Interaction of C60 Derivatives and ssDNA from Simulations

Abstract

We report atomistic modeling studies on the interaction of water-soluble C{sub 60} derivatives and single-stranded DNA (ssDNA) segments in phosphate-buffered solutions. Stable hybrids are formed by C{sub 60} derivatives and ssDNA segments, with binding energies in the range of -23 to -47 kcal/mol. By contrast, the typical binding energy between two C{sub 60} derivative molecules is -11 to -15 kcal/mol. The binding pattern of C{sub 60} derivatives with ssDNA molecules depends on the size and shape of the C{sub 60} functional groups. For C{sub 60} derivatives with functional groups that contain aromatic rings, strong ? stacking was observed between the ssDNA base rings and the functional benzene rings. For C{sub 60} derivatives with a long hydrophilic chain, the binding is greatly enhanced by the hydrophilic interaction from the entanglement between the chain and the ssDNA backbone. Stable hydrogen bonds were observed between the hydroxyl hydrogen on the functional chain and the phosphate oxygen on the ssDNA backbone. For C{sub 60} derivative with short hydrophilic groups, at least two binding patterns were observed, one of which is dominated by the hydrophobic interaction between the C{sub 60} surface and bases on ssDNA, and the other involves multiple weak hydrogen bonds between themore » functional carboxylic groups and ssDNA.« less