Thymine Dimerization in DNA Is an Ultrafast Photoreaction

Abstract

Femtosecond time-resolved infrared spectroscopy was used to study the formation of cyclobutane dimers in the all-thymine oligodeoxynucleotide (dT)18 by ultraviolet light at 272 nanometers. The appearance of marker bands in the time-resolved spectra indicates that the dimers are fully formed approximately 1 picosecond after ultraviolet excitation. The ultrafast appearance of this mutagenic photolesion points to an excited-state reaction that is approximately barrierless for bases that are properly oriented at the instant of light absorption. The low quantum yield of this photoreaction is proposed to result from infrequent conformational states in the unexcited polymer, revealing a strong link between conformation before light absorption and photodamage.

UV degradation of deoxyribonucleic acid

“…In fact, the cyclobutane pyrimidine dimer is the most abundant lesion caused by ultraviolet radiation and consists of a reaction of the carbon-carbon double bonds of two proximal pyrimidine bases to form a cyclobutane ring. This reaction has been recently investigated by femtosecond time-resolved infrared spectroscopy [34] and it was revealed that in DNA samples irradiated at 266 nm, the intensity of infrared bands due to double-band stretch associated with the two carbonyl groups and the …”

Ultrafast excited-state dynamics of RNA and DNA C tracts

“…Raman measurements on (dC) 10 were interpreted in terms of a complex equilibrium between duplex, tetraplex, and even octaplex structures [57]. The two-dimensional NMR spectra of Snoussi et al suggest that (rC) 5 adopts multiple intercalation topologies perhaps including an i-motif core terminated by double-stranded hemiprotonated duplexes or unpaired dangling strands [54].…”

“…In recent years, ultrafast laser spectroscopy has provided many new insights into excited states in nucleic acids [3][4][5][6][7][8][9][10]. Experiments on single bases are easier to interpret than those on multiple base systems ("base multimers"), and are more amenable to quantum chemical modeling [11][12][13][14][15].…”

Picosecond infrared probing of the vibrational spectra of transients formed upon UV excitation of stacked G-tetrad structures

“…4 To fully understand the nature of the molecular specific interactions, it is essential to employ techniques that can interrogate the structural modifications underpinning these processes, and here we apply ultrafast time-resolved infrared spectroscopy (TRIR) for this purpose. ps-TRIR is now being demonstrated as a powerful technique for probing the photophysical properties of DNA, [5][6][7][8] and its strength stems from its ability to yield kinetic and structural information that goes beyond that obtainable from fluorescence or transient UV/visible absorption techniques.In this communication, we describe how ps-TRIR can be employed to investigate conformationally dependent photophysical properties of base-base interactions. Guanine is known to aggregate to form stacked species at high concentrations.…”