To explore the feasibility of capsid-targeted viral inactivation for dengue virus infection, a newly-discovered antiviral strategy, a mammalian cell line stably expressing staphylococcal nuclease fused to the capsid protein of dengue 2 virus was established and the effects on the production of infectious virus particles were examined. The results presented evidence that the enzymatically active staphylococcal nuclease fused to capsid protein could be incorporated into the nascent virions during wild virus assembly, resulting in degradation of viral genomic RNA and decrease in infectivity. Comparing the effects of incorporated SN and SN*, an enzymatically inactive missense mutant form of SN, on the infectivity of progeny virions, nucleolytic activity of incorporated SN was responsible for the major antiviral effects. These results paved the road of developing capsid-targeted viral inactivation as a new antiviral strategy against dengue.