RNA hairpin loop stability depends on closing base pair

• Published in: Nucleic acids research Vol. 21; no. 16; pp. 3845 - 3849
• Main Authors: Serra, Martin J., Lyttle, Matthew H., Axenson, Theresa J., Schadt, Calvin A., Turner, Douglas H.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 11.08.1993
• Subjects: Analytical, structural and metabolic biochemistry; Base Composition; Base Sequence; Biological and medical sciences; Chromatography, High Pressure Liquid; Fundamental and applied biological sciences. Psychology; Molecular Sequence Data; Nucleic Acid Conformation; Nucleic acids; RNA - chemistry; Rna, ribonucleoproteins; Thermodynamics; Hairpin loop; Stability; RNA; Thermodynamic parameter
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/21.16.3845

Thermodynamic parameters are reported for hairpin formation in 1 M NaCl by RNA sequences of the type GGXAUAAUAYCC. where X and Y are CG, GC, AU, UA, GU, or UG. A nearest neighbor analysis of the data indicates the free energy change for loop formation at 37°C, Δ°G/,37, averages 3.4 kcal/mol for hairpin loops closed with C·G , G·C, and G·U pairs. In contrast, ΔG/,37 averages 4.6 kcal/mol for loops closed with A·U, U·A, or U·G pairs. Thus the stability of an RNA hairpin depends on the closing base pair. The hairpin with a GA mismatch that is formed by GGCGUAAUAGCC is more stable than the corresponding hairpin with an AA mismatch. Thus hairpin stability also depends on loop sequence. These effects are not included in current algorithms for prediction of RNA structure from sequence.