Adsorption dynamics of double-stranded DNA on a graphene oxide surface with both large unoxidized and oxidized regions

Abstract

The adsorption dynamics of double-stranded DNA (dsDNA) molecules on a graphene oxide (GO) surface are important for applications of DNA/GO functional structures in biosensors, biomedicine and materials science. In this work, molecular dynamics simulations were used to examine the adsorption of different length dsDNA molecules (from 4 bp to 24 bp) on the GO surface. The dsDNA molecules could be adsorbed on the GO surface through the terminal bases and stand on the GO surface. For short dsDNA (4 bp) molecules, the double-helix structure was partially or totally broken and the adsorption dynamics was affected by the structural fluctuation of short dsDNA and the distribution of the oxidized groups on the GO surface. For long dsDNA molecules (from 8 bp to 24 bp) adsorption is stable. By nonlinear fitting of the contact angle between the axis of the dsDNA molecule and the GO surface, we found that a dsDNA molecule adsorbed on a GO surface has the chance of orienting parallel to the GO surface if the length of the dsDNA molecule is longer than 54 bp. We attributed this behavior to the flexibility of dsDNA molecules. With increasing length, the flexibility of dsDNA molecules also increases, and this increasing flexibility gives an adsorbed dsDNA molecule more chance of reaching the GO surface with the free terminal. This work provides a whole picture of adsorption of dsDNA molecules on the GO surface and should be of benefit for the design of DNA/GO based biosensors.