Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair

Thermodynamic parameters measured by optical melting are reported for forma tion of RNA duplexes containing tandem noncanonical pairs with at least one guanosine-guanosine (GG) pair. For selected sequences, imino proton NMR pr ovides evidence that the desired duplex forms and that the structure of a G G pair adjacent to a noncanonical pair depends on context. A GG pair next t o a different noncanonical pair is more stable than expected from measureme nts of adjacent GG pairs. This is likely due to an unfavorable stacking int eraction between adjacent GG pairs, where areas of high negative charge pro bably overlap. The results suggest a model where tandem noncanonical pairs closed by two GC pairs are assigned the following free energy increments at 37 degreesC: 0.8 kcal/mol for adjacent GG pairs, 1.0 kcal/mol for GG next to UU, and -0.3 kcal/mol for all others. These values are adjusted by 0.65 kcal/ mol for each closing AU pair.