Kinetic analysis of hole migration through DNA

The mechanism of hole migration through donor-DNA-acceptor systems is studied using a kinetic model, in which the time evolution of the hole population at guanine sites is expressed in terms of the hopping rates between neighboring guanine-cytosine (GC) base pairs. The hole hopping rates are empirically determined and effectively include all important factors of the hole migration process. We present quantitative and qualitative descriptions of hole migration along DNA by analyzing such quantities as survival probabilities, mean residence times, and mean first passage times for a number of different donor-DNA-acceptor systems. The sequence dependence and distance-dependence of the hole-migration mechanism are examined in depth for both short and long donor-DNA-acceptor systems. Some important consequences obtained from our analysis are as follows: (i) The path that a hole takes in going through cross-linked adenine-thymine (AT) base pairs is 1.5 times longer than the typical base-stacking distance; thus, the hole transfer rate decreases about twice as fast for each cross-linked AT base pair as for a directly linked one. (ii) If the GC and AT base pairs are properly arranged the hole migration time can be changed, while keeping the transfer rate the same. (iii) A formula is derived for estimating the maximal length of regular DNA bridges for use in hole-migration experiments.