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PMID: 2449689 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

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

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 85 ·No. 5 ·1988-03-00 ·Pages 1364-8

Tuerk C, Gauss P, Thermes C, Groebe DR, Gayle M, Guild N, Stormo G, d'Aubenton-Carafa Y, Uhlenbeck OC, Tinoco I

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.

MeSH Terms
Base Sequence Nucleic Acid Conformation RNA RNA, Messenger/genetics RNA, Viral/genetics RNA-Directed DNA Polymerase/metabolism T-Phages/genetics Templates, Genetic Thermodynamics Transcription, Genetic
Chemicals
RNA, Messenger RNA, Viral RNA RNA-Directed DNA Polymerase
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Tuerk C
Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309.
Gauss P
Thermes C
Groebe D R
Gayle M
Guild N
Stormo G
d'Aubenton-Carafa Y
Uhlenbeck O C
Tinoco I
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.85.5.1364
Published
1988-03-00
Pages
1364-8
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC279771
Subset
IM
Grants
NIGMS NIH HHS · GM19963 · United States
External Links
PubMed source DOI: 10.1073/pnas.85.5.1364 PMC Full Text View journal details
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