Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
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DOI：
10.1073/pnas.0401799101
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发表时间：
2004-05-11
影响因子：
11.1
通讯作者：
Turner, DH
中科院分区：
文献类型：
--
作者：
Mathews, DH;Disney, MD;Turner, DH
用于预测 RNA 二级结构的动态编程算法已被修改，以适应由化学修饰确定的折叠约束，并包括当螺旋相邻或由单个错配分开时，螺旋同轴堆叠的自由能增量。此外，对自由能参数进行了修改，以考虑末端失配和发夹、凸出、内部和多分支环的最新实验结果。为了证明该方法的适用性，使用 1-环己基-3-(2-吗啉乙基)碳二亚胺甲对甲苯磺酸盐、硫酸二甲酯和酮醛对大肠杆菌和白色念珠菌中的 5S rRNA 进行体内修饰。通过使用修饰约束，大肠杆菌序列的预测结构中已知碱基对的百分比从 26.3% 增加到 86.8%。对于白色念珠菌，无论是否修改数据，准确度均保持为 87.5%。平均而言，对于这些序列以及一组具有已知二级结构和来自文献的化学修饰数据的 14 个序列，准确度从 67% 提高到 76%。这一增强主要反映了预测的三个序列的改进
A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch. Furthermore, free energy parameters are revised to account for recent experimental results for terminal mismatches and hairpin, bulge, internal, and multibranch loops. To demonstrate the applicability of this method, in vivo modification was performed on 5S rRNA in both Escherichia coli and Candida albicans with 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate, dimethyl sulfate, and kethoxal. The percentage of known base pairs in the predicted structure increased from 26.3% to 86.8% for the E. coli sequence by using modification constraints. For C albicans, the accuracy remained 87.5% both with and without modification data. On average, for these sequences and a set of 14 sequences with known secondary structure and chemical modification data taken from the literature, accuracy improves from 67% to 76%. This enhancement primarily reflects improvement for three sequences that are predicted with