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Binding affinity and selectivity are critical properties of aptamers that must be optimized for any application. The sulforhodamine B binding RNA aptamer (SRB-2) is a somewhat promiscuous aptamer that can bind ligands that vary markedly in shape, size and charge. Here we categorize potential ligands based on their binding mode and structural characteristics required for high affinity and selectivity. Several known and potential ligands of SRB-2 were screened for binding affinity using LSPR, ITC and NMR spectroscopy. The study shows that rhodamine B has the ideal structural and electrostatic properties for selective and high-affinity binding of the SRB-2 aptamer. • Smaller alkyl groups and reduced negative charge result in higher binding affinity. • The single ring and one negative charge are required for binding specificity. • Size and shape of the alkyl amine groups is crucial for binding affinity. • Rhodamine B is the ideal SRB-2 ligand among those tested here. [ABSTRACT FROM AUTHOR]