Fluorescence of Natural DNA: From the Femtosecond to the Nanosecond Time Scales

Probing the Conical Intersection Dynamics of the RNA Base Uracil by UV-Pump Stimulated-Raman-Probe Signals; Ab Initio Simulations

Nonadiabatic electron and nuclear dynamics of photoexcited molecules involving conical intersections is of fundamental importance in many reactions such as the self-protection mechanism of DNA and RNA bases against UV irradiation. Nonlinear vibrational spectroscopy can provide an ultrafast sensitive probe for these processes. We employ a simulation protocol that combines nonadiabatic on-the-fly molecular dynamics with a mode-tracking algorithm for the simulation of femtosecond stimulated Raman spectroscopy (SRS) signals of the high frequency C–H- and N–H-stretch vibrations of the photoexcited RNA base uracil. The simulations rely on a microscopically derived expression that takes into account the path integral of the excited state evolution and the pulse shapes. Analysis of the joint time/frequency resolution of the technique reveals a matter chirp contribution that limits the inherent temporal resolution. Characteristic signatures of relaxation dynamics mediated in the vicinity of conical intersection are predicted. The C–H and N–H spectator modes provide high sensitivity to their local environment and act as local probes with submolecular and high temporal resolution.

Ultrafast photo-initiated molecular quantum dynamics in the DNA dinucleotide d(ApG) revealed by broadband transient absorption spectroscopy

The ultrafast photo-initiated quantum dynamics of the adenine-guanine dinucleotide d(ApG) in aqueous solution (pH 7) has been studied by femtosecond time-resolved spectroscopy after excitation at lambda = 260 nm. The results reveal a hierarchy of processes on time scales from tau < 100 fs to tau > 100 ps. Characteristic spectro-temporal signatures are observed indicating the transformation of the molecules in the electronic relaxation from the photo-excited state to a long-lived exciplex. In particular, broadband UV/VIS excited-state absorption (ESA) measurements detected a distinctive absorption by the excited dinucleotide around lambda = 335 nm, approximately 0.5 eV to the blue compared to the maximum of the broad and unstructured ESA spectrum after excitation of an equimolar mixture of the mononucleotides dAMP and dGMP. A similar feature has been identified as signature of the excimer in the dynamics of the adenine dinucleotide d(ApA). The lifetime of the d(ApG) exciplex was found to be tau = 124 +/- 4 ps both from the ESA decay time and from the ground-state recovery time, far longer than the sub-picosecond lifetimes of excited dAMP or dGMP. Fluorescence-time profiles measured by the up-conversion technique indicate that the exciplex state is reached around approximately 6 ps after excitation. Very weak residual fluorescence at longer times red-shifted to the emission from the photo-excited state shows that the exciplex is almost optically dark, but still has enough oscillator strength to give rise to the dual fluorescence of the dinucleotide in the static fluorescence spectrum.

State-specific heavy-atom effect on intersystem crossing processes in 2-thiothymine: a potential photodynamic therapy photosensitizer

Thiothymidine has a potential application as a photosensitizer in cancer photodynamic therapy (PDT). As the chromophore of thiothymidine, 2-thiothymine exhibits ultrahigh quantum yield of intersystem crossing to the lowest triplet state T(1) (ca. 100%), which contrasts with the excited-state behavior of the natural thymine that dissipates excess electronic energy via ultrafast internal conversion to the ground state. In this work, we employed high-level complete-active space self-consistent field and its second-order perturbation methods to explore the photophysical mechanism of a 2-thiothymine model. We have optimized the minimum energy structures in the low-lying seven electronic states, as well as ten intersection points. On the basis of the computed potential energy profiles and spin-orbit couplings, we proposed three competitive, efficient nonadiabatic pathways to the lowest triplet state T(1) from the initially populated singlet state S(2). The suggested mechanistic scenario explains well the recent experimental phenomena. The origin responsible for the distinct photophysical behaviors between thymine and 2-thiothymine is ascribed to the heavy-atom effect, which is significantly enhanced in the latter. Additionally, this heavy-atom effect is found to be state-specific, which could in principle be used to tune the photophysics of 2-thiothymine. The present high-level electronic structure calculations also contribute to understand the working mechanism of thiothymidine in PDT.

Monitoring Non-Adiabatic Dynamics of the RNA Base Uracil by UV-Pump-IR-Probe Spectroscopy

Resolving the excited state dynamics of DNA- and RNA- nucleobases has attracted considerably attention. UV irradiation of the isolated nucleobases leads to the population of an electronic excited state which is quenched by internal conversion mediated by conical intersections on an ultrafast timescale. We present non-adiabatic on-the-fly molecular dynamics simulations of the UV-pump-IR-probe signal of the pyrimidine nucleobase uracil using a novel semiclassical protocol which takes into account the path integral over the excited state vibrational dynamics and properly describes the joint temporal and spectral resolution of the technique. Simulations of vibrational motions of carbonyl fingerprint modes in the electronically excited states reveal clear signatures of different relaxation pathways on a timescale of hundreds of femtoseconds which arise from an ultrafast branching in the excited state. We show that the inherent temporal and spectral resolution of the technique is not purely instrumental but also depends on the vibrational fluctuation timescale.

Electronically excited states of DNA oligonucleotides with disordered base sequences studied by fluorescence spectroscopy

DNA double-stranded oligomers are studied by steady-state and time-resolved fluorescence spectroscopy from the femtosecond to the nanosecond time-scale, following excitation at 267 nm. It is shown that emission arises from three types of excited states. (i) Bright ππ* states emitting around 330 nm and decaying on the sub-picosecond time-scale with an average lifetime of ca. 0.4 ps and a quantum yield lower than 4 × 10(-6). (ii) Excimers/exciplexes emitting around 430 nm and decaying on the sub-nanosecond time-scale. (iii) Excited states emitting mainly at short wavelengths (λ < 330 nm) and decaying on the nanosecond time-scale, possibly correlated to GC pairs. The properties of the examined duplexes, exhibiting significant disorder with respect to the nearest neighbour base sequence, are radically different than those of the much longer and disordered calf thymus DNA. Such behaviour suggests that long range and/or sequence effects play a key role in the fate of excitation energy.

Femtosecond Intersystem Crossing in the DNA Nucleobase Cytosine

Ab initio molecular dynamics including nonadiabatic and spin-orbit couplings on equal footing is used to unravel the deactivation of cytosine after UV light absorption. Intersystem crossing (ISC) is found to compete directly with internal conversion in tens of femtoseconds, thus making cytosine the organic compound with the fastest triplet population calculated so far. It is found that close degeneracy between singlet and triplet states can more than compensate for very small spin-orbit couplings, leading to efficient ISC. The femtosecond nature of the ISC process highlights its importance in photochemistry and challenges the conventional view that large singlet-triplet couplings are required for an efficient population flow into triplet states. These findings are important to understand DNA photostability and the photochemistry and dynamics of organic molecules in general.

Probing electronic coupling between adenine bases in RNA strands from synchrotron radiation circular dichroism experiments

Circular dichroism spectra (176-330 nm) of RNA adenine oligomers, (rA)(n) (n = 1-10, 12, 15, and 20), reveal electronic coupling between two bases in short strands. The number of interacting bases in long strands is more and larger than that reported previously for the corresponding DNA strands.

Analysis of Excitonic and Charge Transfer Interactions from Quantum Chemical Calculations

A procedure for a detailed analysis of excited states in systems of interacting chromophores is proposed. By considering the one-electron transition density matrix, a wealth of information is recovered that may be missed by manually analyzing the wave function. Not only are the position and spatial extent given, but insight into the intrinsic structure of the exciton is readily obtained as well. For example, the method can differentiate between excitonic and charge resonance interactions even in completely symmetric systems. Four examples are considered to highlight the utility of the approach: interactions between the nπ* states in a formaldehyde dimer, excimer formation in the naphthalene dimer, stacking interaction in an adenine dimer, and the excitonic band structure in a conjugated phenylenevinylene oligomer.

Absorption by DNA single strands of adenine isolated in vacuo: the role of multiple chromophores

The degree of electronic coupling between DNA bases is a topic being up for much debate. Here we report on the intrinsic electronic properties of isolated DNA strands in vacuo free of solvent, which is a good starting point for high-level excited states calculations. Action spectra of DNA single strands of adenine reveal sign of exciton coupling between stacked bases from blueshifted absorption bands (~3 nm) relative to that of the dAMP mononucleotide (one adenine base). The bands are blueshifted by about 10 nm compared to those of solvated strands, which is a shift similar to that for the adenine molecule and the dAMP mononucleotide. Desolvation has little effect on the bandwidth, which implies that inhomogenous broadening of the absorption bands in aqueous solution is of minor importance compared to, e.g., conformational disorder. Finally, at high photon energies, internal conversion competes with electron detachment since dissociation of the bare photoexcited ions on the microsecond time scale is measured.

Label-free 3D visualization of cellular and tissue structures in intact muscle with second and third harmonic generation microscopy

Second and Third Harmonic Generation (SHG and THG) microscopy is based on optical effects which are induced by specific inherent physical properties of a specimen. As a multi-photon laser scanning approach which is not based on fluorescence it combines the advantages of a label-free technique with restriction of signal generation to the focal plane, thus allowing high resolution 3D reconstruction of image volumes without out-of-focus background several hundred micrometers deep into the tissue. While in mammalian soft tissues SHG is mostly restricted to collagen fibers and striated muscle myosin, THG is induced at a large variety of structures, since it is generated at interfaces such as refraction index changes within the focal volume of the excitation laser. Besides, colorants such as hemoglobin can cause resonance enhancement, leading to intense THG signals. We applied SHG and THG microscopy to murine (Mus musculus) muscles, an established model system for physiological research, to investigate their potential for label-free tissue imaging. In addition to collagen fibers and muscle fiber substructure, THG allowed us to visualize blood vessel walls and erythrocytes as well as white blood cells adhering to vessel walls, residing in or moving through the extravascular tissue. Moreover peripheral nerve fibers could be clearly identified. Structure down to the nuclear chromatin distribution was visualized in 3D and with more detail than obtainable by bright field microscopy. To our knowledge, most of these objects have not been visualized previously by THG or any label-free 3D approach. THG allows label-free microscopy with inherent optical sectioning and therefore may offer similar improvements compared to bright field microscopy as does confocal laser scanning microscopy compared to conventional fluorescence microscopy.

Following G-quadruplex formation by its intrinsic fluorescence

We characterized and compared the fluorescence properties of various well-defined G-quadruplex structures. The increase of intrinsic fluorescence of G-rich DNA sequences when they form G-quadruplexes can be used to monitor the folding and unfolding of G-quadruplexes as a function of cations and temperature. The temperature-dependent fluorescence spectra of different G-quadruplexes also exhibit characteristic patterns. Thus, the stability and possibly also the structure of G-quadruplexes can be characterized and distinguished by their intrinsic fluorescence spectra.

Formation mechanism and structure of a guanine-uracil DNA intrastrand cross-link

The formation and structure of the 5'-G[8-5]U-3' intrastrand cross-link are studied using density functional theory and molecular dynamics simulations due to the potential role of this lesion in the activity of 5-halouracils in antitumor therapies. Upon UV irradiation of 5-halouracil-containing DNA, a guanine radical cation reacts with the uracil radical to form the cross-link, which involves phosphorescence or an intersystem crossing and a rate-determining step of bond formation. Following ionizing radiation, guanine and the uracil radical react, with a rate-limiting step involving hydrogen atom removal. Although cross-link formation from UV radiation is favored, comparison of calculated reaction thermokinetics with that for related experimentally observed purine-pyrimidine cross-links suggests this lesion is also likely to form from ionizing radiation. For the first time, the structure of 5'-G[8-5]U-3' within DNA is identified by molecular dynamics simulations. Furthermore, three conformations of cross-linked DNA are revealed, which differ in the configuration of the complementary bases. Distortions, such as unwinding, are localized to the cross-linked dinucleotide and complementary nucleotides, with minimal changes to the flanking bases. Global changes to the helix, such as bending and groove alterations, parallel cisplatin-induced distortions, which indicate 5'-G[8-5]U-3', may contribute to the cytotoxicity of halouracils in tumor cell DNA using similar mechanisms.

A comparative picosecond transient infrared study of 1-methylcytosine and 5'-dCMP that sheds further light on the excited states of cytosine derivatives

The role of N1-substitution in controlling the deactivation processes in photoexcited cytosine derivatives has been explored using picosecond time-resolved IR spectroscopy. The simplest N1-substituted derivative, 1-methylcytosine, exhibits relaxation dynamics similar to the cytosine nucleobase and distinct from the biologically relevant nucleotide and nucleoside analogues, which have longer-lived excited-state intermediates. It is suggested that this is the case because the sugar group either facilitates access to the long-lived (1)n(O)π* state or retards its crossover to the ground state.