RNA recognition by a Staufen double-stranded RNA-binding domain

The double-stranded RNA-binding domain (dsRBD) is a common RNA-binding moti f found in many proteins involved in RNA maturation and localization. To de termine how this domain recognizes RNA, we have studied the third dsRBD fro m Drosophila Staufen, The domain binds optimally to RNA stem-loops containi ng 12 uninterrupted base pairs, and we have identified the amino acids requ ired for this interaction. By mutating these residues in a staufen transgen e, we show that the RNA-binding activity of dsRBD3 is required in vivo for Staufen-dependent localization of bicoid and oskar mRNAs, Using high-resolu tion NMR, we have determined the structure of the complex between dsRBD3 an d an RNA stem-loop. The dsRBD recognizes the shape of A-form dsRNA through interactions between conserved residues within loop 2 and the minor groove, and between loop 4 and the phosphodiester backbone across the adjacent maj or groove. In addition, helix al interacts with the single-stranded loop th at caps the RNA helix, Interactions between helix al and single-stranded RN A may be important determinants of the specificity of dsRBD proteins.