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Molecule Reclame

The hole density is found principally on guanines G, G, and G.Structural relaxation of the vertically ionized DNA redistributes the hole density and lowers the ionization potential, thereby creating a selftrapped polaron.The most signicant structural changes are not of the DNA itself but of the surrounding medium.The role that steric effects can play in reactions at GG steps was probed through a combination of experiments and theoretical simulations.Quantum mechanical calculations of the hole spatial distribution in ionized DNA oligomers containing the sequences XGGX, where X stands for T or uracil, show that the radical cation density on the guanines in the sequences TGGT and UGGU are essentially identical.Access to C occurs through a coneshaped region extending from the side of the guanine oriented along the direction of the developing carbonoxygen bond.The MD simulations reveal {|Targetmol’s {Endurobol|Amiodarone little change in access to the G of a GG pair for the TGGT and UGGU sequences, while the methyl group of T is found to signicantly hinder access of HO to the C of the G.Thus, the preference for reaction at the G of UGGU compared with TGGT appears to be a result of steric inhibition of reaction at the G by the methyl group on thymine.In general, the relative rate for reaction at a particular nucleobase radical cation in DNA is determined by factors that are comprised of both electronic and steric effects.First, an ensemble of congurations, characterized by their high abundance, were selected from a roomtemperature MD simulation.Removal of an electron from these congurations gives a DNA radical cation, and those congurations of the ionized DNA having the lowest vertical IP were further relaxed.Several of the tightly bound solvating HO molecules are shown.The atoms are coded as follows: P, yellow; C, gray; N, light blue; O, red; H, white.This structure was selected from among many highprobability congurations revealed by the MD simulation.The DNA was ionized, and the resulting DNA radical cation and the solvating HO molecules were relaxed to give the structures shown here.This predicted path is supported experimentally; the reaction yield is reduced when the phosphate group adjacent to the GG step is replaced with a methylphosphonate group, which is electrically neutral.Signicantly, related protoncoupled electron transfer reactions are now being found to underlie a number of important processes.Atoms not directly involved in the reaction are not shown.Further evolution along the reaction coordinate leads to step where the formation of a hydroxy,dihydroguanyl radical is accompanied by generation of HO.Irradiation of the duplex sequence ATATAAA causes reaction at the thymine bases of the TT steps revealed as distancedependent strand cleavage when the irradiated samples are treated with hot piperidine.If a GG step is incorporated in a duplex that otherwise is comprised only of TA base pairs, reaction occurs primarily at the GG sequence even if it is much farther from the site of radical cation injection than the TT steps.That is, when there is a GG step in the oligonucleotide, the nsequence changes its character from that of a trap to that of a shuttle.

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