Improved free-energy parameters for predictions of RNA duplex stability.

作者：Susan M. Freier, Ryszard Kierzek, John A. Jaeger, Naoki Sugimoto, Marvin H. Caruthers, Thomas Neilson, Douglas H. Turner · 发表于：Proceedings of the National Academy of Sciences · 年份：1986 · DOI：10.1073/pnas.83.24.9373 · 被引用次数：1494 · 研究领域：RNA and protein synthesis mechanisms、Bacterial Genetics and Biotechnology、RNA modifications and cancer

Thermodynamic parameters for prediction of RNA duplex stability are reported. One parameter for duplex initiation and 10 parameters for helix propagation are derived from enthalpy and free-energy changes for helix formation by 45 RNA oligonucleotide duplexes. The oligomer sequences were chosen to maximize reliability of secondary structure predictions. Each of the 10 nearest-neighbor sequences is well-represented among the 45 oligonucleotides, and the sequences were chosen to minimize experimental errors in delta GO at 37 degrees C. These parameters predict melting temperatures of most oligonucleotide duplexes within 5 degrees C. This is about as good as can be expected from the nearest-neighbor model. Free-energy changes for helix propagation at dangling ends, terminal mismatches, and internal G X U mismatches, and free-energy changes for helix initiation at hairpin loops, internal loops, or internal bulges are also tabulated.