Thermodynamic parameters for DNA sequences with dangling ends
Thermodynamic parameters for DNA sequences with dangling ends
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DOI：
10.1093/nar/28.9.1929
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发表时间：
2000-05-01
影响因子：
14.9
通讯作者：
SantaLucia, J
中科院分区：
文献类型：
--
作者：
Bommarito, S;Peyret, N;SantaLucia, J
报告了 Watson-Crick 对上所有 32 个可能的单核苷酸悬空末端双链体形成的热力学贡献。在大多数情况下，悬空端稳定，自由能贡献范围为 +0.48 ((GT)(A)) 至 -0.96 kcal/mol ((AC)(G))。相比之下，Watson-Crick 最近邻增量范围为 -0.58 (TA/AT) 到 -2.24 (GC/CG) kcal/mol。因此，在某些情况下，悬空末端对双链体稳定性的贡献与 Watson-Crick A-T 碱基对一样大。讨论了这些结果对 DNA 探针设计的影响。对悬端稳定性的序列依赖性的分析表明，闭合碱基对的性质在很大程度上决定了稳定性。然而，对于给定的闭合碱基对，腺嘌呤悬空末端总是与其他悬空核苷酸更稳定或同等稳定。此外，5' 悬空端是可移动的，或者与 3' 悬空端一样稳定。 DNA 与 RNA 悬空末端基序的比较表明，具有 5' 悬空末端的 DNA 基序对稳定性的贡献与对应的 RNA 相同或更高。相反，RNA 3' 悬挂末端对稳定性的贡献与 DNA 对应物相同或更多。该数据集已被纳入DNA二级结构预测算法（DNA MFOLD）（http://mfold2.wustl.edu/，类似于mfold/dna/form1.cgi）以及DNA杂交预测算法（HVTHER（TM））（http：jsI1.chem.wayne.edu/Hyther/hythermenu.html）。
The thermodynamic contributions to duplex formation of all 32 possible single-nucleotide dangling ends on a Watson-Crick pair are reported. In most instances, dangling ends are stabilizing with free energy contributions ranging from +0.48 ((GT)(A)) to -0.96 kcal/mol ((AC)(G)). In comparison, Watson-Crick nearest-neighbor increments range from -0.58 (TA/AT) to -2.24 (GC/CG) kcal/mol. Hence, in some cases, a dangling end contributes as much to duplex stability as a Watson-Crick A-T base pair. The implications of these results for DNA probe design are discussed. Analysis of the sequence dependence of dangling-end stabilities show that the nature of the closing base pair largely determines the stabilization. For a given closing base pair, however, adenine dangling ends are always more or equally as stable as the other dangling nucleotides. Moreover, 5' dangling ends are move or equally as stabilizing as their 3' counterparts. Comparison of DNA with RNA dangling-end motifs shows that DNA motifs with 5' dangling ends contribute to stability equally or more than their RNA counterparts. Conversely, RNA 3' dangling ends contribute to stability equally or more than their DNA counterparts. This data set has been incorporated into a DNA secondary structure prediction algorithm (DNA MFOLD) (http://mfold2.wustl.edu/ similar to mfold/dna/ form1.cgi) as well as a DNA hybridization prediction algorithm (HVTHER(TM))(http:jsI1.chem.wayne.edu/ Hyther/hythermenu.html).