DNA is an ideal target for single-molecule, manipulations. The conformation of stacked basepairs in DNA depends sensitively on various factors such. as temperature, the kind of solvent and counterions, changes in the backbone, applied forces, etc. This raises the question of whether the rate of charge transfer (CT) through the stack can be considerably enhanced by tuning of "observed" DNA conformations. Using a stochastic approach to account for the effects of thermal fluctuations, we study how the efficiency of CT in poly(dA)-poly(dT) and poly(dG)-poly(dC) sequences will change by variation of the pi stack structure. The CT process is shown to be not very sensitive to the torsional angle (twist) while affected more strongly by altering translation modes (shift and slide). We conclude that the design of basepair stacks with significantly improved electrical conductivity, as compared to poly(dG)-poly (dC), appears to be quite elusive. Specific changes of the pi stack structure can increase the efficiency of CT by a factor of similar to 3 (e.g., in systems with negative shift); much stronger effects can hardly be expected. This result, formally derived for molecular ensembles, should also be applicable for single-molecule systems because of the strong effects of dynamical disordering.