Nucleic Acids Research, 1995, Vol. 23, No. 14 2706-2714
© 1995
MOLECULAR BIOLOGY |
The trinucleotide repeat sequence d(GTC)15 adopts ahairpin conformation
Department of Biochemistry and Molecular Biology, Oklahoma State University, 246 Noble Research Center Stillwater, OK 74078, USA, 1Department of Pharmaceutical Sciences 1985 Zonal Avenue, Los Angeles, CA 90033, USA 2Department of Biochemistry and Molecular Biology, University of Southern California 1985 Zonal Avenue, Los Angeles, CA 90033, USA
*To whom correspondence should be addressed
Received March 23, 1995. Accepted June 7, 1995.
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.
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