Molecular Cell Biology

Oneelectron oxidation of the duplex oligomer containing the sequence results in essentially equivalent reaction at each of its six GG steps.In this case, a semilogarithmic plot of strand cleavage yield versus distance from the AQ has a slope indistinguishable from zero.In contrast, the GG step closest to the AQ of the duplex oligomer containing the sequence reacts with much higher yield than those that are farther away.The hopping model reveals that these slopes are related to the ratio of two generic pseudorstorder rate constants: one for reversible hopping that leads to damaged bases.If khopektrap, the reaction is under kinetic control and sites closer to the site of initial oxidation react with greater probability.The situation is more complicated for DNA oligomers that do not have a regularly repeating pattern of nucleobases.For these mixed sequence oligomers, reactivity depends on the identity and sequence of all the other bases in the oligomer, and the semilogarithmic plots are often not linear and have little meaning.The shading represents the relative amount of strand cleavage observed at each site.Critically, the behavior of a set of nucleobases is context dependent; for example, in one circumstance a sequence can act as a trap and in another as a shuttle.Traps, shuttles, and barriers can be combined to create relative potential energy landscapes that enable the qualitative prediction of reactivity patterns.For example, the TGTGTGTGT sequence is a trap in the duplex DNA where oxidation results in equivalent amounts of reaction at each of the four guanines.The character of the TGTGTGTGT sequence changes to that of shuttle in the duplex DNA where the two anking GG steps behave as traps because of their signicantly lower oxidation potential and higher reactivity than that of an isolated G.The amount of strand cleavage observed at both GG steps in this oligomer is essentially the same even though one is more than farther from the site of initial oxidation than the other.In this oligomer, the TGTGTGTGT sequence shuttles the radical cation between the GG steps, and the entire reaction is under thermodynamic control because hopping is always faster than trapping.It is possible to transform a GG step from a trap to part of a shuttle.The oxoG is a deep trap with such high reactivity that once the radical cation arrives at that position it is always consumed.However, reaction at the oxoG can be {|buy {Endurobol|Amiodarone prevented by the introduction of a kinetic barrier to charge migration.The TTTT sequence has this property in the duplex. The oneelectron oxidation reaction of these two oligomers is under kinetic control because a trapping rate is greater than the rate of hopping.The key to the application of this approach is the realizat ion thatthe cha rac terofa part icu larnuc leobaseor sequence of bases cannot be determined without consideration of the entire oligonucleotide.The DNA duplex contains the minimum essential features required to simulate charge hopping, a donor base pair. A portion of the network of tightly bound solvating HO molecules is also shown with their oxygen atoms represented as orange spheres.The blue and green shadings in structure A represent the signs of the isosurfaces of the like HOMO, which is located primarily on the GG step.

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