Drosophila SNF is a member of the U1A/U2B/SNF protein family that is found in U1 and U2 snRNPs, where it binds to Stemloop II and Stemloop IV of U1 and U2 snRNA, respectively. SNF also binds to the U2A protein, but only in the U2 snRNP. Although previous reports have implicated U2A as a necessary auxiliary protein for the binding of SNF to Stemloop IV, there are no mechanisms that explain the partitioning of U2A to the U2 snRNP and its absence from the U1 snRNP. Using in vitro RNA binding isotherms and isothermal titration calorimetry, the thermodynamics of SNF/RNA/U2A ternary complex formation have now been characterized. There is a very large binding cooperativity unique to Stemloop IV that favors formation of the SLIV/SNF/U2A complex. The binding cooperativity, or heterotropic linkage, is interpreted with respect to linked conformational equilibria of both SNF and its RNA ligand and so represents an example of protein-RNA allostery.