Thermal transitions in E. coli +RNA fMet and two of its molecular fragments

Melting curves of tRNA^fMet and two fragments derived from this molecule by limited ribonuclease T1 digestion (i.e., the anticodon arm and loop [K fragment] and the larger fragment representing three-fourths of the tRNA chain from the 3′ terminus including two potential limbs of the cloverleaf structure [L fragment]) are presented. The profiles observed are consistent with the presence of base paired structures in all those molecules. At low salt concentration (0.02M Na⁺) the stabilities of these molecules measured by the apparent midpoints of the denaturation profiles are in the order K > L > tRNA. The relative stabilities approach each other at 0.2M Na⁺ (the tRNA profile being biphasic), while at high salt (2M) the L fragment seems to be more stable than either K or t-RNA ^fMet. Estimation of the enthalpy of denaturing the K structure in 0.02M Na⁺ gives a value of 40 ± 3 kcal/mole corresponding to an enthalpy per effective G.C. base pair disrupted of 10 ± 1 kcal/mole.