Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States.
Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States.
J Phys Chem B. 2023 Mar 23;127(11):2351-2361. doi: 10.1021/acs.jpcb.2c08915. Epub 2023 Mar 10.
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 region. Following the fruitful applications in proteins, C 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 C 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 C isotope labeling technique can potentially be applied to characterize the stacking configurations and secondary structures of nucleic acids.
羰基伸缩模式已广泛应用于线性和二维红外（IR）光谱学中，以探测核酸的构象、相互作用和生物学功能。然而，由于它们在碱基中的普遍存在，核酸的 IR 吸收带在 1600-1800 cm 区域往往高度拥挤。在蛋白质中取得丰硕成果后，C 同位素标记已被引入到寡核苷酸的 IR 测量中，以揭示其特定部位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谱，开发了一种理论策略，该策略可直接从分子动力学模拟中对带有 C 标记的寡核苷酸的 IR 光谱进行建模。我们将理论方法应用于核苷 5'-单磷酸酯和 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时的变化。使用双螺旋作为示例，我们表明计算出的 IR 光谱与实验吻合良好，并且 C 同位素标记技术有可能被应用于表征核酸的堆积构型和二级结构。
