Nearest-neighbor thermodynamics of internal A•C mismatches in DNA:: Sequence dependence and pH effects
Nearest-neighbor thermodynamics of internal A•C mismatches in DNA:: Sequence dependence and pH effects
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DOI：
10.1021/bi9803729
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发表时间：
1998-06-30
期刊：
影响因子：
2.9
通讯作者：
SantaLucia, J
中科院分区：
文献类型：
--
作者：
Allawi, HT;SantaLucia, J
根据 UV 吸光度与温度解链曲线确定了 27 种具有内部 A.C 错配的寡核苷酸在两个不同 pH 值下的热力学。将数据与四个文献值相结合，并用于推导所有 16 个在 pH 7.0 和 5.0 下具有内部 A.C 错配的三聚体序列的最近邻参数。结果表明，单个 A.C 错配对双链体稳定性的贡献很大程度上取决于溶液 pH 值和最近邻环境。平均而言，内部 A.C 错配的质子化使双链体的 Delta G(37) 度稳定为 1.39 kcal/mol，T-M 稳定为 7.0 摄氏度。最近邻参数预测本研究中提出的寡核苷酸的 Delta G(37) 度、Delta H 度、Delta S 度和 T-M 平均偏差为 6.3%、11.0%、12.2% 和pH 7.0 时分别为 1.8 摄氏度，pH 5.0 时分别为 4.7%、5.9%、6.1% 和 1.3 摄氏度。在 pH 7.0 时，单个 A.C 错配对螺旋稳定性的贡献范围为 TCA/AAT 的 2.25 kcal/mol 到 GCG/CAC 的 1.22 kcal/mol。然而，在 pH 5.0 时，A(+).C 错配的影响范围为 TCT/AAA 的 1.09 kcal/mol 到 GCC/CAG 的 -0.43 kcal/mol。讨论了结果对复制保真度和错配修复的影响。
Thermodynamics of 27 oligonucleotides with internal A.C mismatches at two different pHs were determined from UV absorbance versus temperature melting profiles. The data were combined with four literature values and used to derive nearest-neighbor parameters for all 16 trimer sequences with internal A.C mismatches at pH 7.0 and 5.0. The results indicate that the contribution of single A.C mismatches to duplex stability is strongly dependent on the solution pH and the nearest-neighbor context. On average, the protonation of an internal A.C mismatch stabilizes the duplex by 1.39 kcal/mol for Delta G(37)degrees and 7.0 degrees C for the T-M The nearest-neighbor parameters predict Delta G(37)degrees Delta H degrees, Delta S degrees and T-M of oligonucleotides presented in this study with average deviations of 6.3%, 11.0%, 12.2%, and 1.8 degrees C, respectively, at pH 7.0 and 4.7%, 5.9%, 6.1%, and 1.3 degrees C, respectively, at pH 5.0. At pH 7.0, the contribution of single A.C mismatches to helix stability ranges from 2.25 kcal/mol for TCA/AAT to 1.22 kcal/mol for GCG/CAC. At pH 5.0, however, the contribution of A(+).C mismatches ranges from 1.09 kcal/mol for TCT/AAA to -0.43 kcal/mol for GCC/CAG. Implications of the results for replication fidelity and mismatch repair are discussed.