Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States.
Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States.
J Phys Chem B. 2021 Jul 22;125(28):7613-7627. doi: 10.1021/acs.jpcb.1c01351. Epub 2021 Jul 8.
Measuring the strength of the hydrogen bonds between DNA base pairs is of vital importance for understanding how our genetic code is physically accessed and recognized in cells, particularly during replication and transcription. Therefore, it is important to develop probes for these key hydrogen bonds (H-bonds) that dictate events critical to cellular function, such as the localized melting of DNA. The vibrations of carbonyl bonds are well-known probes of their H-bonding environment, and their signals can be observed with infrared (IR) spectroscopy. Yet, pinpointing a single bond of interest in the complex IR spectrum of DNA is challenging due to the large number of carbonyl signals that overlap with each other. Here, we develop a method using isotope editing and infrared (IR) spectroscopy to isolate IR signals from the thymine (T) C2═O carbonyl. We use solvatochromatic studies to show that the TC2═O signal's position in the IR spectrum is sensitive to the H-bonding capacity of the solvent. Our results indicate that C2═O of a single T base within DNA duplexes experiences weak H-bonding interactions. This finding is consistent with the existence of a third, noncanonical CH···O H-bond between adenine and thymine in both Watson-Crick and Hoogsteen base pairs in DNA.
测量 DNA 碱基对之间氢键的强度对于理解我们的遗传密码在细胞中如何被物理访问和识别至关重要，特别是在复制和转录过程中。因此，开发用于这些关键氢键（H 键）的探针非常重要，这些氢键决定了细胞功能的关键事件，例如 DNA 的局部熔化。羰基键的振动是其氢键环境的已知探针，并且可以通过红外（IR）光谱观察到它们的信号。然而，由于羰基信号彼此重叠的数量很大，因此在 DNA 的复杂 IR 光谱中精确定位单个感兴趣的键是具有挑战性的。在这里，我们使用同位素编辑和红外（IR）光谱开发了一种方法，用于分离胸腺嘧啶（T）C2═O 羰基的 IR 信号。我们使用溶剂化变色研究表明，IR 光谱中 TC2═O 信号的位置对溶剂的氢键能力敏感。我们的结果表明，DNA 双链体中单个 T 碱基的 C2═O 经历弱氢键相互作用。这一发现与 DNA 中 Watson-Crick 和 Hoogsteen 碱基对中腺嘌呤和胸腺嘧啶之间存在第三种非经典 CH···O H 键是一致的。
