Environmental and Nuclear Quantum Effects on Double Proton Transfer in the Guanine–Cytosine Base Pair,The Journal of Physical Chemistry Letters

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Environmental and Nuclear Quantum Effects on Double Proton Transfer in the Guanine–Cytosine Base Pair
The Journal of Physical Chemistry Letters ( IF 4.8 ) Pub Date : 2023-05-30 , DOI: 10.1021/acs.jpclett.3c00747
Federica Angiolari ₁ , Simon Huppert ₂ , Fabio Pietrucci ₃ , Riccardo Spezia ₁

Affiliation

In the present letter, we investigate the double proton transfer (DPT) tautomerization process in guanine–cytosine (GC) DNA base pairs. In particular, we study the influence of the biological environment on the mechanism, the kinetics and thermodynamics of such DPT. To this end, we present a molecular dynamics (MD) study in the tight-binding density functional theory framework, and compare the reactivity of the isolated GC dimer with that of the same dimer embedded in a small DNA structure. The impact of nuclear quantum effects (NQEs) is also evaluated using Path Integral based MD. Results show that in the isolated dimer, the DPT occurs via a concerted mechanism, while in the model biological environment, it turns into a stepwise process going through an intermediate structure. One of the water molecules in the vicinity of the proton transfer sites plays an important role as it changes H-bond pattern during the DPT reaction. The inclusion of NQEs has the effect of speeding up the tautomeric-to-canonical reaction, reflecting the destabilization of both the tautomeric and intermediate forms.

中文翻译：

鸟嘌呤-胞嘧啶碱基对中双质子转移的环境和核量子效应

在这封信中，我们研究了鸟嘌呤-胞嘧啶 (GC) DNA 碱基对中的双质子转移 (DPT) 互变异构化过程。特别是，我们研究了生物环境对这种 DPT 的机制、动力学和热力学的影响。为此，我们提出了紧束缚密度泛函理论框架中的分子动力学 (MD) 研究，并比较了分离的 GC 二聚体与嵌入小 DNA 结构中的相同二聚体的反应性。还使用基于路径积分的 MD 评估了核量子效应 (NQE) 的影响。结果表明，在分离的二聚体中，DPT 通过协同机制发生，而在模型生物环境中，它变成了通过中间结构的逐步过程。质子转移位点附近的一个水分子起着重要作用，因为它在 DPT 反应期间改变了氢键模式。包含 NQE 具有加速互变异构到规范反应的效果，反映了互变异构和中间体形式的不稳定。

更新日期：2023-05-30

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