Base-stacked structure is an important feature of DNA molecules. But dynamics study on the influences of the stacking effects on charge transfer in DNA is yet rare.In this article, a general rule about the relationship of onsite energies of same bases in a stack is derived by H ̈uckel theory. It is found that the base in the middle position of the stack has lower onsite energy than the bases at the terminals due to squeezing effect, which is different from previous studied neighboring base effect. The former is along-range effect while the latter acts in a short range. Semiempirical MNDO calculations on (A:T) n (n=1∼10) systems verfied the H ̈uckel analysis. From this perspective,the so-called incoherent hopping mechanism is actually somewhat coherent due to the squeezing effect. To understand these stacking effects on charge transfer in DNA,a cross-scale method which combines classical MD simulations, quantum mechanism calculations, Marcus electron transfer theory and kinetic Monte Carlo simulations is developed and applied on hole dynamics in (A:T) n (G:C) (n=1∼10) systems. Although no superexchange mechanism is explicitly involved in the studied systems, a crossover from strong to weak distance-dependency of hole arrival rates, which is an experimentally observed property of hole dynamics in DNA and is thought an evidence of the conversion from superexchange to hopping mechanism, also appears. We attribute it to the stacking effects. Such a result provides a new idea on explaining the crossover of different distance-dependencies of charge transfer rates in DNA. In addition, the squeezing effect may be a new driving force for long-range charge transfer. At the same time, some technical methods developed in the dynamics, e.g. calculations of onsite energies and electronic couplings in a stack, and simulated hole dynamics, etc.,can be generalized to other complex molecular systems with charge transfer behaviors.<br><br>
Stacking Effects on Charge Transfer Dynamics in Fluctuating DNA