Bern Kohler

DNA Excited-State Dynamics: From Single Bases to the Double Helix

Ultraviolet light is strongly absorbed by DNA, producing excited electronic states that sometimes initiate damaging photochemical reactions. Fully mapping the reactive and nonreactive decay pathways available to excited electronic states in DNA is a decades-old quest. Progress toward this goal has accelerated rapidly in recent years, in large measure because of ultrafast laser experiments. Here we review recent discoveries and controversies concerning the nature and dynamics of excited states in DNA model systems in solution. Nonradiative decay by single, solvated nucleotides occurs primarily on the subpicosecond timescale. Surprisingly, excess electronic energy relaxes one or two orders of magnitude more slowly in DNA oligo- and polynucleotides. Highly efficient nonradiative decay pathways guarantee that most excited states do not lead to deleterious reactions but instead relax back to the electronic ground state. Understanding how the spatial organization of the bases controls the relaxation of excess electronic energy in the double helix and in alternative structures is currently one of the most exciting challenges in the field.

Base stacking controls excited-state dynamics in A-T DNA

Solar ultraviolet light creates excited electronic states in DNA that can decay to mutagenic photoproducts. This vulnerability is compensated for in all organisms by enzymatic repair of photodamaged DNA. As repair is energetically costly, DNA is intrinsically photostable. Single bases eliminate electronic energy non-radiatively on a subpicosecond timescale, but base stacking and base pairing mediate the decay of excess electronic energy in the double helix in poorly understood ways. In the past, considerable attention has been paid to excited base pairs. Recent reports have suggested that light-triggered motion of a proton in one of the hydrogen bonds of an isolated base pair initiates non-radiative decay to the electronic ground state. Here we show that vertical base stacking, and not base pairing, determines the fate of excited singlet electronic states in single- and double-stranded oligonucleotides composed of adenine (A) and thymine (T) bases. Intrastrand excimer states with lifetimes of 50–150 ps are formed in high yields whenever A is stacked with itself or with T. Excimers limit excitation energy to one strand at a time in the B-form double helix, enabling repair using the undamaged strand as a template.

Internal conversion to the electronic ground state occurs via two distinct pathways for pyrimidine bases in aqueous solution

The femtosecond transient absorption technique was used to study the relaxation of excited electronic states created by absorption of 267-nm light in all of the naturally occurring pyrimidine DNA and RNA bases in aqueous solution. The results reveal a surprising bifurcation of the initial excited-state population in <1 ps to two nonradiative decay channels within the manifold of singlet states. The first is the subpicosecond internal conversion channel first characterized in 2000. The second channel involves passage through a dark intermediate state assigned to a lowest-energy 1nπ* state. Approximately 10–50% of all photoexcited pyrimidine bases decay via the 1nπ* state, which has a lifetime of 10–150 ps. Three- to 6-fold-longer lifetimes are seen for pyrimidine nucleotides and nucleosides than for the corresponding free bases, revealing an unprecedented effect of ribosyl substitution on electronic energy relaxation. A small fraction of the 1nπ* population is proposed to undergo intersystem crossing to the lowest triplet state in competition with vibrational cooling, explaining the higher triplet yields observed for pyrimidine versus purine bases at room temperature. Some simple correlations exist between yields of the 1nπ* state and yields of some pyrimidine photoproducts, but more work is needed before the photochemical consequences of this state can be definitively determined. These findings lead to a dramatically different picture of electronic energy relaxation in single pyrimidine bases with important ramifications for understanding DNA photostability.

UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases

Excited electronic states created by UV excitation of the diribonucleoside monophosphates ApA, ApG, ApC, ApU, and CpG were studied by the femtosecond transient-absorption technique. Bleach recovery signals recorded at 252 nm show that long-lived excited states are formed in all five dinucleosides. The lifetimes of these states exceed those measured in equimolar mixtures of the constituent mononucleotides by one to two orders of magnitude, indicating that electronic coupling between proximal nucleobases dramatically slows the relaxation of excess electronic energy. The decay rates of the long-lived states decrease with increasing energy of the charge-transfer state produced by transferring an electron from one base to another. The charge-transfer character of the long-lived states revealed by this analysis supports their assignment to excimer or exciplex states. Identical bleach recovery signals were seen for ApA, (A)4, and poly(A) at delay times >10 ps after photoexcitation. This indicates that excited states localized on a stack of just two bases are the common trap states independent of the number of stacked nucleotides. The fraction of initial excitations that decay to long-lived exciplex states is approximately equal to the fraction of stacked bases determined by NMR measurements. This supports a model in which excitations associated with two stacked bases decay to exciplex states, whereas excitations in unstacked bases decay via ultrafast internal conversion. These results establish the importance of charge transfer-quenching pathways for UV-irradiated RNA and DNA in room-temperature solution.

Pulse retrieval in frequency-resolved optical gating based on the method of generalized projections

We use the algorithmic method of generalized projections (GPs) to retrieve the intensity and phase of an ultrashort laser pulse from the experimental trace in frequency-resolved optical gating (FROG). Using simulations, we show that the use of GPs improves significantly the convergence properties of the algorithm over the basic FROG algorithm. In experimental measurements, the GP-based algorithm achieves significantly lower errors than previous algorithms. The use of GPs also permits the inclusion of an arbitrary material response function in the FROG problem.

Quantum control of I2 in the gas phase and in condensed phase solid Kr matrix

We present experimental results and theoretical simulations for an example of quantum control in both gas and condensed phase environments. Specifically, we show that the natural spreading of vibrational wavepackets in anharmonic potentials can be counteracted when the wavepackets are prepared with properly tailored ultrafast light pulses, both for gas phase I2 and for I2 embedded in a cold Kr matrix. We use laser induced fluorescence to probe the evolution of the shaped wavepacket. In the gas phase, at 313 K, we show that molecular rotations play an important role in determining the localization of the prepared superposition. In the simulations, the role of rotations is taken into account using both exact quantum dynamics and nearly classical theory. For the condensed phase, since the dimensionality of the system precludes exact quantum simulations, nearly classical theory is used to model the process and to interpret the data. Both numerical simulations and experimental results indicate that a properly ...

Broadly tunable 30-fs pulses produced by optical parametric amplification

Broadly tunable 30-fs pulses have been generated by parametric amplification of a white-light continuum at kilohertz repetition rates.

Phase and intensity characterization of femtosecond pulses from a chirped-pulse amplifier by frequency-resolved optical gating

Frequency-resolved optical gating (FROG) measurements were made to characterize pulses from a Ti:sapphire chirped-pulse amplified laser system. By characterizing both the pulse intensity and the phase, the FROG data provided the first direct observation to our knowledge of residual phase distortion in a chirped-pulse amplifier. The FROG technique was also used to measure the regenerative amplifier dispersion and to characterize an amplitude-shaped pulse. The data provide an experimental demonstration of the value of FROG for characterizing complex pulses, including tailored femtosecond pulses for quantum control.

Intermolecular vibrational motion in CS2 liquid at 165 ⩽ T⩾ 300 K observed by femtosecond time-resolved impulsive stimulated scattering

Abstract Temperature-dependent molecular dynamics of CS 2 liquid are examined in femtosecond time-resolved impulsive stimulated scattering experiments. At temperatures T ⩽ 240 K, weakly oscillatory time-dependent responses are observed. These are interpreted in terms of librations of molecules about their local potential minima. The librations undergo rapid inhomogeneous dephasing. Temperature-dependent values of the configuration-averaged librational frequency and the extent of inhomogeneity in that frequency are determined.

Molecular dynamics in liquids from femtosecond time-resolved impulsive stimulated scattering

Molecular motions in simple liquids are observed on the femtosecond time scale by means of impulsive simulated scattering. In carbon disulphide and benzene liquids, weakly oscillatory time-dependent responses are observed. These are interpreted in terms of molecular orientational motion which at short times is vibrational (i.e. librational) in character due to intermolecular interactions. In CS/sub 2/, the dephasing of the oscillations is primarily inhomogeneous. Temperature-dependent values of the configuration-averaged librational frequency and the extent of its inhomogeneity are determined. >