Kinetics and thermodynamics of i-DNA formation: phosphodiester versus modified oligodeoxynucleotides
Kinetics and thermodynamics of i-DNA formation: phosphodiester versus modified oligodeoxynucleotides
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DOI：
10.1093/nar/26.21.4797
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发表时间：
1998-11-01
影响因子：
14.9
通讯作者：
Lacroix, L
中科院分区：
文献类型：
--
作者：
Mergny, JL;Lacroix, L
在微酸性或甚至中性的pH值下，包括一段胞苷的寡脱氧核苷酸已被证明形成四聚体结构，其中两个平行链双链的半质子化的C.C+碱基对面对面并完全插入，形成所谓的i基序。富含胞嘧啶的嘧啶寡脱氧核苷酸可以形成分子内的i基序，我们已经研究了几种DNA类似物折叠成这种结构的能力。热变性提供了折叠的证据。我们已经证明，硫代磷酸酯和磷酸二酯低聚脱氧核苷酸，而不是甲基膦酸或PNA低聚物，可以形成i-基序。四种不同的PS低聚脱氧核苷酸与它们的PO对应物进行了比较，在所有情况下，硫代磷酸酯低聚物的熔化温度（T-m）等于或略低于天然低聚脱氧核苷酸的熔化温度（2-3℃）。pH值的微小变化会导致完全不同的熔化曲线：pH值在6.4或更低时曲线是可逆的，pH值在6.8或更高时出现滞后；冷却和加热曲线没有重叠，使我们能够确定结合（k(on)）和解离（k(off)）的速率常数作为温度的函数：这些速率常数给出线性阿伦尼乌斯图，与结合-解离两态模型的预测一致。活化能E-on是强烈负的，在中性pH下，硫代磷酸酯缔合和解离速度比相同序列的磷酸二酯寡脱氧核苷酸快9倍。
At slightly acidic or even neutral pH, oligodeoxynucleotides that include a stretch of cytidines have been shown to form a tetrameric structure in which two parallel-stranded duplexes have their hemiprotonated C.C+ base pairs face to face and fully intercalated, in a so-called i-motif. Cytosine-rich pyrimidine oligodeoxynucleotides can form an intramolecular i-motif, We have studied the ability of several DNA analogs to fold into this structure. Evidence for folding was provided by thermal denaturation. We have shown that phosphorothioate and phosphodiester oligodeoxynucleotides, but not methylphosphonate or PNA oligomers, may form the i-motif, Four different PS oligodeoxynucleotides were compared with their PO counterparts, In all cases, the melting temperature (T-m) of the phosphorothioate oligomer was equal or slightly inferior (by 2-3 degrees C) to the T-m of the natural oligodeoxynucleotide, For long oligodeoxynucleotides, a small change of pH leads to a completely different melting profile: the curves are reversible at pH 6.4 or lower, and a hysteresis is obtained at pH 6.8 or higher; cooling and heating curves were not superimposed, allowing us to determine the rate constants of association (k(on)) and dissociation (k(off)) as a function of the temperature: these rate constants give linear Arrhenius plots, in agreement with the prediction of the two-state model of association-dissociation. The activation energy E-on is strongly negative and, at neutral pH, the phosphorothioate associates and dissociates nine times faster than the phosphodiester oligodeoxynucleotide of identical sequence.