Sequences and structures present at the 5' and 3' UTRs of RNA viruses play crucial roles in the initiation and regulation of translation, RNA synthesis and viral assembly. In dengue virus, as well as in other mosquito-borne flaviviruses, the presence of complementary sequences at the ends of the genome mediate long-range RNA-RNA interactions. Dengue virus RNA displays two pairs of complementary sequences (CS and UAR) required for genome circularization and viral viability. In order to study the molecular mechanism by which these RNA-RNA interactions participate in the viral life cycle, we developed a dengue virus replicon system. RNA transfection of the replicon in mosquito and mammalian cells allows discrimination between RNA elements involved in translation and RNA synthesis. We found that mutations within CS or UAR at the 5' or 3' ends of the RNA that interfere with base pairing did not significantly affect translation of the input RNA but seriously compromised or abolished RNA synthesis. Furthermore, a systematic mutational analysis of UAR sequences indicated that, beside the role in RNA cyclization, specific nucleotides within UAR are also important for efficient RNA synthesis.