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Long-range Stacking Effects of Nucleobases in Charge Transfer

submitted on 09.08.2020, 10:32 and posted on 10.08.2020, 12:54 by 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.


National Natural Science Foundation of China (Grant No. 21703234).


Email Address of Submitting Author


Dalian Institute of Chemical Physics



ORCID For Submitting Author


Declaration of Conflict of Interest

no interest of confilict

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