Aptamers are RNA molecules that are selected in vitro to bind to small molecules, peptides, proteins, oligosaccharides, or RNA molecules. To better understand the structural basis for how high affinity and specificity are achieved in aptamer-ligand complexes, multidimensional, heteronuclear magnetic resonance spectroscopic studies were initiated on the Class II GTP-binding aptamer. A construct screen was carried out to find a Class II RNA sequence that gave high-quality NMR spectra. Resonance assignment experiments were initiated to assign the exchangeable and non-exchangeable proton resonances in the Class II:GTP complex. GTP resonances were assigned in the complex using a combination of unlabeled RNA and uniformly ¹³C, ¹⁵ N labeled GTP. To aid in the resonance assignment process Class II binding loop mutants were generated and characterized by NMR. The HNN-COSY experiment carried out on the Class II complex showed that the Class II aptamer recognizes GTP by forming an intermolecular Watson-Crick base pair with GTP. ¹³C- and 1⁵N-edited NMR spectra provide evidence for two N1-protonated adenine residues in the Class II complex at pH 6.2. Structural studies of the Class II complex initiated here will expand our understanding of how RNA molecules recognize target ligands with high affinity and specificity.