Structural modeling of DNA mini-hairpin molecules with various loop sequences

We modeled the structures of DNA fragments dGC(GNA)GC (N = A, G, T, and C), which are known to form mini-hairpins, and dGC(GAC)GC and dGC(GAG)GC, which are known not to form mini-hairpins, by using global optimization of conformational energy. For all of the fragments, we obtained mini-hairpins which had similar backbone structures and positions of bases. The conformational energy differences between the energy-optimized structures were small. Our results suggest that the optimized energy values are not sufficient to discriminate which fragments form thermo-stable mini-hairpins and which do not.