Dimitra Markovitsi

Near infrared absorption spectra of lanthanide bis-phthalocyanines

Abstract Near infrared absorption spectra (700–1800 nm) of various lanthanide bis-phthalocyanines (Pc 2 Lu, Pc 2 Yb, Pc 2 Tm, Pc 2 Dy) show two relatively intense bands (ϵ max ≈10 4 M −1 cm −1 ). The higher energy band is assigned to the 1e g →a lu transition of the radical macrocycle (Pc − ) while the lower energy one may be related to an intramolecular charge transfer from one macrocyclic ligand (Pc 2− ) to the other (Pc − ). The corresponding spectra for the reduced and oxidized species (Pc 2 Ln − , Pc 2 Ln + ) are in agreement with these assignments.

Thymine, thymidine and thymidine 5′-monophosphate studied by femtosecond fluorescence upconversion spectroscopy

Abstract We report fluorescence measurements of DNA components performed on the femtosecond time-scale using the fluorescence upconversion technique. Aqueous solutions of thymine (T), thymidine (dT) and thymidine 5′-monophosphate (TMP) were studied in room temperature by excitation at 267 nm and detection at wavelengths between 310 and 380 nm. The fluorescence decays are complex and cannot be described by single exponentials. About 25% of the fluorescence disappears within 150 fs and the remaining part decays more slowly when going from the base through the nucleoside to the nucleotide. The initial fluorescence anisotropy was found to be 0.35±0.03 and did not show any drastic change on the examined time interval.

Adenine, deoxyadenosine and deoxyadenosine 5'-monophosphate studied by femtosecond fluorescence upconversion spectroscopy

Abstract Aqueous solutions of adenine (A), deoxyadenosine (dA) and deoxyadenosine 5′-monophosphate (dAMP) were studied in room temperature by femtosecond fluorescence upconversion. The fluorescence decays cannot be described by single exponentials. They consist of an ultrafast component (230 fs for A, fs for dA and dAMP) and a slower one (8 ps for A, 0.5 ps for dA and dAMP). The slow component constitutes 95% of the total fluorescence (time-integrated) for the base while only 24% for the nucleoside or the nucleotide. The initial fluorescence anisotropy is 0.30±0.03 for A, 0.25±0.05 for dA and dAMP. The anisotropy of the A fluorescence partially decays during its lifetime due to rotational diffusion.

Dipolar coupling between electronic transitions of the DNA bases and its relevance to exciton states in double helices

The present communication addresses the question of the magnitude of dipolar coupling between the lowest electronic transition moments of the DNA nucleosides and its relevance to Frenkel exciton states in double helices. The transition energies and moments of the nucleosides are determined from absorption spectra recorded for dilute water solutions. Dipolar interactions are computed for some typical nucleoside dimers according to the atomic transition charge distribution model. The properties of the exciton states of two particular double helices, (dA)20·(dT)20 and (dAdT)10·(dAdT)10, are calculated considering three closely lying molecular electronic transitions (S1 and S2 for adenosine, S1 for thymidine). It is shown that (i) the oscillator strength is distributed over a small number of eigenstates, (ii) important mixing of the three monomer electronic transitions may occur, (iii) all eigenstates are spatially delocalised over the whole length of the double helix and (iv) the extent of exciton states over the two strands depends on the base sequence.

Electronic excited states responsible for dimer formation upon UV absorption directly by thymine strands: joint experimental and theoretical study.

The study addresses interconnected issues related to two major types of cycloadditions between adjacent thymines in DNA leading to cyclobutane dimers (T<>Ts) and (6-4) adducts. Experimental results are obtained for the single strand (dT)(20) by steady-state and time-resolved optical spectroscopy, as well as by HPLC coupled to mass spectrometry. Calculations are carried out for the dinucleoside monophosphate in water using the TD-M052X method and including the polarizable continuum model; the reliability of TD-M052X is checked against CASPT2 calculations regarding the behavior of two stacked thymines in the gas phase. It is shown that irradiation at the main absorption band leads to cyclobutane dimers (T<>Ts) and (6-4) adducts via different electronic excited states. T<>Ts are formed via (1)ππ* excitons; [2 + 2] dimerization proceeds along a barrierless path, in line with the constant quantum yield (0.05) with the irradiation wavelength, the contribution of the (3)ππ* state to this reaction being less than 10%. The formation of oxetane, the reaction intermediate leading to (6-4) adducts, occurs via charge transfer excited states involving two stacked thymines, whose fingerprint is detected in the fluorescence spectra; it involves an energy barrier explaining the important decrease in the quantum yield of (6-4) adducts with the irradiation wavelength.

Excited states and energy transfer among DNA bases in double helices

The study of excited states and energy transfer in DNA double helices has recently gained new interest connected to the development of computational techniques and that of femtosecond spectroscopy. The present article points out contentious questions regarding the nature of the excited states and the occurrence of energy transfer and shows how they are currently approached. Using as example the polymer poly(dA) . poly(dT), composed of about 2000 adenine-thymine pairs, a model is proposed on the basis of time-resolved measurements (fluorescence decays, fluorescence anisotropy decays and fluorescence spectra, obtained with femtosecond resolution), associated to steady-state spectra. According to this qualitative model, excitation at 267 nm populates excited states that are delocalized over a few bases (excitons). Ultrafast internal conversion directs the excited state population to the lower part of the exciton band giving rise to fluorescence. Questions needing further investigations, both theoretical and experimental, are underlined with particular emphasis on delicate points related to the complexity and the plasticity of these systems.

Base Pairing Enhances Fluorescence and Favors Cyclobutane Dimer Formation Induced upon Absorption of UVA Radiation by DNA

The photochemical properties of the DNA duplex (dA)(20)·(dT)(20) are compared with those of the parent single strands. It is shown that base pairing increases the probability of absorbing UVA photons, probably due to the formation of charge-transfer states. UVA excitation induces fluorescence peaking at ∼420 nm and decaying on the nanosecond time scale. The fluorescence quantum yield, the fluorescence lifetime, and the quantum yield for cyclobutane dimer formation increase upon base pairing. Such behavior contrasts with that of the UVC-induced processes.

Fluorescence of natural DNA: from the femtosecond to the nanosecond time-scales

The fluorescence of calf thymus DNA is studied by steady-state and time-resolved spectroscopy combining fluorescence upconversion and time-correlated single photon counting. The fluorescence spectrum is very similar to that of a stoichiometric mixture of monomeric chromophores, arising from bright pi pi* states, and contrasts with the existing picture of exciplex emission in natural DNA. Yet, the DNA fluorescence decays span over five decades of time, with 98% of the photons being emitted at times longer than 10 ps. These findings, in association with recent studies on model duplexes, are explained by the involvement of dark states, possibly related to charge separation, serving as a reservoir for the repopulation of the bright pi pi* states.

Electronic Excitation Energy Transfer between Nucleobases of Natural DNA

Transfer of the electronic excitation energy in calf thymus DNA is studied by time-resolved fluorescence spectroscopy. The fluorescence anisotropy, after an initial decay starting on the femtosecond time scale, dwindles down to ca. 0.1. The in-plane depolarized fluorescence decays are described by a stretched exponential law. Our observations are consistent with one-dimensional transfer mediated by charge-transfer excited states.

Conformational Control of TT Dimerization in DNA Conjugates. A Molecular Dynamics Study

The paper presents quantum yield results for the [2+2] and 6-4 photodimerization of TT steps in several DNA structures, including hairpins where the context dependence of the photodimerization yield is determined, and it develops a theoretical model that correctly describes the trends in dimerization yield with DNA structure. The DNA conjugates considered include dT(20), dA(20)dT(20), and three alkane-linked hairpins that contain a single TT step. The theoretical modeling of the [2+2] process is based on CASSCF electronic structure calculations for ethylene + ethylene, which show that photoexcitation of low-lying excited states leads to potential surfaces that correlate without significant barriers to a conical intersection with the ground state surface at geometries close to the dimer structure. The primary constraint on dimerization is the distance d between the two double bonds, and it is found that d < 3.52 A leads to quantum yield trends that match the observed trends within a factor of 3. Constraints on the dihedral angle between the two double bonds are not as important, and although it is possible to generate better dimerization yield predictions for some structures by including these constraints, the best overall picture is obtained with no constraint. For 6-4 dimerization, a distance g < 2.87 A and no constraint on dihedral angle provide an accurate description of the yield.