Excited States in DNA

The interaction of UV radiation with nucleic acids is of great importance since it can lead to UV-induced damage in DNA with profound consequences, including photocarcinogenesis [1,2]. The nucleobases are the primary chromophores in DNA and RNA, and consequently, the photophysical and photochemical behavior of the nucleobases has been the focus of extensive theoretical and experimental work over the years [4, 6, 81, 82], 

Upon absorption of UV radiation from sunlight the bases can proceed through photochemical reactions that can lead to photodamage in the nucleic acids. Photochemical reactions do occur in the bases, with thymidine dimerization being a primary result, but at low rates. The bases are quite stable to photochemical damage, having efficient ways to dissipate the harmful electronic energy, as indicated by their ultrashort excited state lifetimes. It had been known for years that the excited states were short lived, and that fluorescence quantum yields are very low for all bases [4, 81, 82], Femtosecond laser spectroscopy has, in recent years, enabled a much 

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In conclusion, we present herein a rather compelling model for the short-time dynamics of the excited states in DNA chains that incorporates both charge-transfer and excitonic transfer. It is certainly not a complete model and parametric refinements are warranted before quantitative predictions can be established. For certain, there are various potentially important contributions we have left out disorder in the system, the fluctuations and vibrations of the lattice, polarization of the media, dissipation, quantum decoherence. We hope that this work serves as a starting point for including these physical interactions into a more comprehensive description of this system. 

Role of excited states in DNA damage experimental and theoretical results... 

Harpe, K. de La 8c Kohler, B. (2011). Observation of long-lived excited states in DNA oligonucleotides with significant base sequence disorder. The Journal of Physical Chemistry Letters, 2, 133. 

Bases stacked rather than hydrogen bonded have also been studied with quantum chemical methods [182, 244-247]. The nature of excited states in these systems has been debated and theoretical calculations are called to decide on the degree of excited state localization or delocalization, as well as the presence and energy of charge transfer states. The experimentally observed hypochromism of DNA compared to its individual bases has been known for decades [248], Accurate quantum chemical calculations are limited in these systems because of their increased size. Many of the reported studies have used TDDFT to calculate excited states of bases stacked with other bases [182, 244, 246, 247], However, one has to be cautious when us-... 

Oxygen-free reactions of psoralens, when in close proximity to the target, proceed via the first excited states in which the 3,4-and the 4, 5 7r-bonds of the pyrone and furan moieties, respectively, can undergo C4-cyclization reactions with, e.g., unsaturated bonds of lipids, or the C5=C6 double bonds of thymine in DNA. In reactions with DNA the psoralen is believed to intercalate with DNA in the dark. Subsequent irradiation at 400 nm usually leads to furan-side 4, 5 -monoadduct formation, whereas irradiation at 350 nm increases the formation of crosslinks in which the furan and pyrone rings form C4 cycloadducts to thymines on opposite strands [95], Subsequent irradiation of the 4, 5 -monoadducts at 350 nm leads to formation of crosslinks and conversion into pyrone-side 3,4-monoadducts. Shorter wave-... 

Abstract. We consider here the theoretical and quantum chemical description of the photoexcitated states in DNA duplexes. We discuss the motivation and limitations of an exciton model and use this as the starting point for more detailed excited state quantum chemical evaluations. In particular, we focus upon the role of interbase proton transfer between Watson/Crick pairs in localizing an excitation and then quenching it through intersystem crossing and charge transfer. 

An important issue in the nature of the excited states in stacks of DNA bases is whether or not the states extended over a number of the bases are neutral Frenkel excitons or if they carry some degree of charge transfer character (exciplex or excimer).3 [2-4] A purely excitonic model neglects configurations... 

Beaumont, PC., Parsons, B.J., Navaratnam, S., Phillips, G.O., and Allen, J.C. (1980) The reactivities of furocoumarin excited states with DNA in solution. A laser flash photolysis and fluorescence study, Biochim. Biophys. Acta, 608, 259-265. 

Intercalation of the luminescent cyclometalated [Pt(C6ANAN)(MeCN)]+ 46 (HC6ANAN=2,9-diphenyl-l,10-phenanthroline) and [Pt2(C1 ANAN)2(/U-dppm)]2+ 7b complexes into calf-thymus DNA leads to a dramatic enhancement of their photoluminescence [16d]. The intercalation is likely to prohibit the solvent-induced quenching process, which typically occurs at the coor-dinative unsaturated platinum site for the MLCT excited state. The DNA-in-tercalating platinum(II) complex, [Pt(dppz)(tNAC)]CF3S03 (dppz=dipyri-do[3,2-a 2, 3 -c]phenazine, fNACH=4-ferf-butyl-2-phenylpyridine) 47 similarly exhibits an increase in emission intensity at Amax 650 nm on addition of calf thymus DNA (Fig. 22) [46]. 

Experimental studies of ground state properties of DNA bases have been carried out for many years. This includes studies of their molecular structures. Although one can conclude that the ground state of these important DNA constituents is well characterized, data concerning their excited state properties is scarce. The molecular geometry of such complex systems like DNA bases cannot be determined by experimental methods. It creates a need for theoretical studies that could shed light on the properties of DNA bases in the excited state. In the last chapter of this volume, M.K. Shukla and J. Leszczynski discuss available experimental data of DNA bases, base pairs, and their complexes with water. The discussion is enhanced by an overview of the results of recent... 

The ability to survive electronic excitation is a fundamental property of DNA [1]. While excited states of DNA nucleobases are important in mutation and repair processes, the average lifetime of these states is 1 ps [2]. DNA excited states dissipate in a variety of ways with the dominant mechanism being non-radiative decay. Other decay pathways are important due to their health implications ... 

Phenol has been interesting many chemists as a model system to study how photo-excited bases in DNA can deactivate to the ground state without resulting in mutation. Not only in such biology-oriented studies, this molecule shows many other interesting features when put in surrounding molecules, clusters, and solvents. Small ammonia clusters are frequently used in place of water-molecule clusters, because ammonia is more proton-attractive than water, and very extensive studies have been performed... 

Kumar, A., 8c Sevilla, M. D. (2008b). The role of Tier excited states in electron-induced DNA strand break formation A time-dependent density functional theory study. Journal of the American Chemical Society, 130, 2130. 

A. W. Lange and J. M. Herbert,/. Am. Chem. Soc., 131, 3913-3922 (2009). Both Intra- and Interstrand Charge-Transfer Excited States in B-DNA are Present at Energies Comparable to, or Just above, the Excitonic Bright States. 

Resonance Raman Spectroscopy. If the excitation wavelength is chosen to correspond to an absorption maximum of the species being studied, a 10 —10 enhancement of the Raman scatter of the chromophore is observed. This effect is called resonance enhancement or resonance Raman (RR) spectroscopy. There are several mechanisms to explain this phenomenon, the most common of which is Franck-Condon enhancement. In this case, a band intensity is enhanced if some component of the vibrational motion is along one of the directions in which the molecule expands in the electronic excited state. The intensity is roughly proportional to the distortion of the molecule along this axis. RR spectroscopy has been an important biochemical tool, and it may have industrial uses in some areas of pigment chemistry. Two biological appHcations include the deterrnination of helix transitions of deoxyribonucleic acid (DNA) (18), and the elucidation of several peptide stmctures (19). A review of topics in this area has been pubHshed (20). 

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