Sequence Specific Targeting of Nucleic Acids Using Intramolecular Triplexes: Energetics and Hydration

这个项目的重点是核酸三股螺旋的热力学，这已经牵连到细胞过程的控制内源性或外源性机制。 长期目标是了解核苷酸序列、链组成、阳离子、pH和水合作用对分子内和分子间三链体稳定性的作用。 光谱，量热，密度和声学技术的组合用于获得完整的热力学配置文件的三链体形成作为双链体构象，pH值，盐浓度，并纳入错配和凸起的函数。 具体而言，相图的三链体的稳定性将被测量作为盐浓度和pH值的函数，然后，压力扰动量热和热应力技术将被用来探测其展开和水合的变化。 将结果与它们的声学和体积测量进行比较，从而分别通过双链体和三链体形成获得它们的水合性质和在靶向核酸单链或双链体中的水合作用。 一个全面的数据库将产生设计有用的三链体试剂靶向特定的核酸序列和序列特异性的局部构象重排的能量预测。水合作用在大分子识别中的作用是分子生物科学中一个重要的研究领域。 水在生物大分子的整体性质中起着至关重要的作用。 大分子水合作用的定量描述对于将序列与结构、能量学、动力学和功能联系起来是重要的。 这些结果将提高我们目前对水合作用如何控制核酸三链体的稳定性，构象和熔融行为的理解，提供对溶液中全球水的深入了解，有助于分子建模和理论计算。 更广泛的影响：该项目的教育意义在于指导学生;该项目将涉及核酸的生物物理化学及其与配体的相互作用的复杂方法和分析方面的培训。 此外，研究结果将纳入本科和研究生课程的讲座。在这个项目中产生的数据库将是有用的其他研究人员解释和分析结果，从许多类型的结构和生物物理实验。

This project focuses on the thermodynamics of nucleic acid triple helices, which have been implicated in the control of cellular processes by endogenous or exogenous mechanisms. The long-term goal is to understand the role of nucleotide sequence, strand composition, cations, pH, and hydration on the stability of intramolecular and intermolecular triplexes. A combination of spectroscopic, calorimetric, density and acoustical techniques is used to obtain complete thermodynamic profiles of triplex formation as a function of duplex conformation, pH, salt concentration, and incorporation of mismatches and bulges. Specifically, phase diagrams of the stability of triplexes will be measured as a function of salt concentration and pH; then, pressure-perturbation calorimetric and osmotic-stress techniques will be used to probe their unfolding and hydration changes. The results will be compared with their acoustical and volume measurements, allowing obtaining their hydration properties and the hydration effects in the targeting of nucleic acid single strands or duplexes via duplex and triplex formation, respectively. A comprehensive database will be produced for designing useful triplex reagents for targeting specific nucleic acid sequences and for energy predictions of sequence-specific local conformational rearrangements.The role of hydration in macromolecular recognition is an important understudied research area in molecular biosciences. Water plays a crucial role in the overall properties of biological macromolecules. A quantitative description of macromolecular hydration is important for correlating sequence with structure, energetics, dynamics and function. The results will improve our current understanding of how hydration controls the stability, conformation and melting behavior of nucleic acid triplexes, providing an insight into global water in solution, useful in molecular modeling and theoretical calculations. Broader impact: The educational significance of the project is in the mentoring of students; the project will involve training in sophisticated methodology and analysis in biophysical chemistry of nucleic acids and of their interactions with ligands. Furthermore, the research findings will be incorporated into lectures of undergraduate and graduate courses. The database generated in this project will be useful to other investigators for interpreting and analyzing results from many types of structural and biophysical experiments.