GNA Trinucleotide Loop Sequences Producing Extraordinarily Stable DNA Minihairpins

d(GCGAAAGC) and d(GCGAAGC) fragments form extraordinarily stable DNA minihairpins containing only two G-C base pairs and a GAAA or GAA loop, respectively, with a Tm of 76 degrees C. These sequences are frequently found in some important regions such as replication origins and promoter regions for transcription. We examined all 64 possible DNA fragments, d(GCNNNGC), in which the triloop region of the d(GCGAAGC) minihairpin was randomized and found that only four fragments, d(GCGNAGC) (N = A, G, C, or T), formed extraordinarily stable minihairpins as shown by their gel mobility and resistance to a single-stranded DNA-specific exonuclease. Structural and thermodynamic analyses suggest that the extraordinary stability is caused by a unique structural property of the trinucleotide sequences corresponding to the GNA loop.