Base- and Structure-Dependent DNA Dinucleotide–Carbon Nanotube Interactions: Molecular Dynamics Simulations and Thermodynamic Analysis

Abstract

Wrapping of single-wall carbon nanotubes (SWCNTs) by singlestranded DNA (ssDNA) was found to be sequence-dependent, offering properties such as the facilitation of SWCN sorting, ultrafast DNA sequencing, and construction of chemical sensors. Although the interactions of nucleic acids with SWCNTs have been studied thoroughly, the DNAÀCNT hybrid especially for the oligonucleotides containing more than one nucleotide has not yet been fully understood.To address this, we have examined new and unconventional DNA dinucleotides involving all 16 combinations of two DNA nucleotides attached with chiral (8,4) and armchair (6,6) SWCNTs using all-atom molecular dynamics simulations and thermodynamic analyses. The 16 dinucleotides with different sequence compositions are found to readily adsorb onto SWCNTs and display interesting binding behaviors such as base flipping, local dynamic stability of structure, and conformational shifting. Four dinucleotides, i.e., AC, AG, GC, and GT, share similar dynamic properties (base turning and conformation transformation) in (8,4) and (6,6) systems. The different dynamic profiles between the compositional isomers with the reverse sequences such as the AG and GA show that the sequence order also impacts the dynamic recognition and binding energy of the ssDNAÀCNT hybrid. Clustering-analysis-derived representative conformations imply that general dinucleotides are inclined to spread on the SWCNT surface, and the adjacent bases tend to stretch away from each other. Dinucleotides like AC, AT, CG, CT, GC, GG, TA, TC, TG, and TT adopt similar geometries on both CNTs, suggesting that their structures are not predominantly influenced by the nanotube chirality but controlled by the identity of the base sequence, sequence order, and the basic cylindric structure of SWCNT. In addition, the nucleotide bases have a high degree of orientational order on the nanotube surface and the orientations of each base are significantly affected by the sequence of DNA and the chirality of nanotube, emphasizing that the structural order plays an important role in the binding of DNA and CNTs. However, our energy analysis shows that due to small different curvatures of the CNT surface, the binding affinity of most dinucleotides (except AG, CA, CG, and TG) to the chiral and armchair nanotube is not significantly different. Generally, the dinucleotides constituted with purine and thymine exhibit the lowest binding free energy, resulting from the van der Waals interactions and solvent effects. The thymine-based dinucleotides reduce the solvation free energy of the SWCNT in aqueous solution more effectively as compared to other bases. The present work also demonstrates that the total binding free energy is sequence specific but not merely a sum of individual baseÀSWCNT binding free energies.

Investigation of thermodynamic and structural properties of drug delivery system based on carbon nanotubes as a carboplatin drug carrier by molecular dynamics simulations

“…The solvation energy (G solv )can be obtained from an implicit description of the solvent and divided into the polar and nonpolar parts. Since the difference of TDS was very small considering the similarity of the systems, the contribution of the entropy (TDS) is negligible [54]. Therefore, the free energy and other values are relative in all simulated systems.…”

“…The AMBER12 simulation package was employed for the molecular dynamics simulations [50], which had been successfully carried out in the study of the carbon nanotubes [51][52][53][54][55]. All calculations were performed in the isothermal-isobaric ensemble at 1 atm and 300 K using the SANDER module in the AMBER 12 program.…”

Dendrimer assisted dispersion of carbon nanotubes: a molecular dynamics study

“…Several recent studies 32,33 have shown that single stranded DNA (ssDNA) and SWCNT form a stable hybrid structure in the aqueous solution and thus make dispersion of CNTs easier. Molecular dynamics (MD) studies [34][35][36][37][38][39] have reported that the hydrophobic nucleobases of ssDNA wrapped around the SWCNT surface via π-π base stacking interaction whereas the hydrophilic phosphate backbone is exposed to the aqueous environment. Thus the ssDNA-SWCNT forms a stable hybrid structure making it soluble in the aqueous medium.…”

Functionalization of Carbon Nanotubes with Stimuli- Responsive Molecules and Polymers

“…DNA or RNA molecules can interact with the CNT sidewall via π-π stacking. In particular, single-strand DNA (ssDNA) oligomers and polymers have been extensively explored as SWNT dispersants and the interactions were found to be sequence-dependent [45][46][47][48][49][50][51]. Such properties have enabled fascinating applications including precise sorting of SWNTs, DNA sequencing, and chemical sensing applications [52].…”