Induction of type I interferon by RNA viruses: cellular receptors and their substrates

Baum, Alina; García-Sastre, Adolfo

Apart from translocation and ATP hydrolysis, the helicase domain also appears to have an important role in RNA binding. In vitro RNA binding assays show that the RNA affinity of purified RD alone is not as strong as that of the full-length protein. Interestingly, analysis of helicase deletion mutants demonstrated impaired binding affinity to dsRNA but had little effect on in vitro transcribed RNA binding, suggesting that the RD and helicase domains likely recognize different PAMPs within the same RNA molecule . The contribution of the helicase domain to RNA recognition and binding is further clarified by competition experiments which show that while the RD domain alone has a preference for any 5 0 ppp molecule (either double or single stranded) the full length protein prefers to bind dsRNA with 5 0 OH groups than 5 0 ppp ssRNA ). However, in vitro binding analysis of the purified helicase domain, failed to show dsRNA interaction. Therefore, it appears that the RD and the helicase domain within the full length protein exhibit cooperative binding properties, as neither domain alone possesses the complete RNA affinity of the full length molecule (Takahasi et al. 2008) . Together these findings support the notion that the helicase domain may only recognize dsRNA molecules, while the RD domain has specificity to both dsRNA and the 5 0 ppp.