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submitted on 09.08.2020 and posted on 10.08.2020by Zhongwei Li, Keli Han
Base-stacked structure is an important feature of DNA molecules. Previous studies on the stacking effect concerning DNA-mediated hole transfer have revealed the influence of neighboring bases on onsite energies. But the neighboring base effect acts only in a short-distance. Besides it, a long-range (longer than three base pairs) stacking effect called squeezing effect in this paper has not yet been reported. Such a squeezing effect causes the bases near the middle of a sequence consisting of same type base pairs have lower onsite energies than the bases near the terminals. We predict it by H ̈uckelanalysis in an unconventional way and confirmed it by semiempirical calculations combinated with molecular dynamics simulations. The results suggest that in order to obtain a reasonable onsite energy map when study charge transfer on DNA, the stacking effects should be considered in a long-distance as possible. The consideration of squeezing effect also provides a new suggestion on the driving force of fluctuation-assisted DNA charge transfer. The method used to calculate the onsite energies in abase stack can be generalized to other π-stacked systems.