Radical cations migration in DNA

Base Sequence Effects on Radical Cation Migration in DNA -... 

Fig. 4 Schematic representation of long-distance radical cation migration in DNA. In AQ-DNA(l), irradiation of the anthraquinone group linked at the 5 -terminus leads to reaction at GG steps that are 27 A and 44 A from the site of charge injection. The amount of reaction observed at each guanine is represented approximately by the length of the solid arrow. In UAQ-DNA(2), irradiation of the anthraquinone leads to reaction at each of the eight GG steps. However, replacement of a G by 7,8-dihydro-8-oxoguanine (8-OxoG) introduces a deep trap that inhibits reaction at guanines on the same side of the DNA as the trap...

The mechanism of long-range radical cation migration in DNA has been reported... 

Having an ATA sequence between assigned polarons does not always create a high barrier for radical cation migration. In AQ-DNA(IO), we assign... 

Abdou IM, Sartor V, Cao H, Schuster GB (2001) Long-distance radical cation migration in Z-form DNA. J Am Chem Soc 123 6696-6697... 

Liu C-S, Schuster GB (2003) Base sequence effects in radical cation migration in duplex DNA support for the polaron-like hopping model. J Am Chem Soc 125 6098-6102 Llano J, Eriksson LA (2004) First principles electrochemical study of redox events in DNA bases and chemical repair in aqueous solution. Phys Chem Chem Phys 6 2426-2433... 

Therefore, the sequence of reactions illustrated in Fig. 1 catalytically (the anthraquinone is regenerated) injects a radical cation into a DNA oligonucleotide that does not simultaneously contain a radical anion. As a result, the lifetime of this radical cation is determined by its relatively slow bimolecular reaction with H20 (or some other diffusible reagent such as 02- ) and not by a rapid intramolecular charge annihilation reaction. This provides sufficient time for the long distance migration of the radical cation in DNA to occur. 

The anthraquinone group of the UAQ sensitizer is intercalated on the 3 -side of its linkage site [15]. Use of UAQ permits assessment of the directionality of long-range radical cation migration. Both AQ and UAQ enable the selective and efficient introduction of a radical cation in duplex DNA, whose lifetime is controlled by its relatively slow bimolecular reaction primarily with H20. 

GG8, the radical cation must traverse five A/T base pairs. Electrochemical measurements in solution have shown that the purine bases (A and G) have considerably lower Eox than the pyrimidines (C and T), with the Eox of G estimated to be about 0.25 V below that of A [20]. It is not very likely that the Eox of bases in DNA will be the same as they are in solution, but it is generally assumed that the order of Eox will remain the same. Consequently, the radical cation at Gi of AQ-DNA(l) must traverse a bridge of five A bases to reach GG8. The process whereby the radical cation crosses such bridges has been a major point of debate in consideration of long distance radical cation migration mechanisms in DNA this issue will be discussed fully below. 

The primary conclusion that follows from the effect of base sequence on the efficiency of radical cation migration through duplex DNA is that base pairs cannot be considered in isolation. For example, the effect of placing a T in a sequence of purines depends critically on the nature and number of purines. In this regard, the effect of base sequence on radical cation transport emerges from examination of collective properties of the DNA. This is a clear indication that the charge is delocalized over several base pairs, a conclusion that is supported by extensive quantum calculations. 

The pattern and efficiencies of strand cleavage at GG steps in duplex DNA reflect the ability of a radical cation to migrate from its initial position through a sequence of base pairs. In an illustrative example, we consider the photochemistry of AQ-DNA(l), which is shown in Fig. 4. AQ-DNA(l) is a 20-mer that contains an AQ group linked to the 5 -end of one strand and has two GG steps in the complementary strand. The proximal GG step is eight base pairs, ca. 27 A, from the 5 -end linked to the AQ, and the distal GG step is 13 base pairs (ca. 44 A) away. The complementary strand is labeled with 32P at its 5 -terminus (indicated by a in Fig. 4). 

The results from irradiation of AQ-DNA(l) show conclusively that a radical cation introduced at one site, Gi at the 3/-terminus of the complementary strand in this case, can migrate through duplex DNA and cause reaction at remote sites. To migrate from its point of injection at Gi to where it reacts at... 

The experiments described above, and those carried out in other laboratories, leave no doubt that a radical cation introduced at one location in DNA can migrate to and cause reaction at a remote location. The mechanism of this long-distance process has been enthusiastically debated and three broad possibilities have emerged ... 

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