The trinucleotide repeat sequence d(GTC)15 adopts ahairpin conformation

Adong Yu, Jeffrey Dill, Sara S. Wirth, George Huang, Vincent H. Lee, Ian S. Haworth, Michael Mitas

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The structure of a single-stranded (ss) oligonucleotide containing (GTC)15 ' ss GTC)15 ' was examined. As a control, parallel studies were performed with ss(CTG)15, an oligonucleotide that forms a hairpin. Electrophoretic mobility, KMnO4 oxidation and P1 nuclease studies demonstrate that, similar to ss(CTG)15, ss(GTC)15 forms a hairpin containing base paired and/or stacked thymines in the stem. Electrophoretic mobility melting profiles performed In ∼1 mM Na+ revealed that the melting temperatures of ss(GTC)15 and ss(CTG)15 were 38 and 48°C respectively. The loop regions of ss{GTC)15 and ss{CTG)15 were cleaved by single-strand-specific P1 nuclease at the T25-C29 and G26-C27 phosphodlester bonds respectively (where the loop apex of the DNAs is T28). Molecular dynamics simulations suggested that in ss(GTC)15 the loop was bent towards the major groove of the stem, apparently causing an increased exposure of the T25-C29 region to solvent. In ss(CTG)15 guanine-guanine stacking caused a separation of the G26 and C27 bases, resulting in exposure of the intervening phosphodiester to solvent. The results suggest that ss(GTC)15 and ss(CTG)is form similar, but distinguishable, hairpin structures.

Original languageEnglish
Pages (from-to)2706-2714
Number of pages9
JournalNucleic Acids Research
Issue number14
StatePublished - 25 Jul 1995
Externally publishedYes


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