Structure of RNA aptamer for HIV Tat complexed with Tat-derived peptide

An RNA aptamer containing two binding sites exhibits extremely high affinity to the HIV Tat protein. We previously reported the structure of the aptamer complexed with argininamide as the simplest analogue of Tat. Here, we have analyzed the structure of the aptamer complexed with the partial peptide of Tat, RKKRR. The profile of chemical sift perturbations for the aptamer upon complex formation with RKKRR revealed that RKKRR can be a realistic analogue of Tat to address the interactions between the arginine-rich motif of Tat and the aptamer. It was suggested that the aptamer interacts with different arginine residues of RKKRR simultaneously at the two binding sites, which can explain the extremely high affinity to Tat.