Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues

Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.

On the use of the spectral luminescent method for studying acid-base equilibria of uracil derivatives in aqueous solutions

The effect of pH on fluorescence parameters (spectral composition, intensity I_fl, and quantum yield φ) of thymine (T), 5-fluorouracil (FU) and 6-aminouracil (AU) have been investigated in aqueous solutions. As found, there is the regularity of the changes in the spectral composition, intensity, and quantum yields of uracil fluorescence depending on pH. The constants of the acid-base equilibria of uracils (pK_a) determined by the fluorescence titration method are: 9.9 (T), 8.0 (FU), and 9.1 (AU) at 298 K. These pK_a1 values satisfactorily agree with the previous estimates obtained by independent experimental or quantum chemical methods. The possibilities of the spectral fluorescence method for the quantitative description of the acid-base equilibria of uracils depending on the fluorescent features of the pyrimidinedione and its conjugate base are discussed.

The methyl- and aza-substituent effects on nonradiative decay mechanisms of uracil in water: a transient absorption study in the UV region

The C5, C6 methyl- and aza-substituent effects on the decay mechanism of uracil and vibrational cooling dynamics are investigated using a continuous UV probe.

Ultrafast Excited-State Dynamics of 6-Azauracil Studied by Femtosecond Transient Absorption Spectroscopy

The excited-state dynamics of 6-azauracil in different solvents have been studied using femtosecond transient absorption spectroscopy. The molecule is populated to the S2 state with a pump pulse at 264 nm. Broad-band white light continuum which covers from 320 to 600 nm is used as the probe. With a global fitting analysis of the measured transient spectra, three decay time constants, i.e., <0.3, 5.2 ± 0.1, and >1000 ps, are directly obtained in the solvent of acetonitrile. These newly observed lifetime constants are important in clarifying its decay dynamics as well as in providing a criterion for the ultrafast dynamics simulations in 6-azauracil using quantum chemical theories. In combination with previous theoretical works, the main decay channel is proposed: the initially populated S2 decays to S1 through internal conversion in <0.3 ps, followed by an intersystem crossing from S1 to T1 in 5.2 ± 0.1 ps. The >1000 ps component is due to the decay of the T1 state. A comparison of the excited-state dynamics in different solvents reveals that the decay from S1 to T1 shows a clear dependence on the polarity of the solvents. With higher polarity, the S1 excited state decays faster. This observation is in line with the prediction by Etinski et al. [ Phys. Chem. Chem. Phys. 2010 , 12 , 15665 - 15671 ], where a blue-shift of the T1 state potential energy surface leading to an increase of the intersystem crossing rate was proposed. With the new information obtained in the present measurement, a clearer picture of the decay dynamics of 6-azauracil on the S2 excited state is provided.

Two-dimensional fourier transform spectroscopy of adenine and uracil using shaped ultrafast laser pulses in the deep UV

We compare two-dimensional (2D) ultrafast Fourier transform spectroscopy measurements in the deep UV (262 nm) for adenine and uracil in solution. Both molecules show excited-state absorption on short time scales and ground-state bleaching extending for over 1 ps. While the 2D spectrum for uracil shows changes in the center of gravity during the first few hundred femtoseconds, the center of gravity of the 2D spectrum for adenine does not show similar changes. We discuss our results in light of ab initio electronic structure calculations.

Excited-state dynamics of dGMP measured by steady-state and femtosecond fluorescence spectroscopy

The room-temperature fluorescence of 2'-deoxyguanosine 5'-monophosphate (dGMP) in aqueous solution is studied by steady-state and time-resolved fluorescence spectroscopy. The steady-state fluorescence spectrum of dGMP shows one band centered at 334 nm but has an extraordinary long red tail, extending beyond 700 nm. Both the fluorescence quantum yield and the relative weight of the 334 nm peak increase with the excitation wavelength. The initial fluorescence anisotropy after excitation at 267 nm is lower than 0.2 for all emission wavelengths, indicating an ultrafast S(2) --> S(1) internal conversion. The fluorescence decays depend strongly on the emission wavelength, getting longer with the wavelength. A rise time of 100-150 fs was observed for wavelengths longer than 450 nm, in accordance with a gradual red shift of the time-resolved spectra. The results are discussed in terms of a relaxation occurring mainly on the lowest excited (1)pi pi*-state surface toward a conical intersection with the ground state, in line with recent theoretical predictions. Our results show that the excited-state population undergoes a substantial "spreading out" before reaching the CI, explaining the complex dynamics observed.