Probing the TRAP-RNA interaction with nucleoside analogs

The trp RNA-binding Attenuation Protein (TRAP) from Bacillus subtilis binds a series of GAG and UAG repeats separated by 2-3 nonconserved spacer nucle otides in trp leader mRNA. To identify chemical groups on the RNA required for stability of the TRAP-RNA complex, we introduced several different nucl eoside analogs into each pentamer of the RNA sequence 5'-(UAGCC)-3' repeate d 11 times and measured their effect on the TRAP-RNA interaction. Deoxyribo nucleoside substitutions revealed that a 2'-hydroxyl group (2'-OH) is requi red only on the guanosine occupying the third residue of the RNA triplets f or high-affinity binding to TRAP. The remaining hydroxyl groups are dispens able. Base analog substitutions identified all of the exocyclic functional groups and N1 nitrogens of adenine and guanine in the second and third nucl eotides, respectively, of the triplets as being involved in binding TRAP. I n contrast, none of the substitutions made in the first residue caused any detectable changes in affinity, indicating that elements of these bases are not necessary for complex formation and stability. Studies using abasic nu cleotides in the first residue of the triplets and in the two spacer residu es confirmed that the majority of the specificity and stability of the TRAP -RNA complex is provided by the AG dinucleotide of the triplet repeats. In addition to direct effects on binding, we demonstrate that the N7-nitrogen of adenosine and guanosine in UAG triplet and the 2'-OHs of (UAGCC)(11) RNA are involved in the formation of an as yet undetermined structure that int erferes with TRAP binding.