The stability of RNA hairpin loops containing A–U–G: An–U–G–Um

Abstract

RNA oligomers with the sequence A_n‐U‐G‐U_m, n = 7–9, m = 5–10, have been synthesized and found to form hairpin loops in 21 mM or 101 mM Na⁺. The hairpin loops displayed melting temperatures 13°–29°C greater than that of the hairpin loop A₆‐C₈‐U₆ in the same solvent. The increased stability of these hairpin loops is attributed to the presence of the trinucleotide A‐U‐G in the loop.Circular dichroism (CD) spectra were taken of the hairpin loops A₇‐U‐G‐U_6,7,8, A₈‐U‐G‐U_6,7,8, and A₉‐U‐G‐U₆ in 21 mM Na⁺, and compared with circular dichroism spectra of A₆‐U₆ in 1 M Na⁺. Difference spectra were calculated between each A_n‐U‐G‐U_m and 11.5 mM (nucleotide) A₆‐U₆ at similar temperatures and identical singlestrand fractions to give the “experimental” CD spectrum of the unbase‐paired nucleotides in the loop, assuming, five, six, or seven base pairs. CD spectra were calculated for each of the assumed unbase‐paired sequences using the measured CD spectra of ApA, A‐U‐G‐, A, and U, and compared with the experimental spectra. The best agreement was found for hairpin‐loop models containing five base pairs and five to eight unbase‐paired nucleotides in the loop.