Ti(PO4)(H2PO4)·(2-x)H2O, β-Ti(PO4)(H2PO4) and Ti(PO4)(H2P2O7)0.5 were found to crystallise at 323, 373 and 748 K, respectively. A new tetragonal three-dimensional phosphate phase called τ-Zr(HPO4)2 was prepared, and subsequently its structure was determined and refined using the Rietveld method. In the high-temperature transformation from τ-Zr(HPO4)2 to cubic α-ZrP2O7 two new orthorhombic intermediate phases were found. The first intermediate phase, ρ-Zr(HPO4)2, forms at 598 K, and the second phase, β-ZrP2O7, at 688 K. Their respective structures were solved using direct methods and refined using the Rietveld method. In-situ high-pressure studies of τ-Zr(HPO4)2 revealed two new phases, tetragonal ν-Zr(HPO4)2 and orthorhombic ω-Zr(HPO4)2 that crystallise at 1.1 and 8.2 GPa. The structure of ν-Zr(HPO4)2 was solved and refined using the Rietveld method. The high-pressure properties of the pyrophosphates ZrP2O7 and TiP2O7, and the pyrovanadate ZrV2O7 were studied up to 40 GPa. Both pyrophosphates display smooth compression up to the highest pressures, while ZrV2O7 has a phase transformation at 1.38 GPa from cubic to pseudo-tetragonal β-ZrV2O7 and becomes X-ray amorphous at pressures above 4 GPa. In-situ high-pressure studies of trigonal α-ZrMo2O8 revealed the existence of two new phases, monoclinic δ-ZrMo2O8 and triclinic ε-ZrMo2O8 that crystallises at 1.1 and 2.5 GPa, respectively. The structure of δ-ZrMo2O8 was solved by direct methods and refined using the Rietveld method.

Dynamics of fluorescence fluctuations in green fluorescent protein observed by fluorescence correlation spectroscopy

We have investigated the pH dependence of the dynamics of conformational fluctuations of green fluorescent protein mutants EGFP (F64L/S65T) and GFP-S65T in small ensembles of molecules in solution by using fluorescence correlation spectroscopy (FCS). FCS utilizes time-resolved measurements of fluctuations in the molecular fluorescence emission for determination of the intrinsic dynamics and thermodynamics of all processes that affect the fluorescence. Fluorescence excitation of a bulk solution of EGFP decreases to zero at low pH (pKa = 5.8) paralleled by a decrease of the absorption at 488 nm and an increase at 400 nm. Protonation of the hydroxyl group of Tyr-66, which is part of the chromophore, induces these changes. When FCS is used the fluctuations in the protonation state of the chromophore are time resolved. The autocorrelation function of fluorescence emission shows contributions from two chemical relaxation processes as well as diffusional concentration fluctuations. The time constant of the fast, pH-dependent chemical process decreases with pH from 300 μs at pH 7 to 45 μs at pH 5, while the time-average fraction of molecules in a nonfluorescent state increases to 80% in the same range. A second, pH-independent, process with a time constant of 340 μs and an associated fraction of 13% nonfluorescent molecules is observed between pH 8 and 11, possibly representing an internal proton transfer process and associated conformational rearrangements. The FCS data provide direct measures of the dynamics and the equilibrium properties of the protonation processes. Thus FCS is a convenient, intrinsically calibrated method for pH measurements in subfemtoliter volumes with nanomolar concentrations of EGFP.

Transport in the blood of an anti-tumor water-soluble rutheniun cyclopentadienyl complex: a fluorescence study on albumin binding

Dissertação de mestrado, Qualidade em Análises, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2014

Fluorescence of nitrobenzoxadiazole (NBD)-labeled lipids in model membranes is connected not to lipid mobility but to probe location

Nitrobenzoxadiazole (NBD)-labeled lipids are popular fluorescent membrane probes. However, the understanding of important aspects of the photophysics of NBD remains incomplete, including the observed shift in the emission spectrum of NBD-lipids to longer wavelengths following excitation at the red edge of the absorption spectrum (red-edge excitation shift or REES). REES of NBD-lipids in membrane environments has been previously interpreted as reflecting restricted mobility of solvent surrounding the fluorophore. However, this requires a large change in the dipole moment (Dm) of NBD upon excitation. Previous calculations of the value of Dm of NBD in the literature have been carried out using outdated semi-empirical methods, leading to conflicting values. Using up-to-date density functional theory methods, we recalculated the value of Dm and verified that it is rather small (B2 D). Fluorescence measurements confirmed that the value of REES is B16 nm for 1,2-dioleoyl-sn-glycero-3- phospho-L-serine-N-(NBD) (NBD-PS) in dioleoylphosphatidylcholine vesicles. However, the observed shift is independent of both the temperature and the presence of cholesterol and is therefore insensitive to the mobility and hydration of the membrane. Moreover, red-edge excitation leads to an increased contribution of the decay component with a shorter lifetime, whereas time-resolved emission spectra of NBD-PS displayed an atypical blue shift following excitation. This excludes restrictions to solvent relaxation as the cause of the measured REES and TRES of NBD, pointing instead to the heterogeneous transverse location of probes as the origin of these effects. The latter hypothesis was confirmed by molecular dynamics simulations, from which the calculated heterogeneity of the hydration and location of NBD correlated with the measured fluorescence lifetimes/REES. Globally, our combination of theoretical and experiment-based techniques has led to a considerably improved understanding of the photophysics of NBD and a reinterpretation of its REES in particular.

Photophysical properties of a photocytotoxic fluorinated chlorin conjugated to four beta-cyclodextrins

A meso-tetrakis(pentafluorophenyl)-chlorin with the reduced pyrrole ring linked to an isoxazolidine ring (FC) has been conjugated to four beta-cyclodextrins (CDFC). The CDFC exhibits excellent water solubility and is a potent photosensitizer towards proliferating NCTC 2544 human keratinocytes. The study by conventional steady state absorption and fluorescence spectroscopies and by time-resolved femto- and nanosecond laser flash spectroscopies suggests that in ethanol and pH 7 buffer the beta-cyclodextrins embed the highly hydrophobic tetrakis(pentafluorophenyl)-chlorin macrocycle and strongly interact with the chlorin rings in the singlet and triplet manifolds. In these solvents, femtosecond spectroscopy suggests that the conjugate undergoes a rapid relaxation in the upper excited singlet states induced by photochemical and/or conformation change(s) at a rate of about 5 ps(-1) to fluorescent states whose lifetime is similar to 8 ns. This interaction is destroyed upon addition of Triton X100 to buffer. Both FC and CDFC strongly fluoresce (Phi(F) similar to 0.5) in micelles. Similar behavior is observed at the triplet level. In ethanol and water, the initial transient triplet state absorbance decays within 1-3 mu s yielding a longer lived triplet with spectral properties indistinguishable from that of original difference absorbance spectra. The determination of the molar absorbance in the 440-460 nm region (similar to 35 000 M(-1) cm(-1)) leads to an estimate of similar to 0.2 for the triplet formation quantum yield of FC in toluene and of FC and CDFC in Triton X100 micelles. Quenching of the CDFC triplets by dioxygen in buffer produces (1)O(2) in a good yield consistent with the effective photocytotoxicity of the chlorin-cyclodextrins conjugate towards cultured NCTC 2544 human keratinocytes. By contrast, FC which aggregates in buffer produces little if any (1)O(2).