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首页> 外文期刊>Journal of Biophysical Chemistry >Spin effects govern DNA/RNA nucleotide polymerization
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Spin effects govern DNA/RNA nucleotide polymerization

机译：自旋效应决定DNA / RNA核苷酸聚合

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摘要

A new radical mechanism of nucleotide polymerization is found. The finding is based on the Car-Parrinello molecular dynamics computations at 310 K with an additional spin-spin coupling term for 31P and 1H atoms and a radical pair spin term included. The mechanism is initiated by a creation of a high-energy spin-separated Mg-ATP complex in a triplet state in which the Mg prefers an uncommon chelation to the O2-O3 oxygens of the ATP. The cleavage of the complex produces the .AMP- and .O- radicals. The latter captures a proton from acidic solution (the Zundel cation) that converts it into the .OH radical. The process agrees with the protoncoupled electron transfer (PCET) mechanism. Through interacting with the HO-C3' group of the deoxyribose/ribose the .OH radical captures its hydrogen atom. The process is accompanied by producing water and the .AMP radical. The .AMP- and .AMP radicals then interact yielding a dimer. The described mechanism is easily generalized for a bigger number of adjoining nucleotides and their type. The radical mechanism is highly sensitive to the .AMP-..OH radical pair spin symmetry and the radius of the .OH diffusion. This confines the operation of the radical mechanism: it is applicable to nucleotide polymerization through the HO-C3’ group of deoxyribose/ribose (DNA/RNA polymerization) and inapplicable through the HO-C2’ group of ribose (RNA) . a result that nature has developed over evolution.
机译：发现了核苷酸聚合的新的自由基机理。该发现基于310 K时的Car-Parrinello分子动力学计算，并包含31P和1H原子的附加自旋-自旋耦合项和一个自由基对自旋项。该机理是通过以三重态产生高能自旋分离的Mg-ATP络合物来启动的，其中Mg比ATP的O2-O3氧更倾向于不常见的螯合。复合物的裂解产生.AMP-和.O-基团。后者从酸性溶液（Zundel阳离子）捕获质子，将其转化为.OH自由基。该过程与质子耦合电子转移（PCET）机制相符。通过与脱氧核糖/核糖的HO-C3'基相互作用，.OH自由基捕获其氢原子。该过程伴随产生水和.AMP自由基。然后，.AMP-和.AMP自由基相互作用产生二聚体。对于大量的邻接核苷酸及其类型，很容易概括出所描述的机制。自由基机理对.AMP-.OH自由基对自旋对称性和.OH扩散半径非常敏感。这限制了自由基机制的操作：它适用于通过脱氧核糖/核糖的HO-C3'组进行的核苷酸聚合（DNA / RNA聚合），不适用于通过核糖的HO-C2'组进行的核苷酸聚合（RNA）。大自然比进化发展的结果。

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