Katharina Röttger

Dynamics and Couplings of N-H Stretching Excitations of Guanosine-Cytidine Base Pairs in Solution

N-H stretching vibrations of hydrogen-bonded guanosine-cytidine (G·C) base pairs in chloroform solution are studied with linear and ultrafast nonlinear infrared (IR) spectroscopy. Assignment of the IR-active bands in the linear spectrum is made possible by combining structural information on the hydrogen bonds in G·C base pairs with literature results of density functional theory calculations, and empirical relations connecting frequency shifts and intensity of the IR-active vibrations. A local mode representation of N-H stretching vibrations is adopted, consisting of ν(G)(NH(2))(f) and ν(C)(NH(2))(f) modes for free NH groups of G and C, and of ν(G)(NH(2))(b), ν(G)(NH), and ν(C)(NH(2))(b) modes associated with N-H stretching motions of hydrogen-bonded NH groups. The couplings and relaxation dynamics of the N-H stretching excitations are studied with femtosecond mid-infrared two-dimensional (2D) and pump-probe spectroscopy. The N-H stretching vibrations of the free NH groups of G and C have an average population lifetime of 2.4 ps. Besides a vibrational population lifetime shortening to subpicosecond values observed for the hydrogen-bonded N-H stretching vibrations, the 2D spectra reveal vibrational excitation transfer from the ν(G)(NH(2))(b) mode to the ν(G)(NH) and/or ν(C)(NH(2))(b) modes. The underlying intermode vibrational couplings are on the order of 10 cm(-1).

Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution

Ultrafast deactivation pathways bestow photostability on nucleobases and hence preserve the structural integrity of DNA following absorption of ultraviolet (UV) radiation. One controversial recovery mechanism proposed to account for this photostability involves electron-driven proton transfer (EDPT) in Watson-Crick base pairs. The first direct observation is reported of the EDPT process after UV excitation of individual guanine-cytosine (G⋅C) Watson-Crick base pairs by ultrafast time-resolved UV/visible and mid-infrared spectroscopy. The formation of an intermediate biradical species (G[-H]⋅C[+H]) with a lifetime of 2.9 ps was tracked. The majority of these biradicals return to the original G⋅C Watson-Crick pairs, but up to 10% of the initially excited molecules instead form a stable photoproduct G*⋅C* that has undergone double hydrogen-atom transfer. The observation of these sequential EDPT mechanisms across intermolecular hydrogen bonds confirms an important and long debated pathway for the deactivation of photoexcited base pairs, with possible implications for the UV photochemistry of DNA.

N–H Stretching Vibrations of Guanosine–Cytidine Base Pairs in Solution: Ultrafast Dynamics, Couplings, and Line Shapes

Dynamics and couplings of N-H stretching vibrations of chemically modified guanosine-cytidine (G·C) base pairs in chloroform are investigated with linear infrared spectroscopy and ultrafast two-dimensional infrared (2D-IR) spectroscopy. Comparison of G·C absorption spectra before and after H/D exchange reveals significant N-H stretching absorption in the region from 2500 up to 3300 cm(-1). Both of the local stretching modes ν(C)(NH(2))(b) of the hydrogen-bonded N-H moiety of the cytidine NH(2) group and ν(G)(NH) of the guanosine N-H group contribute to this broad absorption band. Its complex line shape is attributed to Fermi resonances of the N-H stretching modes with combination and overtones of fingerprint vibrations and anharmonic couplings to low-frequency modes. Cross-peaks in the nonlinear 2D spectra between the 3491 cm(-1) free N-H oscillator band and the bands centered at 3145 and 3303 cm(-1) imply N-H···O═C hydrogen bond character for both of these transitions. Time evolution illustrates that the 3303 cm(-1) band is composed of a nearly homogeneous band absorbing at 3301 cm(-1), ascribed to ν(G)(NH(2))(b), and a broad inhomogeneous band peaking at 3380 cm(-1) with mainly guanosine carbonyl overtone character. Kinetics and signal strengths indicate a <0.2 ps virtually complete population transfer from the excited ν(G)(NH(2))(b) mode to the ν(G)(NH) mode at 3145 cm(-1), suggesting lifetime broadening as the dominant source for the homogeneous line shape of the 3301 cm(-1) transition. For the 3145 cm(-1) band, a 0.3 ps population lifetime was obtained.

Electronic Deactivation of Guanosine in Extended Hydrogen-Bonded Self-Assemblies

Guanosine (G) derivatives in nonpolar aprotic solvents self-assemble to intricate hydrogen-bonded supramolecular architectures, including dimers, ribbons, and cyclic quartets. Considerable interest exists in the nature of the excited electronic states, their lifetimes and the radiationless deactivation mechanisms of the molecules in those environments. Here, we report on the electronic relaxation of G in the extended H-bridged networks in solution in n-hexane. The resulting architectures were sampled by FTIR, UV, and CD spectroscopies. The dynamics after 260 nm photoexcitation were investigated by femtosecond fluorescence up-conversion, broadband UV-vis absorption, and single-color deep-UV measurements. The observed temporal profiles reveal a hierarchy of relaxation processes, with lifetimes τ1 = 0.63 ± 0.03 ps, τ2 = 5.9 ± 0.3 ps, and τ3 = 62 ± 7 ps. Moreover, about 10% of the photoexcited molecules transform to much longer-lived product states with lifetime τ4 ≈ 3.6 ± 1.0 ns. These excited-state lifetimes are much longer than in the G monomer or the G·G dimers studied previously, hinting at sizable energy shifts among the excited ππ* and nπ* states and trapping of excited-state population in the supramolecular networks by potential energy barriers along the optimal electronic deactivation pathways of the molecules.

Is UV-Induced Electron-Driven Proton Transfer Active in a Chemically Modified A·T DNA Base Pair?

Transient electronic and vibrational absorption spectroscopies have been used to investigate whether UV-induced electron-driven proton transfer (EDPT) mechanisms are active in a chemically modified adenine-thymine (A·T) DNA base pair. To enhance the fraction of biologically relevant Watson-Crick (WC) hydrogen-bonding motifs and eliminate undesired Hoogsteen structures, a chemically modified derivative of A was synthesized, 8-(tert-butyl)-9-ethyladenine (8tBA). Equimolar solutions of 8tBA and silyl-protected T nucleosides in chloroform yield a mixture of WC pairs, reverse WC pairs, and residual monomers. Unlike previous transient absorption studies of WC guanine-cytosine (G·C) pairs, no clear spectroscopic or kinetic evidence was identified for the participation of EDPT in the excited-state relaxation dynamics of 8tBA·T pairs, although ultrafast (sub-100 fs) EDPT cannot be discounted. Monomer-like dynamics are proposed to dominate in 8tBA·T.

Ultrafast Electronic Deactivation Dynamics of Xanthosine Monophosphate

Ultrafast energy dissipation is a crucial factor for the photostability of DNA and RNA, but even some of the key electronic deactivation pathways in monomeric nucleic acid building stones are still controversial. Here, we report on the excited-state dynamics of the rare nucleotide xanthosine monophosphate as a function of deprotonation state (XMP vs. XMP−) and excitation wavelength (λpump= 278–243 nm) by femtosecond time-resolved fluorescence and absorption spectroscopy. We show that the predominating relaxation channel leads to a return of the photo-excited molecules to the electronic ground state in τ∼1 ps. The mechanism likely involves an out-of-plane deformation of the five-membered ring, different from the main electronic deactivation pathways in the canonical purine bases adenine and guanine. The results are discussed in terms of the structural and electronic differences of XMP compared to the canonical nucleotides.

Ultrafast electronic deactivation dynamics of the inosine dimer--a model case for H-bonded purine bases.

The structural properties and ultrafast electronic deactivation dynamics of the inosine dimer in CHCl3 have been investigated by two-dimensional (1)H NMR and static FTIR spectroscopy and by femtosecond time-resolved transient absorption spectroscopy, respectively. The (1)H NMR and IR spectra show the formation of a well-defined, symmetric dimer with an association equilibrium constant of KI·I = 690 ± 100 M(-1). The excited-state dynamics after photoexcitation at λpump = 260 nm monitored by ultrafast absorption spectroscopy show great similarity with those of the monomer inosine in an aqueous solution and are governed by a decay time of τ = 90 ± 10 fs, which is one of the shortest electronic lifetimes of all nucleobases and nucleobase dimers studied so far. On the basis of these observations, the inosine dimer is expected to follow a similar relaxation pathway as the monomer, involving an out-of-plane deformation of the six-membered ring. The importance of the C(2) position for the electronic deactivation of hypoxanthine and guanine is discussed. The obtained well-determined structure and straightforward dynamics qualify the inosine dimer as an excellent reference case for more complicated systems such as the G·G dimer and the G·C and A·T Watson-Crick pairs.

Detection of the G(–H)• Radical in the Electronic Deactivation of the G–C Watson-Crick Base Pair

Transient absorption spectroscopy of the G-C base pair revealed the formation of the G(-H)● radical with lifetime 3 ps in the electronic deactivation. This radical is the key intermediate in an electron-coupled proton transfer.

Dynamics of N-H Stretching Excitations of Guanosine-Cytidine Base Pairs in Solution

The NH-stretching region of guanosine-cytidine base pairs in chloroform was investigated with 2D-IR and pump-probe spectroscopy. Structural motifs are correlated with spectral features through off-diagonal couplings and observation of energy transfer