Bulky Lesion Bypass Requires Dpo4 Binding in Distinct Conformations.

Translesion DNA synthesis is an essential process that helps resume DNA replication at forks stalled near bulky adducts on the DNA. Benzo[a]pyrene (B[a]P) is a polycyclic aromatic hydrocarbon (PAH) that can be metabolically activated to benzo[a]pyrene diol epoxide (BPDE), which then can react with DNA to form carcinogenic DNA adducts. Here, we have used single-molecule florescence resonance energy transfer (smFRET) experiments, classical molecular dynamics simulations, and nucleotide incorporation assays to investigate the mechanism by which the model Y-family polymerase, Dpo4, bypasses a (+)-cis-B[a]P-N 2-dG adduct in DNA. Our data show that when (+)-cis-B[a]P-N 2-dG is the templating base, the B[a]P moiety is in a non-solvent exposed conformation stacked within the DNA helix, where it effectively blocks nucleotide incorporation across the adduct by Dpo4. However, when the media contains a small amount of dimethyl sulfoxide (DMSO), the adduct is able to move to a solvent-exposed conformation, which enables error-prone DNA replication past the adduct. When the primer terminates across from the adduct position, the addition of DMSO leads to the formation of an insertion complex capable of accurate nucleotide incorporation.

Mechanism of aromatic amine carcinogen bypass by the Y-family polymerase, Dpo4.

Bulky DNA damage inhibits DNA synthesis by replicative polymerases and often requires the action of error prone bypass polymerases. The exact mechanism governing adduct-induced mutagenesis and its dependence on the DNA sequence context remains unclear. In this work, we characterize Dpo4 binding conformations and activity with DNA templates modified with the carcinogenic DNA adducts, 2-aminofluoene (AF) or N-acetyl-2-aminofluorene (AAF), using single-molecule FRET (smFRET) analysis and DNA synthesis extension assays. We find that in the absence of dNTPs, both adducts alter polymerase binding as measured by smFRET, but the addition of dNTPs induces the formation of a ternary complex having what appears to be a conformation similar to the one observed with an unmodified DNA template. We also observe that the misincorporation pathways for each adduct present significant differences: while an AF adduct induces a structure consistent with the previously observed primer-template looped structure, its acetylated counterpart uses a different mechanism, one consistent with a dNTP-stabilized misalignment mechanism.

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.

Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates.

Flap endonuclease 1 (Fen1) is a highly conserved structure-specific nuclease that catalyses a specific incision to remove 5' flaps in double-stranded DNA substrates. Fen1 plays an essential role in key cellular processes, such as DNA replication and repair, and mutations that compromise Fen1 expression levels or activity have severe health implications in humans. The nuclease activity of Fen1 and other FEN family members can be stimulated by processivity clamps such as proliferating cell nuclear antigen (PCNA); however, the exact mechanism of PCNA activation is currently unknown. Here, we have used a combination of ensemble and single-molecule Förster resonance energy transfer together with protein-induced fluorescence enhancement to uncouple and investigate the substrate recognition and catalytic steps of Fen1 and Fen1/PCNA complexes. We propose a model in which upon Fen1 binding, a highly dynamic substrate is bent and locked into an open flap conformation where specific Fen1/DNA interactions can be established. PCNA enhances Fen1 recognition of the DNA substrate by further promoting the open flap conformation in a step that may involve facilitated threading of the 5' ssDNA flap. Merging our data with existing crystallographic and molecular dynamics simulations we provide a solution-based model for the Fen1/PCNA/DNA ternary complex.

Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment.

Y-family DNA polymerases play a crucial role in translesion DNA synthesis. Here, we have characterized the binding kinetics and conformational dynamics of the Y-family polymerase Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) using single-molecule fluorescence. We find that in the absence of dNTPs, the binary complex shuttles between two different conformations within ∼1 s. These data are consistent with prior crystal structures in which the nucleotide binding site is either occupied by the terminal base pair (preinsertion conformation) or empty following Dpo4 translocation by 1 base pair (insertion conformation). Most interestingly, on dNTP binding, only the insertion conformation is observed and the correct dNTP stabilizes this complex compared with the binary complex, whereas incorrect dNTPs destabilize it. However, if the n+1 template base is complementary to the incoming dNTP, a structure consistent with a misaligned template conformation is observed, in which the template base at the n position loops out. This structure provides evidence for a Dpo4 mutagenesis pathway involving a transient misalignment mechanism.

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.