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CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes.
Open accessAbstract
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.
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Cites
Improved free-energy parameters for predictions of RNA duplex stability.
Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., & Turner, D. H. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.24.9373 · Cited by 1,470
Cited by
Mathews, D. H., Sabina, J., Zuker, M., & Turner, D. H. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2700 · Cited by 3,795
Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops".
Woese, C. R., Winker, S., & Gutell, R. R. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.21.8467 · Cited by 522
Harborth, J., Elbashir, S. M., Vandenburgh, K., Manninga, H., Scaringe, S. A., Weber, K., & Tuschl, T. (2003) · Antisense and Nucleic Acid Drug Development · doi:10.1089/108729003321629638 · Cited by 474
Structurally Complex and Highly Active RNA Ligases Derived from Random RNA Sequences
Ekland, E. H., Szostak, J. W., & Bartel, D. P. (1995) · Science · doi:10.1126/science.7618102 · Cited by 422
Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage
Riesenberg, S., Helmbrecht, N., Kanis, P., Maricic, T., & Pääbo, S. (2022) · Nature Communications · doi:10.1038/s41467-022-28137-7 · Cited by 109
Metadata
- Authors
- Tuerk, C., Gauss, P., Thermes, C., Groebe, D. R., Gayle, M., Guild, N., Stormo, G., d'Aubenton-Carafa, Y., Uhlenbeck, O. C., & Tinoco, I.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 1988-03
- Volume
- 85
- Issue
- 5
- Pages
- 1364-1368
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2012268010
- Cited by
- 354
- References
- 1
- FWCI
- 9.02
- Type
- journal article
- Language
- en
- Open access
- green
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- Tuerk, C., Gauss, P., Thermes, C., Groebe, D. R., Gayle, M., Guild, N., Stormo, G., d'Aubenton-Carafa, Y., Uhlenbeck, O. C., & Tinoco, I. (1988). CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.85.5.1364
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