Interaction of the trp RNA-binding attenuation protein (TRAP) of Bacillus subtilis with RNA: effects if the number of GAG repeats, the nucleotides separating adjacent repeats, and RNA secondary structure

The ability of trp (ribonucleotide) RNA-binding attenuation protein (TRAP) of Bacillus subtilis to bind with RNA and the resulting formation of TRAP-RNA complexes is dependent on the number of GAG repeats. The overall stability of the TRAP-RNA complexes is dependent on the specific nucleotide sequence of the spacers that separate the GAG repeats. The TRAP binding site to the RNA duplex is composed of single stranded RNA with 11 GAG repeats that are separated by two UU or AU spacers.