Sequence strand cleavage

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. 

In contrast to the overwhelming affect of conversion of an A/T base pair in AQ-DNA(4) to a T/A base pair in AQ-DNA(5) on radical cation transport, the identical change in AQ-DNA(6) and AQ-DNA(7) has no measurable effect on the amount of strand cleavage observed at GG7 or GG2i [27]. It is apparent from consideration of these results that the effect of a change in base sequence must be considered in the context of the surrounding base pairs and not in isolation. 

The linear distance dependence seen for AQ-DNA(3) is not observed to be universally independent of specific DNA base sequence. This is clearly revealed by examination of AQ-DNA(4) and AQ-DNA(5). Plots of the distance dependence of strand cleavage at the GG steps in these oligomers are shown in Fig. 11. Both show stepped rather than linear behavior, and the size of... 

Fig. 2 Photocleavage of GG-containing oligomers complementary to the corresponding dCNBPu-containing strands. dCNBPU was located opposite to the A at position 0 (shown in red). Partial sequences of ODNs are shown and the sites of strand cleavage are underlined. Single Gs proximal to the dCNBPU-A base pair are shown in bold face. Efficiencies at the major cleavage sites were 18.5% (at position -4, ODN 5), 1.9% (at position +5, ODN 1), and 1.5% (at position -5, ODN 7)...

Although the strand cleavage is normally a sequence neutral reaction, runs of A-T appear to show enhanced reactivity [189]. The preferential reaction in this area is believed to be due to stronger binding of the to such extended... 

Figure 10 shows that the values of kag for the oxidation of G and GG are close to one another, and are smaller by a factor of only -1.7 than the value of kag for the oxidation of guanine in the GGG sequence. Estimates by Lewis et al. [89] have shown that even small differences in the rate constants can provide modest selectivities for alkali-labile strand cleavage observed in a number of experimental studies [83-90]. 

Absalon MJ, Kozarich JW, Stubbe J (1995) Sequence-specific double-strand cleavage of DNA by Fe-bleomycin. I. The detection of sequence-specific double-strand breaks using hairpin oligonucleotides. Biochemistry 34 2065-2075... 

The affinity towards a complementary RNA strand can be improved by using peptide nucleic acids (PNAs) [20]. These DNA mimics, in which the nucleic acid bases are linked to a polyamide backbone [21], usually exhibit improved binding properties with a complementary DNA or RNA strand [22]. The use of an excess PNA-DETA adduct 20 in a Tris-HCl buffer (pH 7), in the presence of NaCl and EDTA at 40 °C, resulted in a sequence-selective cleavage of the RNA strand 21... 

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