Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson–Crick base pairs
Abstract
Improved thermodynamic parameters for prediction of RNA duplex formation are derived from optical melting studies of 90 oligoribonucleotide duplexes containing only Watson-Crick base pairs. To test end or base composition effects, new sets of duplexes are included that have identical nearest neighbors, but different base compositions and therefore different ends. Duplexes with terminal GC pairs are more stable than duplexes with the same nearest neighbors but terminal AU pairs. Penalizing terminal AU base pairs by 0.45 kcal/mol relative to terminal GC base pairs significantly improves predictions of DeltaG degrees37 from a nearest-neighbor model. A physical model is suggested in which the differential treatment of AU and GC ends accounts for the dependence of the total number of Watson-Crick hydrogen bonds on the base composition of a duplex. On average, the new parameters predict DeltaG degrees37, DeltaH degrees, DeltaS degrees, and TM within 3.2%, 6.0%, 6.8%, and 1.3 degreesC, respectively. These predictions are within the limit of the model, based on experimental results for duplexes predicted to have identical thermodynamic parameters.
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The nearest-neighbor model was used to predict RNA and DNA duplex stabilities.
“To estimate ΔGn,m, we use the nearest-neighbor model for predicting RNA and DNA duplex stabilities (31,32,33).”
From The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA (2011) · cites this paper as [33]
The energy terms used for stacking and mismatches have an error of around 5-10%.
“These energy terms have an error of around 5–10% (32,33,35).”
From The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA (2011) · cites this paper as [33]
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- Authors
- Xia, T., SantaLucia, J., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C., & Turner, D. H.
- Affiliations
- Wayne State University (US)
- Corresponding author
- Turner, Douglas H.
- ORCID
- Venue
- Biochemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 1998-10-01
- Volume
- 37
- Issue
- 42
- Pages
- 14719-14735
- ISSN
- 0006-2960 (ISSN-L)
- 1520-4995
- OpenAlex
- W2051713039
- Cited by
- 1,140
- References
- 92
- Citations by year
- 2026: 27 · 2025: 35 · 2024: 33 · 2023: 41 · 2022: 58 · 2021: 32 · 2020: 30 · 2019: 53 · 2018: 43 · 2017: 40 · 2016: 44 · 2015: 61 · 2014: 54 · 2013: 55 · 2012: 65
- FWCI
- 4.88
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Biochemistry (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Francis Crick Institute
- National Cancer Institute (P30CA086862)
- National Institute of General Medical Sciences (GM 22939, R01GM022939)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- RNA duplex formation, Watson-Crick base pairing, free energy prediction, enthalpy and entropy, melting point, hydrogen bonding
- MeSH terms
- Base Sequence, Hydrogen Bonding, Models, Chemical, Nucleic Acid Conformation, Nucleic Acid Heteroduplexes, RNA, Thermodynamics, Linear Models, Databases, Factual, Base Pairing
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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