The dengue virus helicase protein (NS3) plays a pivotal role in the replication lifecycle of the virus. ATP hydrolysis powers the protein as it unwinds double stranded viral RNA. The release of energy in the ATP binding pocket is coupled to the RNA binding region of NS3 over a distance of 20 Å. Using all-atom molecular dynamics we study six important conformations along the ATP hydrolysis cycle. Analyses suggest that the ATPase substrates have an allosteric influence on two helix motifs located at the entrance of the RNA binding cleft. The dynamics of additional RNA binding regions are also strongly coupled to the bound nucleotide state. Combined, these results provide insight into the process by which ATP hydrolysis powers the motion of NS3 helicase along double stranded viral RNA.