la9b02926_si_001.pdf (1.36 MB)
Effect of Octadecylamine Surfactant on DNA Interactions with Graphene Surfaces
journal contribution
posted on 2020-01-22, 00:29 authored by Ho Shin Kim, Nathanael A. Brown, Stefan Zauscher, Yaroslava G. YinglingUnderstanding
of how to integrate DNA molecules with graphene materials
is important for the development of biosensors and biomolecular logic
circuits. For some of these applications, controlling DNA structural
conformation on the graphene substrate is critically important and
can be achieved through the use of self-assembled monolayers. Here,
we performed all-atom molecular dynamics simulations to understand
how various 1-octadecylamine (ODA) coatings of the graphene surface
affect the conformation of double-stranded DNA (dsDNA) on the surface.
The simulation results demonstrated that dsDNA structures become more
stable as ODA concentration increases due to the formation of DNA–ODA
hydrogen bonds and reduction of DNA–surface interactions, which
aid in retaining internal DNA interactions. Specifically, the interaction
of ODA molecules with DNA prevents nucleobases from forming π–π
stacking interactions with the surface. Some dsDNA conformations,
such as sharp kinks or unwinding, can occur more frequently in DNA
with A–T sequences due to weaker pairing interactions than
with G–C sequences. Furthermore, our results conclude that
both DNA sequence and ODA concentration play an essential role in
experimentally observed conformational changes of DNA on the graphene
surface.