C^sub 60^ Binds to and Deforms Nucleotides

Headnote

ABSTRACT

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 C^sub 60^ in aqueous solution. Despite the hydrophobic nature of C^sub 60^, 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-C^sub 60^ complexes depend on the nature of the nucleotides: C^sub 60^ binds to double-strand DNA, either at the hydrophobic ends or at the minor groove of the nucleotide. C^sub 60^ 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 C^sub 60^ and DNA is stronger and more favorable than that between two C^sub 60^ molecules in water. Therefore, our simulation results suggest that C^sub 60^ molecules have potentially negative impact on the structure, stability, and biological functions of DNA molecules.

INTRODUCTION

Several recent reports have highlighted the potentially hazardous nature of nanomaterials (1-3). For example, it has been shown that carbon nanotubes, arguably the best known nanomaterials, can accumulate in the lungs of rats, and possibly cause the development of granulomas in rats (4,5). The nanomaterials we consider in this work are buckminsterfullerenes (C^sub 60^) (6,7), because they show several promising potential applications in biology and pharmacology (8-11) and are regarded as one of the building blocks for nanotechnology applications.

The interest in biological applications of C^sub 60^, as well as that for possible applications in materials science and in other disciplines,...