Journal article
Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson−Crick Base Pairs
Biochemistry (Easton), Vol.37(42), pp.14719-14735
10/20/1998
DOI: 10.1021/bi9809425
PMID: 9778347
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 ΔG°37 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 ΔG°37, ΔH°, ΔS°, and TM within 3.2%, 6.0%, 6.8%, and 1.3 °C, respectively. These predictions are within the limit of the model, based on experimental results for duplexes predicted to have identical thermodynamic parameters.
Details
- Title: Subtitle
- Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson−Crick Base Pairs
- Creators
- Tianbing Xia - Wayne State UniversityJohn SantaLucia - Wayne State UniversityMark E. Burkard - Wayne State UniversityRyszard Kierzek - Wayne State UniversitySusan J. Schroeder - Wayne State UniversityXiaoqi Jiao - Wayne State UniversityChristopher Cox - Wayne State UniversityDouglas H. Turner - Wayne State University
- Resource Type
- Journal article
- Publication Details
- Biochemistry (Easton), Vol.37(42), pp.14719-14735
- DOI
- 10.1021/bi9809425
- PMID
- 9778347
- ISSN
- 0006-2960
- eISSN
- 1520-4995
- Number of pages
- 17
- Language
- English
- Date published
- 10/20/1998
- Academic Unit
- Internal Medicine
- Record Identifier
- 9984701255502771
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