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C₆₀ Binds to and Deforms Nucleotides

Xiongce Zhao ^*, Alberto Striolo  and Peter T. Cummings ^* 

^* Nanomaterials Theory Institute, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee; and Department of Chemical Engineering, Vanderbilt University, Nashville, Tennessee

Correspondence: Address reprint requests to Xiongce Zhao, E-mail: zhaox{at}ornl.gov.

Atomistic molecular dynamics simulations are performed for up to 20 ns to monitor the formation and the stability of complexes composed of single- or double-strand DNA molecules and C₆₀ in aqueous solution. Despite the hydrophobic nature of C₆₀, our results show that fullerenes strongly bind to nucleotides. The binding energies are in the range –27 to –42 kcal/mol; by contrast, the binding energy of two fullerenes in aqueous solution is only –7.5 kcal/mol. We observe the displacement of water molecules from the region between the nucleotides and the fullerenes and we attribute the large favorable interaction energies to hydrophobic interactions. The features of the DNA-C₆₀ complexes depend on the nature of the nucleotides: C₆₀ binds to double-strand DNA, either at the hydrophobic ends or at the minor groove of the nucleotide. C₆₀ binds to single-strand DNA and deforms the nucleotides significantly. Unexpectedly, when the double-strand DNA is in the A-form, fullerenes penetrate into the double helix from the end, form stable hybrids, and frustrate the hydrogen bonds between end-group basepairs in the nucleotide. When the DNA molecule is damaged (specifically, a gap was created by removing a piece of the nucleotide from one helix), fullerenes can stably occupy the damaged site. We speculate that this strong association may negatively impact the self-repairing process of the double-strand DNA. Our results clearly indicate that the association between C₆₀ and DNA is stronger and more favorable than that between two C₆₀ molecules in water. Therefore, our simulation results suggest that C₆₀ molecules have potentially negative impact on the structure, stability, and biological functions of DNA molecules.