Thermodynamic stability of an RNA duplex is impacted by its environment and the imperfections within the duplex. To explore the effects of RNA structure on stability bulges and internal loops were incorporated into the duplex. Two environments were studied: 1M NaCl and artificial cytoplasm of Eco80 (80% Escherichia coli metabolites) which is an approximation of cellular conditions. Results indicate that structural imperfections are more readily tolerated under in vivo-like conditions.