THE TRINUCLEOTIDE REPEAT SEQUENCE D(GTC)(15) ADOPTS A HAIRPIN CONFORMATION

The structure of a single-stranded (ss) oligonucleotide containing (GT C)(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 demo nstrate that, similar to ss(CTG)(15), ss(GTC)(15) forms a hairpin cont aining base paired and/or stacked thymines in the stem, Electrophoreti c mobility melting profiles performed in similar to 1 mM Na+ revealed that the melting temperatures of ss(GTC)(15) and ss(CTG)(15) were 38 a nd 48 degrees C respectively, The loop regions of ss(GTC)(15) and ss(C TG)(15) were cleaved by single-strand-specific P1 nuclease at the T25- C29 and G26-C27 phosphodiester 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, app arently causing an increased exposure of the T25-C29 region to solvent , In SS(CTG)(15) guanine-guanine stacking caused a separation of the G 26 and C27 bases, resulting in exposure of the intervening phosphodies ter to solvent, The results suggest that ss(GTC)(15) and ss(CTG)(15) f orm similar, but distinguishable, hairpin structures.