Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCFAAAGC)and their effect on DNA sequencing

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Abstract
A small DNA fragment having a characteristic sequence d(GCGAAAGC) has been shown to form an extraordinarily stable mlnl-halrpin structure and to have an unusually rapid mobility in poly aery lam ide gel electrophoresis, even when containing 7M urea. Here, we have studied the stability of the various sequence variants of d(GCGAAAGC) and the corresponding RNA fragments. Many such sequence variants form stable mini-hairplns in a similar manner to the d(GCGAAAGC) sequence. The RNA fragment, r(GCGAAAGC) also forms a mini-hairpin structure with less stability. The DNA mini-hairpins with GAAA or GAA loop are much more stable than DNA and RNA minl-hairpins with other loop sequence so far as has been examined. The stability difference between DNA and RNA mini-hairpins may be deduced to the stem structures formed by DNA (B form) and RNA (A form). The stable hairpins consisting of the GCGAAAGC sequence cause strong band compression on the sequencing gel. This phenomenon should be carefully considered In DNA sequencing.