Structural Studies of an RNA Aptamer Containing GGA Repeats Under Ionic Conditions Using Microchip Electrophoresis, Circular Dichroism, and 1D-NMR

Nuclear magnetic resonance (NMR) studies have shown that RNA/DNA oligomers with GGA repeat sequences contain unique G-quadruplex structures in the presence of K+ or Na+ ions. In this study, we used microchip electrophoresis to study the structure of an RNA aptamer against bovine prion protein that possessed four GGA-triplet repeats (wt2). We analyzed the structural changes and characterized dimer formation of the aptamer. Mutational, circular dichroism, and one-dimensional NMR studies of wt2 revealed that K+ ions induce wt2 to assume a thermostable dimer in an intramolecular G-quadruplex with parallel orientation.