Influence of slight sequence changes on the free energy of a single stranded ribonucleic acid molecule

Single-stranded ribonucleic acid molecules take a variety of secondary structures. The free energy (g) of a given secondary structure of a molecule is calculated from the Boltzmann weighted summation over the states of this molecule taking this secondary structure. Likewise, the free energy (G) of a molecule is calculated from the summation over the states of this molecule, which takes various secondary structures. The g-value can be evaluated by Salser’s method (1977, Cold Spring Harbor Symp. Quantum Biol.42, 985-1002). By use of these values, the G-value can also be obtained. Computer studies utilizing this method reveal that there is a particular class of molecules whose G-values tend to increase when the sequences are slightly changed. As far as we examined, such molecules take few secondary structures that fulfill the following two conditions simultaneously: (i) The g-value is close to that of the optimal secondary structure. (ii) The structure is very different from the optimal secondary structure. Here, the optimal secondary structure means the one with the lowest g-value among all the secondary structures taken by the molecule.