Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States.
J Phys Chem B. 2019 Jan 31;123(4):756-767. doi: 10.1021/acs.jpcb.8b09487. Epub 2019 Jan 22.
In this work, we utilize Fourier transform infrared and temperature-jump (T-jump) infrared (IR) spectroscopy to investigate the melting thermodynamics and kinetics of a series of five DNA sequences ranging from 6 to 14 base pairs long. IR spectroscopy is well suited for the study of DNA because of its ability to distinguish base-specific information, and the nanosecond time resolution of the T-jump apparatus can access the relevant range of kinetics. Eyring analysis of a two-state model examines both the activation enthalpy and entropy, providing new insights into the energetic driving forces and physical processes behind the association and dissociation while also helping to clarify the commonly observed negative activation energy. Global analysis of the thermodynamic and kinetic data applying a linear dependence of activation barriers on oligo length provides a holistic result by producing reasonable agreement between our data and existing nearest-neighbor (NN) thermodynamic parameters blending the experimental results with established predictive models. By studying the trends in the thermodynamics and kinetics as a function of length, this work demonstrates a direct correlation between the effects additional dinucleotides have on the kinetics and the NN parameters for those dinucleotides. This result further supports the development of a kinetic analogue to the thermodynamic NN parameters.
在这项工作中，我们利用傅里叶变换红外和温度跃变（T-jump）红外（IR）光谱研究了一系列长度从 6 到 14 个碱基的五个 DNA 序列的熔融热力学和动力学。由于其能够区分碱基特异性信息，并且 T-jump 仪器的纳秒时间分辨率可以访问相关的动力学范围，因此 IR 光谱非常适合研究 DNA。Eyring 分析二态模型同时考察了活化焓和熵，为关联和解离背后的能量驱动力和物理过程提供了新的见解，同时还有助于澄清通常观察到的负活化能。通过线性依赖寡核苷酸长度的激活势垒对热力学和动力学数据进行全局分析，可以通过产生我们的数据与现有最近邻（NN）热力学参数之间的合理一致性来提供整体结果，将实验结果与既定的预测模型融合在一起。通过研究热力学和动力学随长度的变化趋势，这项工作证明了额外的二核苷酸对动力学的影响与那些二核苷酸的 NN 参数之间存在直接关联。这一结果进一步支持了发展与热力学 NN 参数相类似的动力学参数。
