Thermodynamic Stability of DNA Duplexes Comprising the Simplest T → dU Substitutions
Thermodynamic Stability of DNA Duplexes Comprising the Simplest T → dU Substitutions
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DOI：
10.1021/acs.biochem.8b00676
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发表时间：
2018-10-02
期刊：
影响因子：
2.9
通讯作者：
Marky, Luis A.
中科院分区：
文献类型：
--
作者：
Carr, Carolyn E.;Khutsishvili, Irine;Marky, Luis A.
尿嘧啶-DNA糖基化酶（UDG）家族的成员识别并结合尿嘧啶，将其隔离在结合位点口袋内，并催化脱氧核糖的碱基裂解，留下脱碱基位点。识别和结合是被动的，并且依赖于DNA的固有动态运动，其中碱基对经历热诱导的断裂和构象波动。一旦尿嘧啶从其碱基对断裂，它可以被酶识别和结合，然后改变其构象以进行螯合和催化。我们的研究结果表明，胸腺嘧啶尿嘧啶取代，这仅仅是由一个单一的甲基基团不同，导致双链体热力学的不稳定，这将导致人口的螺旋外状态的增加，并增加尿嘧啶被识别和切除的DNA由UDG的概率。这种不稳定性取决于最近邻碱基对堆叠的身份; G.O最近邻导致热和热不稳定性，其比两个A.T近邻的不稳定性弱。此外，尿嘧啶取代产生的最近邻增加的双链体的互补吸收，但降低了所有取代的双链体的结构水的固定化水平，无论邻居身份或取代的数量。
Members of the uracil-DNA glycosylase (UDG) enzyme family recognize and bind uracil, sequestering it within the binding site pocket and catalyzing the cleavage of the base from the deoxyribose, leaving an abasic site. The recognition and binding are passive and rely on innate dynamic motions of DNA wherein base pairs undergo thermally induced breakage and conformational fluctuations. Once the uracil breaks from its base pair, it can be recognized and bound by the enzyme, which then alters its conformation for sequestration and catalysis. Our results suggest that the thymine to uracil substitution, which differs only by a single methyl group, causes a destabilization of the duplex thermodynamics, which would lead to an increase in the population of the extrahelical state and increase the probability of uracil being recognized and excised from DNA by UDG. This destabilization is dependent on the identity of the nearest-neighbor base-pair stacks; a G.O nearest neighbor leads to thermal and enthalpic destabilization that is weaker that that seen with two A.T neighbors. In addition, uracil substitution yields a nearest-neighbor increase in the counterion uptake of the duplexes but decreases the level of immobilization of structural water for all substituted duplexes regardless of the neighbor identity or number of substitutions.