Resolution of Identity in Gas-Phase Dissociations of Mono- and Diprotonated DNA Trinucleotide Codons by 15 N-Labeling and Computational Structure Analysis
Resolution of Identity in Gas-Phase Dissociations of Mono- and Diprotonated DNA Trinucleotide Codons by 15 N-Labeling and Computational Structure Analysis
复制标题
通过 15 N 标记和计算结构分析解析单质子化和二质子化 DNA 三核苷酸密码子气相解离的同一性
DOI：
10.1021/jasms.2c00194
复制
发表时间：
2022
影响因子：
3.2
通讯作者：
Tureček, František
中科院分区：
文献类型：
--
作者：
Wan, Jiahao;Brož, Břetislav;Liu, Yue;Huang, Shu R.;Marek, Aleš;Tureček, František
用串联质谱研究了DNA三核苷酸密码子作为气相单质子化离子和双质子化离子的解离，使用15 N标记来分辨核碱基丢失和骨架裂解中的同一性。根据核碱基的不同，单价阳离子从5′-、中间和3′-位置显示出不同的核碱基丢失分布，有利于胞嘧啶而不是鸟嘌呤、腺嘌呤和胸腺嘧啶，总体平均比例为62：27：11：<1。5′-、中间和3′-核碱基丢失的分布为49：18：33，有利于5′-核碱基，但也取决于其性质。序列w2+离子的形成明确建立了所有密码子单和dications。通过Born-Oppenheimer分子动力学和密度泛函理论计算，确定了dAAA+、dGGG+、dCCC+、dTTT+、dACA+和dATC+的低吉布斯能原异构体和构象异构体的结构.含有鸟嘌呤的Monocations有利于在鸟嘌呤N7质子化的经典结构。含有腺嘌呤和胞嘧啶的结构产生经典的核碱基质子化异构体以及两性离子，其中两个质子化碱基与磷酸根阴离子结合。胸腺嘧啶的质子化不受欢迎。核碱基损失的低阈值能量允许在解离之前发生广泛的质子迁移。从单价阳离子的核碱基的损失是由相邻基团参与亲核加成或质子提取，以及变构质子迁移远离反应中心的协助。dAAA 2+和dACA 2+的双质子化异构体的优化结构揭示了经典和两性离子结构的组合。从dications的核碱基离子损失的阈值和过渡态能量低，导致涉及胞嘧啶，鸟嘌呤和腺嘌呤的容易解离。
Dissociations of DNA trinucleotide codons as gas-phase singly and doubly protonated ions were studied by tandem mass spectrometry using15N-labeling to resolve identity in the nucleobase loss and backbone cleavages. The monocations showed different distributions of nucleobase loss from the 5′-, middle, and 3′-positions depending on the nucleobase, favoring cytosine over guanine, adenine, and thymine in an ensemble-averaged 62:27:11:<1 ratio. The distribution for the loss of the 5′-, middle, and 3′-nucleobase was 49:18:33, favoring the 5′-nucleobase, but also depending on its nature. The formation of sequencew2+ions was unambiguously established for all codon mono- and dications. Structures of low-Gibbs-energy protomers and conformers of dAAA+, dGGG+, dCCC+, dTTT+, dACA+, and dATC+were established by Born–Oppenheimer molecular dynamics and density functional theory calculations. Monocations containing guanine favored classical structures protonated at guanine N7. Structures containing adenine and cytosine produced classical nucleobase-protonated isomers as well as zwitterions in which two protonated bases were combined with a phosphate anion. Protonation at thymine was disfavored. Low threshold energies for nucleobase loss allowed extensive proton migration to occur prior to dissociation. Loss of the nucleobase from monocations was assisted by neighboring group participation in nucleophilic addition or proton abstraction, as well as allosteric proton migrations remote from the reaction center. The optimized structures of diprotonated isomers for dAAA2+and dACA2+revealed combinations of classical and zwitterionic structures. The threshold and transition-state energies for nucleobase-ion loss from dications were low, resulting in facile dissociations involving cytosine, guanine, and adenine.