Skip to main content
. 2000 Jan 18;97(2):646–651. doi: 10.1073/pnas.97.2.646

Figure 2.

Figure 2

Predicted (continuous lines) and experimental differential melting curves (dashed lines). a, b, c, and e show the results for α operon mRNA fragment and the variants in 100 mM (a, b, and c) or 1,000 mM (e) KCl with 10 mM Mops (33): G16-A72 (a); G36→U (b); AA44→CC, UU55→GG (c); and G16-U127 (e), with added nucleotides at the 3′ end: AU (a, b, and c). d and f show denaturation profiles for E. coli 23S rRNA fragment G1051-C1109 in 1 M KCl with 10 mM Mops (34) and E. coli 5S RNA in 1 M NaCl with 5 mM sodium phosphate and 1 mM EDTA (35), respectively. a and f are from calorimetric experiments, and b, c, and e are from UV absorbance experiments. Because our model energies are from Turner's rules, taken in 1 M NaCl, our model should in general overestimate the melting temperatures (Tm) for experiments in lower salt conditions. Because our model accounts only for the secondary structures, peaks in the experimental curves for the disruption of the tertiary structure (35) (f) were removed. The denaturation curve shows the heat capacity as a function of temperature. The heat capacity C(T) is obtained from the partition function Q(T) by using C(T) = ∂/∂T[kT2(∂/∂T)lnQ(T)]. The computer time scales with the chain length L as L4. For each temperature, the calculation of Q(T) and C(T) took 3 sec on an Intel Pentium Pro 200 computer for the 59-mer sequences (a–d), 30 sec for the 100-mer sequence, and 54-sec for the 120-mer sequence (f). We chose μ = e−2 to give a best fit to the experimental curve in c, and used this value for all other calculations. Small variations in μ (e.g., μ = e−2.5) cause only minor changes of the positions and shapes of the main and satellite peaks, but larger changes in μ lead to significant changes of the melting curves. Although the theory gives good predictions, given the simple approach, it is conceivable that the theory may differ with the experimental denaturation profiles in some details. Improvements can come from accounting for tertiary interactions, treating unpaired terminal nucleotides, and other refinements in the theory.