Molecular Simulation of DNA β-Sheet and β-Barrel Structures on Graphite and Carbon Nanotubes

It has recently been discovered that certain short DNA sequences recognize specific carbon nanotubes (CNTs), allowing a mixture to be sorted into individual types. A novel β-sheet and β-barrel secondary DNA motif has been proposed as the structural basis for this recognition. In this study, using molecular simulation, we investigate a class of DNA structures that can be formed by interstrand hydrogen bonding, their stability in planar and barrel forms, and whether they can form the basis for CNT recognition. We show how a library of DNA β-barrel structures can be built from base-dimer tiling units. Various combinations of the (GT) n family of sequences have been studied in greater detail, both as adsorbed in planar form to graphite and as wrapped helically on a CNT surface. We find that G-quartet formation brings stability to the β-sheet, while diameter and chirality matching between the proposed DNA β-barrel and core CNT appears to stabilize an ordered hybrid structure.