Thermodynamics of a stable yeast 5.8S rRNA hairpin helix

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Abstract
The 5.8S ribosomal RNA of bakers yeast contains one particularly stable hairpin helix which is isolated by partial Tl ribonuclease digestion. Thermal hyperchromism analysis of the hairpin fragment showed that it dissociates cooperatively with 18% hyperchromism, with a Tm of 83°C at 2.7 mM sodium ion concentration, and with a hyperchromic difference spectrum indicative of over 90% G + C content. The probable secondary structure for the fragment was used to predict a helix free energy, Δ G = −16.2 kcal/mole, which was the same as that determined from the melting equilibrium. The predicted enthalpy however, was 77% of the value, δ H = −114 kcal/mole, determined from the van’t Hoff relationship. The effect on these data of a G.U base pair within the 9 base pair helix is discussed.