Modeling the Infrared Spectroscopy of Oligonucleotides with 13C Isotope Labels.
Modeling the Infrared Spectroscopy of Oligonucleotides with 13C Isotope Labels.
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DOI：
10.1021/acs.jpcb.2c08915
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发表时间：
2023-03
期刊：
影响因子：
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通讯作者：
Wenting Meng;Hao-Che Peng;Yuanhao Liu;A. Stelling;Lu Wang
中科院分区：
文献类型：
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作者：
Wenting Meng;Hao-Che Peng;Yuanhao Liu;A. Stelling;Lu Wang
羰基拉伸模式已广泛应用于线性和二维红外光谱中，以探测核酸的构象、相互作用和生物功能。然而，由于它们普遍存在于核碱基中，因此核酸的红外吸收带通常在1600-1800 cm-1区域高度拥挤。随着在蛋白质领域的广泛应用，13C同位素标记已被引入到寡核苷酸的红外测量中，以揭示其特定位点的结构波动和氢键条件。在这项工作中，我们结合最近开发的频率和耦合图来开发一种理论策略，直接从分子动力学模拟中模拟具有13C标签的寡核苷酸的红外光谱。我们将理论方法应用于5'-单磷酸核苷和DNA双螺旋，并演示了振动哈密顿量的元素如何决定光谱特征及其在同位素标记后的变化。以双螺旋结构为例，计算得到的红外光谱与实验结果吻合较好，表明13C同位素标记技术可以应用于核酸的堆叠构型和二级结构表征。
The carbonyl stretching modes have been widely used in linear and two-dimensional infrared (IR) spectroscopy to probe the conformation, interaction, and biological functions of nucleic acids. However, due to their universal appearance in nucleobases, the IR absorption bands of nucleic acids are often highly congested in the 1600-1800 cm-1 region. Following the fruitful applications in proteins, 13C isotope labels have been introduced to the IR measurements of oligonucleotides to reveal their site-specific structural fluctuations and hydrogen bonding conditions. In this work, we combine recently developed frequency and coupling maps to develop a theoretical strategy that models the IR spectra of oligonucleotides with 13C labels directly from molecular dynamics simulations. We apply the theoretical method to nucleoside 5'-monophosphates and DNA double helices and demonstrate how elements of the vibrational Hamiltonian determine the spectral features and their changes upon isotope labeling. Using the double helices as examples, we show that the calculated IR spectra are in good agreement with experiments and the 13C isotope labeling technique can potentially be applied to characterize the stacking configurations and secondary structures of nucleic acids.