Strand cleavage

Mei and Barton [66, 67] have used photo-sensitised damage to DNA by /1-Ru(TMP)3 (induced by 02 formation) as a means of probing A-DNA conformations, and they have compared the damage so caused on a linear 

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Strand Cleavage Stemming from Abstraction of the Cl -Hydrogen Atom 351... 

Strand Cleavage Initiated by Abstraction of the 4 -Hydrogen Atom 353... 

The guanine radical cations (G +) are detected by their reactions with water, which leads after treatment with piperidine or ammonia to selective strand cleavage [14]. A similar charge detection method was used by J.K. Barton, G.B. Schuster and I. Saito as described in their articles in this volume. The cleavage products were separated and quantified by gel electrophoresis. A typical example is shown in Fig. 7 where the GGG unit acts as a thermodynamic sink for the positive charge, and the efficiency of the charge transfer can be measured by the product ratio Pggg/Pg-... 

Fig. 7 Histogram showing the products PG and PGgg> formed after charge injection into G, water trapping of the guanine radical cations and subsequent strand cleavage...

Strand cleavage studies have provided relative rate constants for hole transport versus the rate constant for the initial chemical event leading to strand cleavage [18-20]. However, they do not provide absolute rate constants for hole transport processes. Several years ago we introduced a method based on femtosecond time-resolved transient-absorption spectroscopy for investigating the dynamics of charge separation and charge recombination in synthetic DNA hairpins [21, 22]. Recently, we have found that extensions of this method into the nanosecond and microsecond time domains permit investigation of the dynamics of hole transport from a primary hole... 

GG and GGG sequences have been widely used in strand cleavage studies of hole migration in DNA [4-6]. According to conventional wisdom, GG and GGG sequences serve as hole traps . The calculated gas phase ionization potentials reported by Sugiyama and Saito [14] provide relative energies for G vs GG (0.47 eV) and G vs GGG (0.68 eV) that continue to be cited as evi-... 

To our knowledge, there are no other direct measurements of the dynamics of interstrand hole transport. However, the strand cleavage studies of Meggers et al. [17] have clearly demonstrated that long-distance hole transport can occur via a G-hopping sequence in which guanines are located in both strands. Other workers have assumed that hole transport occurs exclusively via intrastrand pathways [45]. 

The dynamics of inter- vs intrastrand hole transport has also been the subject of several theoretical investigations. Bixon and Jortner [38] initially estimated a penalty factor of ca. 1/30 for interstrand vs intrastrand G to G hole transport via a single intervening A T base pair, based on the matrix elements computed by Voityuk et al. [56]. A more recent analysis by Jortner et al. [50] of strand cleavage results reported by Barton et al. [45] led to the proposal that the penalty factor depends on strand polarity, with a factor of 1/3 found for a 5 -GAC(G) sequence and 1/40 for a 3 -GAC(G) sequence (interstrand hole acceptor in parentheses). The origin of this penalty is the reduced electronic coupling between bases in complementary strands. 

Our data provide a ratio of 1 0.2 0.1 for reactivity at G, GG, and GGG sites on a per-G basis. These relationships are summarized in Table 2. The small difference in G vs GG vs GGG hole stability and lower reactivity of the more stable sites is, of course, precisely the combination of stability and reactivity that is required for the observation of hole transport over long distances containing multiple G and GG sites. Hole transport between two GGG sites separated by a TTGTT sequence appears to be somewhat slower than cleavage at the initially oxidized GGG site [12]. To our knowledge, the efficiency of strand cleavage in duplexes possessing more than two GGG sites has not been studied. 

In the second limiting case, the rate of reaction with H20 is presumed to be much slower than the rate of radical cation migration and independent of the specific base pair sequence surrounding the GG step. Under these circumstances, each GG step will be equally reactive, and just as much strand cleavage will be observed at the GG step farthest from the AQ as at the one closest to it. 

Therefore, analysis of the efficiency and pattern of strand cleavage provides information on the relative rate of radical cation migration through different DNA sequences. This is powerful information for analysis of the charge migration mechanism. 

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 relative amount of strand cleavage at each site of AQ-DNA(l) is indicated by the length of the solid vertical arrow shown in Fig. 4. As is often observed, the 5 -G of the GG steps react more often than do the 3 -G. In the case of AQ-DNA(l), the relative reactivity is ca. 1 3, but this ratio depends upon the specific base pair sequence surrounding a GG step, which may be an indication of radical cation delocalization to bases adjacent to the GG sequence. It is worth pointing out again that these reactions are carried out under single-hit conditions where the relative strand cleavage efficiency seen at various locations of AQ-DNA(l) reflect the statistical probability that the radical cation will be trapped by H20 at that site. 

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