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Nucleic Acids Research, 1988, Vol. 16, No. 24 11725-11735
© 1988

CHEMISTRY

Characterization of RNA hairpin loop stability

Duncan R. Groebe and Olke C. Uhlenbeck

Department of Chemistry and Biochemistry, University of Colorado Boulder, CO 80309-0215, USA

Received October 4, 1988. Revised November 10, 1988. Accepted November 10, 1988.

Fifteen RNA hairpins that share the same stem sequence and have homopolymer loops of A, C and U residues which vary in length from three to nine nucleotides were synthesized and their thermal stabilities determined. Tm varys as a function of loop size but is almost independent of loop composition. Loops of four or five nucleotides are found to be the most stable loop size. This is consistent with the observation that four-membered loops are the most prevalent loop size in 16S-like RNAs. The contribution of each loop to hairpin stability was calculated by subtracting the known contribution of the helical stem. These data should be useful for predicting the stability of other hairpins.


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