Characterization of RNA hairpin loop stability

Duncan R. Groebe*, Olke C. Uhlenbeck

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

156 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)11725-11735
Number of pages11
JournalNucleic acids research
Issue number24
StatePublished - Dec 23 1988

ASJC Scopus subject areas

  • Genetics


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