Pipas J M, McMahon J E
Proc Natl Acad Sci U S A. 1975 Jun;72(6):2017-21. doi: 10.1073/pnas.72.6.2017.
We report a method for predicting the most stable secondary structure of RNA from its primary sequence of nucleotides. The technique consists of a series of three computer programs interfaced to take the nucleotide sequence of any RNA and (a) list all possible helical regions, using modified Watson-Crick base-pairing rules; (b) create all possible secondary structures by forming permutations of compatible helical regions; and (c)evaluate each structure for total free energy of formation from a completely extended chain. A free energy distribution and the base-by-base bonding interactions of each possible structure are catalogued by the system and are readily available for examination. The method has been applied to 62 tRNA sequences. The total free-energy of the predicted most stable structures ranged from -19 to -41 kcal/mole (-22 to -49 kJ/mole). The number of structures created was also highly sequence-dependent and ranged from 200 to 13,000. In nearly all cases the cloverleaf is predicted to be the structure with the lowest free energy of formation.
我们报告了一种从RNA的核苷酸一级序列预测其最稳定二级结构的方法。该技术由一系列三个计算机程序组成，这些程序相互连接，以获取任何RNA的核苷酸序列，并（a）使用修改后的沃森-克里克碱基配对规则列出所有可能的螺旋区域；（b）通过形成兼容螺旋区域的排列来创建所有可能的二级结构；（c）从完全伸展的链评估每个结构形成的总自由能。系统会编目每个可能结构的自由能分布和逐个碱基的键合相互作用，并且随时可供检查。该方法已应用于62个tRNA序列。预测的最稳定结构的总自由能范围为-19至-41千卡/摩尔（-22至-49千焦/摩尔）。创建的结构数量也高度依赖于序列，范围从200到13000。几乎在所有情况下，预测三叶草结构是形成自由能最低的结构。
