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Nucleic Acids Research, 1985, Vol. 13, No. 22 8259-8274
© 1985

Articles

Anomalous hairpin formation in an oligodeoxyribonucleotide

J.G. Nadeau and P.T. Gilham

Department of Biological Sciences, Purdue University West Lafayette, IN 47907, USA

Received July 8, 1985. Revised October 21, 1985. Accepted October 21, 1985.

An accurate method for deriving polar absorptivity-tenperature profiles applied to a set of single-stranded oligodeoxyribonucleotides shows that the undecamer CGAGTTTGACGp exists in a hairpin conformation involving Watson-Crick base pairing between the two terminal CG dinucleotides. The hairpin, which has a transition midpoint of 40 °C in 0.115 M Na+, is unusually stable in comparison with previously reported hairpins. A non-linear least squares analysis of the undecamer's profile in terms of a two-state equilibrium model indicates that the hairpin-to-coil transition occurs with an enthalpy change about twice that expected if only combinations of Watson-Crick base-paired stacking interactions are considered. The analogous hairpin structure (containing an identical CG/CG stem) assignable to the complementary strand CGTCAAACTCGp does not form above 0 °C. Measurements on the two undecamers indicate that variation in non Watson-Crick interactions within the loops of two similar hairpins can produce a difference in stability of at least 2.2 kcal/mol (25 /C, 0.115 H Na+), roughly equal to the amount contributed to a double helix by a 5'-CG-3'/5'-CG-3' base-paired stacking interaction.


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