Computational Modeling of Ring DNA-carbon Nanotube Sensors

Non-covalent interactions between single-stranded DNA (ssDNA) oligonucleotides and carbon nanotubes have provided a unique class of tunable chemistries for applications in nanotube chirality purification, gene delivery, electrochemistry, and nanosensor development. However, mechanistic insight into both the photophysical and intermolecular phenomena underlying their utility in such applications is lacking, resulting in non-systematic approaches to producing DNAnanotube based technologies. In this work, we explore the molecular interactions between ssDNA polymers, in particular (GT)6, and single-walled carbon nanotubes (SWNT) in an ultrasensitive nanosensor for a modulatory neurotransmitters dopamine. Classical molecular dynamics simulations show that (GT)6 oligonucleotides adopt ordered, ring-like conformations around SWNT in contrast to the helical adsorption pattern observed for most previously used longer SWNT-adsorbed ssDNA sequences. We also performed replica exchange molecular dynamics simulations to produce a free energy landscape of (GT)6 conformations at SWNT, and determined that the ring-like structure of (GT) 6 at SWNT is one of the most stable conformations, i.e. a free energy minimum structure. Our results show that the ring-like and helical conformations of ssDNA also leave two distinct electrostatic potential footprints at the SWNT surface. We show that adsorbed dopamine has a synergistic effect on ssDNA-SWNT hybrid materials. It leads to disruption of ssDNA conformation and their electrostatic footprint at SWNT surface, explaining more intense optical response of SWNT upon adsorption of dopamine