Contribution of the intercalated adenosine at the helical junction to the stability of the gag-pro frameshifting pseudoknot from mouse mammary tumor virus

Abstract

The mouse mammary tumor virus (MMTV) gag-pro frameshifting pseudoknot is an H-type RNA pseudoknot that contains an unpaired adenosine (A14) at the junction of the two helical stems required for efficient frameshifting activity. The thermodynamics of folding of the MMTV vpk pseudoknot have been compared with a structurally homologous mutant RNA containing a G[bull ]U to G-C substitution at the helical junction (U13C RNA), and an A14 deletion mutation in that context (U13CΔA14 RNA). Dual wavelength optical melting and differential scanning calorimetry reveal that the unpaired adenosine contributes 0.7 (±0.2) kcal mol⁻¹ at low salt and 1.4 (±0.2) kcal mol⁻¹ to the stability (ΔG°₃₇) at 1 M NaCl. This stability increment derives from a favorable enthalpy contribution to the stability ΔΔH = 6.6 (±2.1) kcal mol⁻¹ with ΔΔG°₃₇ comparable to that predicted for the stacking of a dangling 3′ unpaired adenosine on a G-C or G[bull ]U base pair. Group 1A monovalent ions, NH₄⁺, Mg²⁺, and Co(NH₃)₆³⁺ ions stabilize the A14 and ΔA14 pseudoknots to largely identical extents, revealing that the observed differences in stability in these molecules do not derive from a differential or specific accumulation of ions in the A14 versus ΔA14 pseudoknots. Knowledge of this free energy contribution may facilitate the prediction of RNA pseudoknot formation from primary nucleotide sequence (Gultyaev et al., 1999, RNA 5:609–617).