Influence of an exocyclic guanine adduct on the thermal stability, conformation, and melting thermodynamics of a DNA duplex.
Influence of an exocyclic guanine adduct on the thermal stability, conformation, and melting thermodynamics of a DNA duplex.
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环外鸟嘌呤加合物对 DNA 双链体的热稳定性、构象和熔化热力学的影响。
DOI：
10.1021/bi00163a019
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发表时间：
1992
期刊：
影响因子：
2.9
通讯作者：
Breslauer,KJ
中科院分区：
文献类型：
--
作者：
Plum,GE;Grollman,AP;Johnson,F;Breslauer,KJ
1992年9月28日摘要：作为表征诱变损伤对DNA理化性质影响的整体计划的一部分，我们在此报告了对有和无环外鸟嘌呤损伤的DNA双链体的比较光谱研究结果。具体来说，我们研究了一个由四个13-mer双链体组成的家族，其形式为d（CGCATGYGTACGC）* d（GCGTACZCATGCG），其中Y是正常的脱氧鸟苷残基（G）或环外鸟嘌呤加合物1。A是N-丙脱氧鸟苷（X），而Z是脱氧胞嘧啶（C）或脱氧腺苷（A）。因此，所研究的四个双链体，可以通过它们的中心碱基对的身份来命名，它们是沃森-克里克双链体（GC），具有中心错配的双链体（GA），以及两个具有环外鸟嘌呤损伤的双链体（X），其差异仅在于损伤对面的碱基（XC和XA）。通过对这四种DNA双链体的光谱测量，我们可以评估环外鸟嘌呤损伤以及损伤对面碱基对宿主DNA双链体构象、热稳定性和熔解能量的影响。具体地说，我们的圆二色性（CD）光谱表明，环外鸟嘌呤损伤引起双链体结构的改变，而我们的温度依赖性光学测量显示，这些损伤诱导的结构改变降低了双链体的热稳定性、转变焓和转变自由能。我们还发现，thelection诱导的热不稳定的双链体（ATm）主要是由于修改鸟嘌呤残基的存在下，而相对不敏感的基础上对病变是一个C或A残基（例如，XA和XC具有相同的Tm值）。换句话说，损伤的存在使得双链体的热稳定性对与之相对的碱基不敏感，这一结果与相应的未修饰的双链体GA和GC形成对比，后者表现出显著不同的Tm值。相比之下，我们发现，病变的存在并不改变双链差分热力学稳定性的跨链合作伙伴的影响，。换句话说，GC和GA双链体以及XC和XA双链体在自由能方面表现出相同的差异（）。因此，病变改变了具有C和A交叉链伴侣的双链体的差热稳定性（，），但不改变差热动力学稳定性（）。我们的CD光谱揭示了一个有趣的pH值依赖性的结构转变与一个明显的pKa接近中性的XA双链体是不存在的其他三个双链体。由于A残基在体内优先插入相对于X损伤，这一结果表明，生物修复系统可能面临着两种结构的混合物在生理条件下。我们还发现XA和XC双链体在化学上相似。因此，观察到的生物学偏好插入的A超过C残基对面的损伤不能合理化，只是在热力学差异的最终duplex状态。最后，我们的数据揭示了通过NMR观察到的XA双链体中pH诱导的结构改变的热力学结果（Kouchakdjian埃塔尔，1989年（1990年）是最小的。这一令人惊讶的结果表明，DNA可能足以
Revised Manuscript Received September 28, 1992 abstract: As part of an overall program to characterize the impact of mutagenic lesions on the physiochemical properties of DNA, we report here the results of a comparative spectroscopic study on pairs of DNA duplexes both with and without an exocyclic guanine lesion. Specifically, we have studied a family of four 13-mer duplexes of the form d (CGCATGYGTACGC)* d (GCGTACZCATGCG) in which Y is either the normal deoxyguanosine residue (G) or the exocyclic guanine adduct 1. A^-propanodeoxyguanosine (X), while Z is either deoxycytosine (C) or deoxyadenosine (A). Thus, the four duplexes studied, which can be designatedby the identity of their central· base pair, are a Watson-Crick duplex (GC), a duplex with a central mismatch (GA), and two duplexes with exocyclic guanine lesions (X), that differ only by the base opposite the lesion (XC and XA). The data derived from our spectroscopic measurements on these four duplexes have allowed us to evaluate the influence of the exocyclic guanine lesion, as well as the base opposite the lesion, on the conformation, thermal stability, and melting energetics of the host DNA duplex.To be specific, our circular dichroism (CD) spectra show that the exocyclic guanine lesion induces alterations in the duplex structure, while our temperature-dependent optical measurements reveal that these lesioninduced structural alterations reduce the thermal stability, the transition enthalpy, and the transition free energy of the duplex. We also find that thelesion-induced thermal destabilization of the duplex (ATm) primarily results from the presence of the modified guanine residue, while being relatively insensitive to whether the base opposite the lesion is a C or an A residue (eg, XA and XC have the same Tm values). In other words, the presence of the lesion makes the duplex thermal stability insensitiveto the base opposite it, a result that contrasts with the corresponding unmodified duplexes GA and GCwhich exhibit substantially different Tm values. By contrast, we find that the presence of the lesion does not alter the influence of the cross-strand partner on the duplex differential thermodynamic stability,. In other words, the GC and GA duplexes and the XC and XA duplexes exhibit identical differences in free energy (). Thus, the lesion alters the differential thermal stability (,) but not the differential thermodynamic stability () of duplexes with C and A cross-strand partners. Our CD spectra reveal an intriguing pH-dependent structural transition with an apparent pKA near neutrality for the XA duplex which is absent in the other three duplexes. Because A residues are inserted preferentially opposite X lesions in vivo, this result suggests that the biological repair system may be confronted with a mixture of two structures underphysiological conditions. We also find the XA and XC duplexes to be thermodynamically similar. Consequently, theobserved biological preference for insertion of A over C residues across from thelesion cannot be rationalized simply in terms of thermodynamic differencesbetween the final duplex states. Finally, our data reveal the thermodynamic consequences of the pH-induced, structural alterations in the XA duplex observed by NMR (Kouchakdjian etal., 1989, 1990) to be minimal. This surprising result suggests that DNA may be sufficiently