GNA TRINUCLEOTIDE LOOP SEQUENCES PRODUCING EXTRAORDINARILY STABLE DNAMINIHAIRPINS

d(GCGAAAGC) and d(GCGAAGC) fragments form extraordinarily stable DNA m inihairpins containing only two G-C base pairs and a GAAA or GAA loop, respectively, with a T-m of 76 degrees C. These sequences are frequen tly found in some important regions such as replication origins and pr omoter regions for transcription. We examined all 64 possible DNA frag ments, d(GCNNNGC), in which the triloop region of the <d(GC(GAA)under bar GC)> minihairpin was randomized and found that only four fragments , d(GCGNAGC) (N = A, G, C, or T), formed extraordinarily stable miniha irpins as shown by their gel mobility and resistance to a single-stran ded DNA-specific exonuclease. Structural and thermodynamic analyses su ggest that the extraordinary stability is caused by a unique structura l property of the trinucleotide sequences corresponding to the GNA loo p.