Effect of salt concentration on the conformation of TAR RNA and its association with aminoglycoside antibiotics.

RNA is an important biological target because it plays essential roles in many pathogenic and normal cellular processes. The design of inhibitors that target RNA involves optimization of noncovalent interactions, including van der Waals, hydrogen bond, and electrostatic interactions. Although sometimes regarded as nonspecific, electrostatic interactions are important in this optimization because the specific position of the phosphates may allow for specific charge charge interactions with bound ligands. In this work, we have investigated the contribution of electrostatic interactions to the binding affinity of aminoglycoside antibiotics for TAR RNA. Because the charges in aminoglycoside antibiotics are provided by protonated amino groups, it is difficult to separate the contribution of hydrogen bonds and electrostatics to their binding specificity. Hence, we have investigated the dependence of the binding affinity on salt concentration, which should affect only the electrostatic contributions. Our results show that four aminoglycoside antibiotics (paromomycin, kanamycin-B, gentamycin, and tobramycin) bind TAR RNA with different affinities. Furthermore, the dependence of the binding affinity on salt concentration is different for kanamycin-B and paromomycin, with kanamycin-B showing a stronger dependence. Because all these antibiotics contain five positive charges, the results suggest that each antibiotic orients its charges in different ways when bound to TAR RNA. Our overall results support the idea that charge charge interactions can contribute significantly to the specific binding of antibiotics to TAR RNA. Hence, the exact position of the charges should be considered in the design of any inhibitor of the interactions of TAR RNA.