Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson - Crick base pairs

Tianbing Xia, John SantaLucia, Mark E. Burkard, Ryszard Kierzek, Susan J. Schroeder, Xiaoqi Jiao, Christopher Cox, Douglas H. Turner

Research output: Contribution to journalArticle

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 T(M) 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.

Original languageEnglish (US)
Pages (from-to)14719-14735
Number of pages17
JournalBiochemistry®
Volume37
Issue number42
DOIs
StatePublished - Oct 20 1998
Externally publishedYes

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Base Composition
Thermodynamics
Base Pairing
RNA
Oligoribonucleotides
Composition effects
Chemical analysis
Freezing
Hydrogen
Hydrogen bonds
Melting

ASJC Scopus subject areas

  • Biochemistry

Cite this

Xia, T., SantaLucia, J., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., ... Turner, D. H. (1998). Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson - Crick base pairs. Biochemistry®, 37(42), 14719-14735. https://doi.org/10.1021/bi9809425

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson - Crick base pairs. / Xia, Tianbing; SantaLucia, John; Burkard, Mark E.; Kierzek, Ryszard; Schroeder, Susan J.; Jiao, Xiaoqi; Cox, Christopher; Turner, Douglas H.

In: Biochemistry®, Vol. 37, No. 42, 20.10.1998, p. 14719-14735.

Research output: Contribution to journalArticle

Xia, T, SantaLucia, J, Burkard, ME, Kierzek, R, Schroeder, SJ, Jiao, X, Cox, C & Turner, DH 1998, 'Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson - Crick base pairs', Biochemistry®, vol. 37, no. 42, pp. 14719-14735. https://doi.org/10.1021/bi9809425
Xia, Tianbing ; SantaLucia, John ; Burkard, Mark E. ; Kierzek, Ryszard ; Schroeder, Susan J. ; Jiao, Xiaoqi ; Cox, Christopher ; Turner, Douglas H. / Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson - Crick base pairs. In: Biochemistry®. 1998 ; Vol. 37, No. 42. pp. 14719-14735.
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