Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
- PMID: 7524072
- PMCID: PMC44783
- DOI: 10.1073/pnas.91.20.9218
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
Abstract
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.
Similar articles
-
Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces.Biochemistry. 1994 Oct 25;33(42):12715-9. doi: 10.1021/bi00208a024. Biochemistry. 1994. PMID: 7522562
-
Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops.Nucleic Acids Res. 1992 Feb 25;20(4):819-24. doi: 10.1093/nar/20.4.819. Nucleic Acids Res. 1992. PMID: 1371866 Free PMC article.
-
Stability of RNA hairpins closed by wobble base pairs.Biochemistry. 1998 Jan 27;37(4):1094-100. doi: 10.1021/bi972050v. Biochemistry. 1998. PMID: 9454601
-
Gel electrophoresis and the structure of RNA molecules.Biotechnol Genet Eng Rev. 1992;10:379-401. doi: 10.1080/02648725.1992.10647893. Biotechnol Genet Eng Rev. 1992. PMID: 1284511 Review. No abstract available.
-
Synthetic oligoribonucleotides carrying site-specific modifications for RNA structure-function analysis.Biochimie. 1994;76(12):1223-34. doi: 10.1016/0300-9084(94)90053-1. Biochimie. 1994. PMID: 7538326 Review.
Cited by
-
Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction.BMC Bioinformatics. 2004 Aug 5;5:105. doi: 10.1186/1471-2105-5-105. BMC Bioinformatics. 2004. PMID: 15296519 Free PMC article.
-
A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme.Acta Crystallogr D Biol Crystallogr. 2007 Jul;63(Pt 7):812-25. doi: 10.1107/S090744490702464X. Epub 2007 Jun 15. Acta Crystallogr D Biol Crystallogr. 2007. PMID: 17582172 Free PMC article.
-
The complete set of H/ACA snoRNAs that guide rRNA pseudouridylations in Saccharomyces cerevisiae.RNA. 2005 Jun;11(6):928-38. doi: 10.1261/rna.2100905. RNA. 2005. PMID: 15923376 Free PMC article.
-
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.Proc Natl Acad Sci U S A. 2004 May 11;101(19):7287-92. doi: 10.1073/pnas.0401799101. Epub 2004 May 3. Proc Natl Acad Sci U S A. 2004. PMID: 15123812 Free PMC article.
-
Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond.Nucleic Acids Res. 2001 Mar 1;29(5):1034-46. doi: 10.1093/nar/29.5.1034. Nucleic Acids Res. 2001. PMID: 11222752 Free PMC article.
References
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials
