Theoretical Studies on the Photophysics and Photochemistry of 5-Formylcytosine and 5-Carboxylcytosine: The Oxidative Products of Epigenetic Modification of Cytosine in DNA,The Journal of Physical Chemistry B

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Theoretical Studies on the Photophysics and Photochemistry of 5-Formylcytosine and 5-Carboxylcytosine: The Oxidative Products of Epigenetic Modification of Cytosine in DNA
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2018-02-22 00:00:00 , DOI: 10.1021/acs.jpcb.7b10218
Jinlu Xing _{1,

2} , Yuejie Ai ₁ , Yang Liu ₁ , Jia Du ₂ , Weiqiang Chen _{1,

2} , Zhanhui Lu ₂ , Xiangke Wang _{1,

3,

4}

Affiliation

Cytosine methylation and demethylation play crucial roles in understanding the genomic DNA expression regulation. The epigenetic modification of cytosine and its continuous oxidative products are called the “new four bases of DNA” including 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). However, compared to the abundant studies on the classical DNA bases, the photophysical and photochemical properties of those new bases have not yet aroused people’s excessive attention. In this contribution, a systematic study on the nonradiative decay and photochemical pathways via excited states or conical intersections upon photoexcitation has been explored through high-level computational approaches such as the complete active space self-consistent field method, complete active space with second-order perturbation theory, and density functional theory. Pathways like the ring-distortion deactivation, hydrogen dissociation, hydrogen transfer, and also Norrish type I and II photochemical reactions have been investigated, and it was proposed that intersystem crossing from the S₁ state to the T₁ state is the most effective route for 5fC. For 5caC, ring-pucking and intramolecular isomerism are effective deactivation ways at both neutral and protonated forms. In the meantime, the influences of two important environmental factors, the solution and acidic environment (i.e., the protonated state), were also considered in this study. From the theoretical perspective, the initial properties of the photostability and photochemical reactivity for 5fC and 5caC have become a crucial aspect to facilitate a further comprehension of their potential role in gene regulation and transcription.

中文翻译：

5-甲酰基胞嘧啶和5-羧基胞嘧啶的光物理和光化学的理论研究：DNA中胞嘧啶的表观遗传修饰的氧化产物

胞嘧啶甲基化和去甲基化在理解基因组DNA表达调控中起关键作用。胞嘧啶及其连续氧化产物的表观遗传修饰被称为“ DNA的新的四个碱基”，包括5-甲基胞嘧啶（5mC），5-羟甲基胞嘧啶（5hmC），5-甲酰基胞嘧啶（5fC）和5-羧基胞嘧啶（5caC）。但是，与对经典DNA碱基的大量研究相比，这些新碱基的光物理和光化学性质尚未引起人们的过多关注。为此，我们通过高级计算方法，例如完整的有源空间自洽场方法，对光激发时通过激发态或圆锥形相交的非辐射衰变和光化学途径进行了系统研究。具有二阶摄动理论和密度泛函理论的完整活动空间。已经研究了诸如环畸变失活，氢解离，氢转移以及Norrish I型和II型光化学反应之类的途径，并提出了与S的体系间交叉_从1状态到T ₁状态是5fC的最有效途径。对于5caC，环折叠和分子内异构是中性和质子化形式的有效失活方式。同时，在这项研究中还考虑了两个重要的环境因素的影响，即溶液和酸性环境（即质子化状态）。从理论上讲，5fC和5caC的光稳定性和光化学反应性的初始性质已成为至关重要的方面，以促进人们进一步了解它们在基因调控和转录中的潜在作用。

更新日期：2018-02-22

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