Stability of RNA hairpin loops: A6-Cm-U6

Olke C. Uhlenbeck*, Philip N. Borer, Barbara Dengler, Ignacio Tinoco

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

130 Scopus citations


The thermodynamics and circular dichroism of a series of A6-Cm-U6 (m = 4, 5, 6 or 8) oligoribonucleotides have been studied. These molecules form intramolecular hairpin loops at low temperatures and therefore are useful models for similar structures which occur in larger, natural RNA molecules. The stability of the helix forming the stem of these loops was found to be considerably greater than an intermolecular helix with the same length and composition. The most stable loop is m = 6. The enthalpy for initiation of the loop is unfavorable; it ranges from + 24 kcal, for m = 4 to + 21 kcal, for m = 6. The maximum in stability for the C6 loop and the large positive enthalpy for loop initiation are in disagreement with expectations from simple theories assuming a Gaussian distribution of end-to-end distances. Loop strain for m = 4 and m = 5 and the unstacking of the cytosines on loop formation are likely physical explanations for these thermodynamic data. The circular dichroism spectrum of cytosine residues in the C6 and C8 loops is very similar to the spectrum of single-stranded oligoribocytidylate. However, the cytosine residues in the C5 loop have a very different circular dichroism spectrum from the corresponding oligo(C5) spectrum. In accordance with the thermodynamic data, we conclude from the circular dichroism data that the C5 loop has an altered conformation from the C5 and C8 loops.

Original languageEnglish (US)
Pages (from-to)483-496
Number of pages14
JournalJournal of Molecular Biology
Issue number4
StatePublished - Feb 5 1973

ASJC Scopus subject areas

  • Molecular Biology
  • Biophysics
  • Structural Biology


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