CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes.

C. Tuerk, P. Gauss, C. Thermes, D. R. Groebe, M. Gayle, N. Guild, G. Stormo, Y. d'Aubenton-Carafa, O. C. Uhlenbeck, I. Tinoco

Research output: Contribution to journalArticle

301 Scopus citations

Abstract

The mRNA of bacteriophage T4 contains a strikingly abundant intercistronic hairpin. Within the 55 kilobases of known T4 sequence, the hexanucleotide sequence CTTCGG is found 13 times in the DNA strand equivalent to mRNA sequences. In 12 of those occurrences, the sequence is flanked by inverted repeats predictive of RNA hairpins with UUCG in the loop. Avian myeloblastosis virus reverse transcriptase, which can traverse hairpins of larger calculated stability, terminates efficiently at these CUUCGG hairpins. Thermal denaturation studies of model hairpins show that the loop sequence UUCG dramatically stabilizes RNA hairpins when compared to a control sequence. These data, when combined with previously described parameters of helix stability, suggest that T4 has utilized this loop sequence to optimize the stability of intercistronic hairpins. The stability of CUUCGG hairpins is also utilized in the RNAs of many organisms besides T4.

Original languageEnglish
Pages (from-to)1364-1368
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Volume85
Issue number5
DOIs
StatePublished - Mar 1988
Externally publishedYes

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