The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.
Open accessAbstract
An RNA model system consisting of an oligomer binding to a 4-nt overhang at the 5' end of a hairpin stem provides thermodynamic parameters for helix-helix interfaces. In a sequence-dependent manner, oligomers bind up to 1000-fold more tightly adjacent to the hairpin stem than predicted for binding to a free tetramer at 37 degrees C. For the interface (/) in [formula: see text] additional free energy change, delta delta G 37 degrees, for binding is roughly the nearest-neighbor delta G 37 degrees for propagation of an uninterrupted helix of equivalent sequence, CGGC. When X and Z are omitted, the delta delta 37 degrees is even more favorable by approximately 1 kcal/mol (1 cal = 4.184J). On average, predictions of 11 RNA secondary structures improve from 67 to 74% accuracy by inclusion of similar stacking contributions.
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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
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Mfold web server for nucleic acid folding and hybridization prediction
Zuker, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg595 · Cited by 13,404
Self-citationMathews, D. H., Sabina, J., Zuker, M., & Turner, D. H. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2700 · Cited by 3,795
Self-citationMathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M., & Turner, D. H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401799101 · Cited by 1,622
Self-citationXia, T., SantaLucia, J., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C., & Turner, D. H. (1998) · Biochemistry · doi:10.1021/bi9809425 · Cited by 1,140
Self-citationMarkham, N. R., & Zuker, M. (2008) · Methods in Molecular Biology™ · doi:10.1007/978-1-60327-429-6_1 · Cited by 1,018
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Metadata
- Authors
- Walter, A. E., Turner, D. H., Kim, J., Lyttle, M. H., Müller, P., Mathews, D. H., & Zuker, M.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 1994-09-27
- Volume
- 91
- Issue
- 20
- Pages
- 9218-9222
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2044595289
- Cited by
- 466
- References
- 1
- FWCI
- 3.43
- Type
- journal article
- Language
- en
- Open access
- green
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- Walter, A. E., Turner, D. H., Kim, J., Lyttle, M. H., Müller, P., Mathews, D. H., & Zuker, M. (1994). Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.91.20.9218
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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