Role of unsatisfied hydrogen bond acceptors in RNA energetics and specificity

RNA plays essential roles in much of biology. These functions are dictated by structures mediated by hydrogen bonding, stacking, electrostatics, and steric interactions. Roles of unsatisfied hydrogen bond functionalities in these structures are less well understood. Herein, we evaluated the energetic contributions of unsatisfied hydrogen bonding groups by placing chemically modified substituents in select internal positions in RNA helices and conducting thermodynamic studies. We find that unsatisfied carbonyl groups make exceptional contributions to structure formation (approximately 3 kcal/mol in free energy), most likely due to a combination of strain and dehydration effects. Thus, unsatisfied hydrogen bonding groups are likely key determinants in the folding energetics and specificity of many RNA and DNA molecules and may be especially important in tertiary structure interactions.