Paper Citing NAMD - Abstract
Zhao, Xiongce
Self-Assembly of DNA Segments on Graphene and Carbon Nanotube Arrays in Aqueous Solution: A Molecular Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY C, 115:6181-6189, APR 14 2011
Molecular dynamics simulations were performed to study the interaction of double-stranded DNA segments with the surfaces of graphene and carbon nanotube arrays in aqueous solution. Several different kinds of self-assembly phenomena were observed. First, it is found that a DNA segment can 'stand up' on the carbon surfaces with its helix axis perpendicular to the surfaces of graphene or nanotube arrays to form a forestlike structure. Second, a DNA segment can also lie on the carbon surface with its axis parallel to the surface if both of its ends can form stable structure with the carbon surfaces. In the latter case, the ending basepairs of the DNA are broken due to severe deformations. Third, it is observed that short DNA segments can concatenate to each other to form a longer DNA when they are placed in the grooves of nanotube bundles. The self-assembly observed in this study usually happens in less than 50 ns. Exploration on the molecular details and self-assembly mechanism indicates the primary driving force is the pi stacking interaction between the ending basepairs of DNA and the carbon rings. This study confirms the dominant role of hydrophobic pi stacking in the interaction between nucleotides and carbon-based nanosurfaces in aqueous environment.
