Influence of sequence-dependent cytosine protonation and methylation on DNA triplex stability
Influence of sequence-dependent cytosine protonation and methylation on DNA triplex stability
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DOI：
10.1021/bi992630n
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发表时间：
2000-05-16
期刊：
影响因子：
2.9
通讯作者：
Weisz, K
中科院分区：
文献类型：
--
作者：
Leitner, D;Schröder, W;Weisz, K
为了详细研究胞嘧啶质子化及其对DNA三链序列依赖的热稳定性的影响，我们对N-15标记的寡核苷酸进行了同核和异核核磁共振实验，这些寡核苷酸被设计在合适的条件下折叠成嘧啶基序的分子内三螺旋。这些实验表明，即使在中性pH下，三倍体中心位置的胞嘧啶也显著质子化。然而，从依赖于pH的测量中确定的单个胞嘧啶碱基的半质子化点根据它们的位置显示出相当大的差异。因此，质子化对相邻的胞嘧啶或三倍体末端的胞嘧啶是不利的，导致对三螺旋体系整体自由能的贡献较小。相反，在三倍体第三链中，5-甲基胞嘧啶取代胞嘧啶后碱基的质子化只受很小程度的影响，甲基取代基对三倍体的稳定主要来自堆积能量和/或疏水效应。
To investigate cytosine protonation and its influence on the sequence-dependent thermal stability of DNA triplexes in detail, we have employed homo- and heteronuclear NMR experiments on specifically N-15-labeled oligodeoxynucleotides that were designed to fold into intramolecular triple helices of the pyrimidine motif under appropriate conditions. These experiments reveal that cytosines in central positions of the tripler are significantly protonated even at neutral pH. However, semiprotonation points for individual cytosine bases as determined from pH-dependent measurements show considerable differences depending on their position. Thus, protonation is disfavored for adjacent cytosines or for cytosines at the tripler termini, resulting in a smaller contribution to the overall free energy of the triple helical system. In contrast, protonation of the base upon substitution of 5-methylcytosine for cytosine in the tripler third strand is only affected to a minor extent, and tripler stabilization by the methyl substituent is shown to primarily arise from stacking energies and/or hydrophobic effects.