Molecular modeling of epsilon RNA from hepatitis B virus

An initial model of the HBV epsilon RNA was built by the Biopolymer module of Insight II. While its three-dimensional structure was obtained through structure optimization based on molecular dynamics simulation, the two active sites were found. A comparison with the experimental result indicated that the active sites may be the binding sites of the epsilon RNA in the RT–epsilon interaction. The result will be helpful to further discussion about the mechanism of RT–epsilon interaction and the study of HBV genome replication.