Stability of the TAR RNA and its complex with arginine

Most stable secondary structures and their stabilization energies of the TAR RNA with +1 to +104 nucleotide-sequence region were calculated at different temperatures by using thermodynamic parameters for RNA structure prediction. The most stable secondary structure has one bulge and one loop within the region of +20 to +40 nucleotide sequence, and its stabilization energy at 37 degrees C was -46.3 kcal mol-1. The interaction of a TAR bulge oligomer (TARBO) with arginine (Arg) which was in the binding site of a Tat protein was also investigated by CD measurements. The addition of Arg did not affect the CD spectrum of TARBO. The result was different from that of the RNA oligomer with both bulge and loop.