Spectroscopic Characterization of Mitochondrial G-Quadruplexes.

Guanine quadruplexes (G4s) are highly polymorphic four-stranded structures formed within guanine-rich DNA and RNA sequences that play a crucial role in biological processes. The recent discovery of the first G4 structures within mitochondrial DNA has led to a small revolution in the field. In particular, the G-rich conserved sequence block II (CSB II) can form different types of G4s that are thought to play a crucial role in replication. In this study, we decipher the most relevant G4 structures that can be formed within CSB II: RNA G4 at the RNA transcript, DNA G4 within the non-transcribed strand and DNA:RNA hybrid between the RNA transcript and the non-transcribed strand. We show that the more abundant, but unexplored, G6AG7 (37%) and G6AG8 (35%) sequences in CSB II yield more stable G4s than the less profuse G5AG7 sequence. Moreover, the existence of a guanine located 1 bp upstream promotes G4 formation. In all cases, parallel G4s are formed, but their topology changes from a less ordered to a highly ordered G4 when adding small amounts of potassium or sodium cations. Circular dichroism was used due to discriminate different conformations and topologies of nucleic acids and was complemented with gel electrophoresis and fluorescence spectroscopy studies.

Fluorescence quenching of the N-methylquinolinium cation by pairs of water or alcohol molecules.

N-Methylquinolinium cation (MQ+) in its first-excited singlet state is a strong oxidant commonly used as a photosensitizer, whose fluorescence is therefore quenched by electron donors. Interestingly, the fluorescence of MQ+ is also quenched by hydroxy compounds such as water and alcohols, more difficult to oxidize. We investigated the quenching mechanism of MQ+ fluorescence by small amounts of water and alcohols in acetonitrile solution. The fluorescence intensities and lifetimes exhibited a nonlinear dependence on the quencher concentration. We found evidence that emissive exciplexes MQ+*-ROH are formed between the excited quinolinium and the hydroxy compounds. An accurate quantitative description of the results was obtained with a model in which the exciplex reacts with a second molecule of the hydroxy compound, which quenches the fluorescence. The rate constant of this process increased as the quencher ionization energy decreased. We showed also that a low basicity of the hydroxy compound inhibits the quenching process. These results are consistent with the existence of a concerted photoinduced proton-coupled electron transfer (PCET) involving an intermediate complex of the excited quinolinium with a H-bonded molecular pair of the hydroxy compounds. In these pairs, a water or an alcohol molecule is able to donate an electron to the photoexcited quinolinium cation and a proton to the second H-bonded hydroxy molecule, showing an enhanced reducing power in comparison with the isolated molecule. The structure of the intermediate complex was investigated using high-level quantum mechanical calculations. At high water concentrations in acetonitrile/water mixtures, the quenching process is slowed down, indicating that higher water aggregates are less effective for a PCET process. The results obtained may be relevant to the study of water oxidation and electron transfer in biological systems.

Towards ratiometric sensing of amyloid fibrils in vitro.

The aggregation of amyloid-ß peptide and its accumulation in the human brain has an important role in the etiology of Alzheimer's disease. Thioflavin T has been widely used as a fluorescent marker for these amyloid aggregates. Nevertheless, its complex photophysical behavior, with strong wavelength dependencies of all its fluorescence properties, requires searching for new fluorescent probes. The use of 2-(2'-hydroxyphenyl)imidazo[4,5-b]pyridine (HPIP), which shows two emission bands and a rich excited-state behavior due to the existence of excited-state intramolecular processes of proton transfer and charge transfer, is proposed. These properties result in a high sensitivity of HPIP fluorescence to its microenvironment and cause a large differential fluorescence enhancement of the two bands upon binding to aggregates of the amyloid-ß peptide. Based on this behavior, a very sensitive ratiometric method is established for the detection and quantification of amyloid fibrils, which can be combined with the monitoring of fluorescence anisotropy. The binding selectivity of HPIP is discussed on the basis of the apparent binding equilibrium constants of this probe to amyloid-ß (1-42) fibrils and to the nonfibrillar protein bovine serum albumin. Finally, an exhaustive comparison between HPIP and thioflavin T is presented to discuss the sensitivity and specificity of these probes to amyloid aggregates and the significant advantages of the HPIP dye for quantitative determinations.

Excited-state proton and charge transfer in protonated amino and methylated derivatives of 2-(2'-hydroxyphenyl)benzimidazole.

We studied the excited-state behavior of a family of mono- and diprotonated derivatives of 2-phenylbenzimidazole in different solvents, using steady-state and time-resolved fluorescence spectroscopy. The species investigated were 2-(4'-amino-2'-hydroxyphenyl)benzimidazole (1), the diethylamino analogue 2-(4'-N,N-diethylamino-2'-hydroxyphenyl)benzimidazole (2) and its N-methylated derivative 1-methyl-2-(4'-N,N-diethylamino-2'-hydroxyphenyl)benzimidazole (3). The O-methoxy derivatives of 2 and 3 (2-OMe and 3-OMe), and the simpler models 2-phenylbenzimidazole (4) and its 4'-amino (5) and 4'-dimethylamino (6) derivatives were also studied. We found that the dications of 1, 2, and 3 (protonated at the benzimidazole N3 and at the amino group) were strong photoacids, which were deprotonated at the hydroxyl group upon excitation in aqueous solution (totally for 2 and 3) to give a tautomer of the ground-state monocation. In contrast, no photodissociation was observed for the monocations of these species. Instead, some of the monocations studied behaved as molecular rotors, for which electronic excitation led to a twisted intramolecular charge transfer (TICT) state. The monocations of 2, 3, 2-OMe, 3-OMe, and 6, protonated at the benzimidazole N3, experienced a polarity- and viscosity-dependent radiationless deactivation associated with a large-amplitude rotational motion. We propose that this process is connected to an intramolecular charge transfer from the dimethylaminophenyl or diethylaminophenyl moiety (donor) to the protonated benzimidazole group (acceptor) of the excited monocation, which yields a twisted charge-transfer species. No fluorescence from this species was detected except for 3 and 3-OMe in low-viscosity solvents.

Moderately Strong Photoacid Dissociates in Alcohols with High Transient Concentration of the Proton-Transfer Contact Pair.

Proton transfer from strong photoacids to hydroxylic solvents is much under debate. Experimentally, the main issue stems from relaxation and diffusion processes that are concomitant with ultrafast proton transfer and blur population dynamics. To overcome this, we propose a fast photodissociation reaction that, however, proceeds slower than solvent relaxation. Fluorescence spectroscopy of the cationic photoacid 2-(1'-hydroxy-2'-naphtyl)benzimidazolium reveals a two-stage mechanism: (a) reversible elementary proton transfer inside the solvent shell and (b) irreversible contact-pair splitting. The time evolution of the fluorescence signal is complex, yet this is explained quantitatively by simultaneous, spectrally overlapping emission of the acid, the conjugate base, and the contact proton-transfer pair. The latter attains high transient concentration in linear alcohols. Microscopic rate constants of dissociation are determined.

Dissociation of a strong acid in neat solvents: diffusion is observed after reversible proton ejection inside the solvent shell.

Strong-acid dissociation was studied in alcohols. Optical excitation of the cationic photoacid N-methyl-6-hydroxyquinolinium triggers proton transfer to the solvent, which was probed by spectral reconstruction of picosecond fluorescence traces. The process fulfills the classical Eigen-Weller mechanism in two stages: (a) solvent-controlled reversible dissociation inside the solvent shell and (b) barrierless splitting of the encounter complex. This can be appreciated only when fluorescence band integrals are used to monitor the time evolution of the reactant and product concentrations. Band integrals are insensitive to solvent dynamics and report relative concentrations directly. This was demonstrated by first measuring the fluorescence decay of the conjugate base across the full emission band, independently of the proton-transfer reaction. Multiexponential decay curves at single wavelengths result from a dynamic red shift of fluorescence in the course of solvent relaxation, whereas clean single exponential decays are obtained if the band integral is monitored instead. The extent of the shift is consistent with previously reported femtosecond transient absorption measurements, continuum theory of solvatochromism, and molecular properties derived from quantum chemical calculations. In turn, band integrals show clean biexponential decay of the photoacid and triexponential evolution of the conjugate base in the course of the proton transfer to solvent reaction. The dissociation step follows the slowest stage of solvation, which was measured here independently by picosecond fluorescence spectroscopy in five aliphatic alcohols. Also, the rate constant of the encounter-complex splitting stage is compatible with proton diffusion. Thus, for this photoacid, both stages reach the highest possible rates: solvation and diffusion control. Under these conditions, the concentration of the encounter complex is substantial during the earliest nanosecond.

Photoinduced proton and charge transfer in 2-(2'-hydroxyphenyl)imidazo[4,5-b]pyridine.

This paper deals with the interplay between solvent properties and isomerism of 2-(2'-hydroxyphenyl)imidazo[4,5-b]pyridine (1), and the proton and charge-transfer processes that the different isomers undergo in the first-excited singlet state. We demonstrate the strong influence of these processes on the fluorescence properties of 1. We studied the behavior of 1 in several neutral and acidified solvents, by UV-vis absorption spectroscopy and by steady-state and time-resolved fluorescence spectroscopy. The fluorescence of 1 showed a strong sensitivity to the environment. This behavior is the result of conformational and isomeric equilibria and the completely different excited-state behavior of the isomers. For both neutral and cationic 1, isomers with intramolecular hydrogen bond between the hydroxyl group and the benzimidazole N undergo an ultrafast excited-state intramolecular proton transfer (ESIPT), yielding tautomeric species with very large Stokes shift. For both neutral and cationic 1, isomers with the OH group hydrogen-bonded to the solvent behave as strong photoacids, dissociating in the excited state in solvents with basic character. The pyridine nitrogen exhibits photobase character, protonating in the excited state even in some neutral solvents. An efficient radiationless deactivation channel of several species was detected, which we attributed to a twisted intramolecular charge-transfer (TICT) process, facilitated by deprotonation of the hydroxyl group and protonation of the pyridine nitrogen.

Fluorescence of methylated derivatives of hydroxyphenylimidazopyridine. Resolution of strongly overlapping spectra and a new ESIPT dye showing very efficient radiationless deactivation.

The ground- and excited-state behaviour of the isomeric species 2-(2'-methoxyphenyl)imidazo[4,5-b]pyridine (1-OMe) and 2-(2'-hydroxyphenyl)-4-methylimidazo[4,5-b]pyridine (1-NMe) in neutral and acid media has been studied by UV-vis absorption spectroscopy, steady-state and time-resolved fluorescence spectroscopy. The new dye 1-NMe is non-fluorescent in neutral media except in trifluoroethanol, where it shows a very weak fluorescence. 1-NMe also exhibits highly solvent-dependent fluorescence intensity in acidic media. We propose that the neutral species experiences a fast excited-state intramolecular proton transfer (ESIPT), relaxing afterwards by intramolecular twisting associated with internal charge transfer (TICT) and subsequent very fast internal conversion of the proton-transferred TICT structure. The behaviour of 1-NMe in acidic media is explained by the existence of a ground-state tautomeric equilibrium between species with intramolecular hydrogen bonds N-HOH and NHO. The first type of tautomers dissociates at the hydroxyl group in water and ethanol, but fluoresces in acetonitrile and trifluoroethanol due to the inability of these solvents to accept the proton. The second type of tautomers is non-emissive due to fast radiationless deactivation through an ESIPT-TICT process. The fluorescence of 1-OMe was investigated in neutral and acidic media, demonstrating the photobasic character of the pyridine nitrogen. A ground-state equilibrium between pyridinium and imidazolium cations was found for this species, showing overlapping absorption and fluorescence spectra. We devised a method to resolve the spectra by applying principal component global analysis to a series of excitation spectra taken at different emission wavelengths, which allowed estimation of the equilibrium constant between the cations.

Solvent-modulated ground-state rotamerism and tautomerism and excited-state proton-transfer processes in o-hydroxynaphthylbenzimidazoles.

The ground-state rotamerism and tautomerism and the excited-state proton-transfer processes of 2-(1'-hydroxy-2'-naphthyl)benzimidazole (1) and 2-(3'-hydroxy-2'-naphthyl)benzimidazole (2) have been investigated in various solvents by means of UV-vis absorption spectroscopy, steady-state and time-resolved fluorescence spectroscopy, and quantum-mechanical ab initio calculations. For both compounds, a solvent-modulated rotameric equilibrium, and also tautomeric for 1, was observed in the ground state. In apolar solvents, both 1 and 2 exist as planar syn normal forms, with the hydroxyl group hydrogen bonded to the benzimidazole N3. In acetonitrile and ethanol, a rotameric equilibrium is established between the syn form and its planar anti rotamer, with the phenyl ring rotated 180 degrees about the C2-C2' bond. In ethylene glycol, glycerol, and aqueous solution with 40% ethanol, a tautomeric equilibrium was detected for 1 between the syn and anti normal forms and the tautomer form, with the hydroxyl proton transferred to the benzimidazole N3. In all of the solvents studied, the syn normal form of 1 and 2 undergoes an ultrafast excited-state intramolecular proton transfer (ESIPT) to yield the excited tautomer. The anti normal forms of 1 and 2, unable to experience ESIPT, give normal form fluorescence. In addition, the anti normal conformer of 2 partly deprotonates at the hydroxyl group in aqueous solution with 40% ethanol, giving the excited anion. The monocations of 1 and 2, protonated at the benzimidazole N3, are strong photoacids that deprotonate completely in aqueous solution with 40% ethanol and to a great extent in ethanol, giving the excited tautomer.

Rotamerism, tautomerism, and excited-state intramolecular proton transfer in 2-(4'-N,N-diethylamino-2'-hydroxyphenyl)benzimidazoles: novel benzimidazoles undergoing excited-state intramolecular coupled proton and charge transfer.

The solvent and temperature dependence of the phototautomerization of 1-methyl-2-(2'-hydroxyphenyl)benzimidazole (4) and the novel compounds 2-(4'-amino-2'-hydroxyphenyl)benzimidazole (1), 2-(4'-N,N-diethylamino-2'-hydroxyphenyl)benzimidazole (2), and 1-methyl-2-(4'-N,N-diethylamino-2'-hydroxyphenyl)benzimidazole (3), together with the ground-state rotamerism and tautomerism of these new compounds, have been studied by UV-vis absorption spectroscopy and steady-state and time-resolved fluorescence spectroscopy. A solvent-modulated rotameric and tautomeric equilibrium is observed in the ground state for 1, 2, and 3. In cyclohexane, these compounds mainly exist as a planar syn normal form, with the hydroxyl group hydrogen-bonded to the benzimidazole N3. In ethanol, the syn form is in equilibrium with its planar anti rotamer (for 1 and 2), with the phenyl ring rotated 180 degrees about the C2-C1' bond and with a nonplanar rotamer for compound 3. In aqueous solution, a tautomeric equilibrium is established between the anti normal form (or the nonplanar rotamer for 3) and the tautomer (with the hydroxyl proton transferred to the benzimidazole N3). The syn normal form of these compounds undergoes in all the solvents an excited-state intramolecular proton-transfer process from the hydroxyl group to the benzimidazole N3 to yield the excited tautomer. The tautomer fluorescence quantum yield of 2, 3, and 4 shows a temperature-, polarity-, and viscosity-dependent radiationless deactivation, connected with a large-amplitude conformational motion. We conclude that this excited-state conformational change experienced by the tautomer is associated with an intramolecular charge transfer from the deprotonated dialkylaminophenol or phenol (donor) to the protonated benzimidazole (acceptor), affording a nonfluorescent charge-transfer tautomer. Therefore, these compounds undergo an excited-state intramolecular coupled proton- and charge-transfer process.

Excited-state intramolecular proton transfer in 2-(3'-hydroxy-2'-pyridyl)benzoxazole. Evidence of coupled proton and charge transfer in the excited state of some o-hydroxyarylbenzazoles.

The influence of solvent, temperature, and viscosity on the phototautomerization processes of a series of o-hydroxyarylbenzazoles was studied by means of ultraviolet-visible (UV-vis) absorption spectroscopy and steady-state and time-resolved fluorescence spectroscopy. The compounds studied were 2-(2'-hydroxyphenyl)benzimidazole (HBI), 2-(2'-hydroxyphenyl)benzoxazole (HBO), 2-(2'-hydroxyphenyl)benzothiazole (HBT), 2-(3'-hydroxy-2'-pyridyl)benzimidazole (HPyBI), and the new derivative 2-(3'-hydroxy-2'-pyridyl)benzoxazole (HPyBO), this one studied in neutral and acid media. All of these compounds undergo an excited-state intramolecular proton transfer (ESIPT) from the hydroxyl group to the benzazole N3 to yield an excited tautomer in syn conformation. A temperature- and viscosity-dependent radiationless deactivation of the tautomer has been detected for all compounds except HBI and HPyBI. We show that this radiationless decay also takes place for 2-(3-methyl-1,3-benzothiazol-3-ium-2-yl)benzenolate (NMeOBT), the N-methylated analog of the tautomer, whose ground-state structure has anti conformation. In ethanol, the radiationless decay shows intrinsic activation energy for HPyBO and HBO; however, it is barrierless for HBT and NMeOBT and controlled instead by the solvent dynamics. The relative efficiency of the radiationless decay in the series of molecules studied supports the hypothesis that this transition is connected with a charge-transfer process taking place in the tautomer, its efficiency being related to the strength of the electron donor (dissociated phenol or pyridinol moiety) and electron acceptor (protonated benzazole). We propose that the charge transfer is associated with a large-amplitude conformational change of the tautomer, the process leading to a nonfluorescent charge-transfer intermediate. The previous ESIPT step generates the structure with the suitable redox pair to undergo the charge-transfer process; therefore, an excited-state intramolecular coupled proton and charge transfer takes place for these compounds.

Two competitive routes in the lactim-lactam phototautomerization of a hydroxypyridine derivative cation in water: dissociative mechanism versus water-assisted proton transfer.

Ground-state tautomerism and excited-state proton-transfer processes of 2-(6'-hydroxy-2'-pyridyl)benzimidazolium in H2O and D2O have been studied by means of UV-vis absorption and fluorescence spectroscopy in both steady-state and time-resolved modes. In the ground state, this compound shows a tautomeric equilibrium between the lactim cation, protonated at the benzimidazole N3, and its lactam tautomer, obtained by proton translocation from the hydroxyl group to the pyridine nitrogen. Direct excitation of the lactam tautomer leads to its own fluorescence emission, while as a result of the increase of acidity of the OH group and basicity at the pyridine N upon excitation, the lactim species undergoes a proton translocation from the hydroxyl group to the nitrogen, favoring the lactam structure in the excited state. No fluorescence emission from the initially excited lactim species was detected due to the ultrafast rate of the excited-state proton-transfer processes. The lactim-lactam phototaumerization process takes place via two competitive excited-state proton-transfer routes: a one-step water-assisted proton translocation (probably a double proton transfer) and a two-step pathway which involves first the dissociation of the lactim cation to form an emissive intermediate zwitterionic species and then the acid-catalyzed protonation at the pyridine nitrogen to give rise to the lactam tautomer.