Microarrays with a pillared patterned double-layer graphene substrate: A molecular dynamics simulation approach

Abstract Microarray technology plays an important role in detecting the sequence of the genome. In the production of microarrays, the formation of a homogeneous and uniform spot due to biodroplet pining is of great importance. In this work, using the molecular dynamics simulation method, it is possible to create homogeneous spots on the surface of graphene-based surfaces. Hence, the behavior of five different types of DNA including homogeneous sequences of adenine, cytosine, guanine, and thymine as well as heterogeneous sequence of bases in the water droplets, was subjected to a double-layer graphene substrate with a pillar structure. The results showed that double layer graphene with pillar pattern are successful in pinning of biodroplet and this substrate leads to the differnet placement of Oligonucleotide probes. Also, the results of wettability demonstrated that the formation of hydrogen bond between a single strand and water molecules reduces the spreading and increases the contact angle and height of biodroplet containing oligonucleotides with respect to the water droplet without oligonucleotides on the surface of the double layer graphene in pillar pattern. The results of the simulation of single-stranded DNA after equilibration showed that single strand of adenine and heterogeneous single strands had the least folding compared to other single strands, and the single strand of adenine produced the most stable structure. Hence, single-stranded adenine is stretched more compared to other single strands, which is due to the lack of tendency of this single strand for internal hydrogen bonds and regular spiral structure resulting from a strong internal π-π stacking interaction. As a result, single strand of adenine is more accessible to detect target single strands for use in microarrays.