Excimers and Exciplexes in Photoinitiated Processes of Oligonucleotides

Abstract

A lot has been learned about the physical and chemical transformations that originate from the absorption of light by DNA, and computational chemistry has played a critical role in revealing the mechanisms of how these transformations occur. Nucleic acids consist of chromophores interacting via π stacking and hydrogen bonding. The fate of these systems after they absorb light is determined by the interplay and competition between pathways involving one chromophore or interacting chromophores. This Perspective highlights the role of π stacking in photophysical and photochemical processes in oligonucleotides and reveals the importance of excimers and exciplexes. Special types of excimers/exciplexes, characterized as bonded excimers/exciplexes, are also found to be important.

Photochemical Formation of Cyclobutane Pyrimidine Dimers in DNA through Electron Transfer from a Flanking Base

“…ET from an external moiety is believed to quench CPD formation, but, in contrast to what is known so far, here we demonstrate that a pathway initiated by ET from a flanking base can also lead to CPD formation. Furthermore, we also illustrate that the methylation of cytosine in T5mCG uses this pathway to enhance CPD formation ,…”

“…ET is also involved in CPD repair by DNA photolyase where a crucial step is ET from its cofactor to CPD.Meanwhile, the methylation of cytosine at the 5 position, an epigenetic mechanism regulating various biological functions, is closely related to the mutational hot spots. The formation of CPD has been shown to be involved in these mutations and enhanced by the presence of 5-methylcytosine, [12] but the mechanistic details of this enhancement are still poorly understood.ET from an external moiety is believed to quench CPD formation, [13][14][15] but, in contrast to what is known so far, here we demonstrate that a pathway initiated by ET from a flanking base can also lead to CPD formation. Furthermore, we also illustrate that the methylation of cytosine in T5mCG uses this pathway to enhance CPD formation.…”

Photophysical properties of pyrrolocytosine, a cytosine fluorescent base analogue

“…Relaxation away from the FC region may stabilize these states leading to minima with CT character and additional decay mechanisms. This behavior has been found in several π-stacked bases including 2AP systems, 66 and could play a role in the PC systems as well.…”

Sequence Dependent Photochemistry of Adenine-Thymine and Thymine-Adenine Dinucleotides

“…The photochemical processes in DNA have attracted much attention owing to their relation with carcinogenic mutations [1,2]. Under UV irradiation, DNA thymine-adenine dinucleotide sequence in DNA promoter and impedes normal gene expression [3,4].…”