Interaction of C₆₀ Derivatives and ssDNA from Simulations

Abstract

We report atomistic modeling studies on the interaction of water-soluble C 60 derivatives and single-stranded DNA (ssDNA) segments in phosphate-buffered solutions. Stable hybrids are formed by C 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 60 derivative molecules is -11 to -15 kcal/mol. The binding pattern of C 60 derivatives with ssDNA molecules depends on the size and shape of the C 60 functional groups. For C 60 derivatives with functional groups that contain aromatic rings, strong π stacking was observed between the ssDNA base rings and the functional benzene rings. For C 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 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 60 surface and bases on ssDNA, and the other involves multiple weak hydrogen bonds between the functional carboxylic groups and ssDNA.

End-to-end attraction of duplex DNA

“…For comparison, a computational investigation of hydrophobic interactions revealed a free energy of −55 kcal/mol for the adhesion of a pair of 11 × 12 Å 2 graphene sheets, or about 10 times the energy per unit surface area ( 45 ). Interactions of similar strength were found to promote DNA–fullerene and ssDNA–carbon nanotube association ( 46 , 47 ).…”

A biophysical perspective of understanding nanoparticles at large

“…Towards understanding genotoxicity induced by nanoparticles computational modelling has previously been used to describe the interactions of fullerene and fullerene derivatives with nucleic acids. 41,42 In a recent study 43 The calculated RDF values indicated that the C 60 (OH) 2 preferentially interacted with the triphosphate oxygens in the dNTP/ssDNA, separated by an average distance of B0.7 nm. While the hydrogen bonding between the C 60 (OH) 20 and the deoxyribose or base moieties of the dNTP/ssDNA was insignificant (1-6%), strong interactions occurred between the nanoparticle and the triphosphate oxygens from the initial C 60 (OH) 20 -dNTP/ssDNA contact (at B2-3 ns) until the end of the simulation (40 ns).…”

Self-Assembly of DNA Segments on Graphene and Carbon Nanotube Arrays in Aqueous Solution: A Molecular Simulation Study

“…In a previous work, we investigated the interaction of DNA segments and CNT/C 60 in aqueous solution via molecular dynamics simulations. We found that C 60 or CNT can interact with nucleotide segments strongly, either through hydrophobic π−π stacking, , or through hydrogen bonding , when the nanoparticles are functionalized. Under either circumstance, the carbon-based nanoparticles form very stable hybrids with the DNA segments, with typical binding energies in the range of −20 to −40 kcal/mol.…”