Thermodynamic Cycles and Relaxation Timescales in Surface Hybridization

ID: MPS/DMR/BMAT(7623) 1206754 PI: Levicky, Rastislav ORG: NYU Polytechnic Institute 标题：表面杂交中的热力学循环和弛豫时间尺度 知识优点：核酸分析正越来越多地融入医疗保健和临床诊断中。 多重表面杂交 (SH) 是一项在通量与经济性相结合方面尤其出色的技术。 临床 SH 测试可用于癌症诊断、囊性纤维化预筛查、病原体检测和药物代谢评估等应用。 这些测试通过监测两条核酸链之间的杂交或关联程度来发挥作用，一条核酸链是固定在固体材料表面上的“探针”，另一条是存在于溶液中的样品“目标”序列。 SH 技术在临床诊断中的到来极大地增强了对基本理解的需求，以便优化诊断性能。 该项目解决了SH应用中使用的材料表面的两个突出挑战：（1）表面杂交热力学与溶液中杂交热力学之间的联系，以及（2）当许多目标序列竞争探针时接近平衡的时间尺度。 第一个主题对于将数十年的溶液杂交研究应用于 SH 应用至关重要，例如优化探针序列的设计和交叉杂交校正算法的开发。 第二个主题集中于当许多目标序列竞争探针时竞争性 SH 中限速瓶颈的识别，目标是推进最小化动力学偏差和增强对低拷贝目标序列的敏感性的策略。 作为这些研究的一部分，将获得分子相互作用的基准热力学数据，包括探针之间的相互作用，这些数据影响密集改性材料表面的杂交反应。 通过阐明表面和溶液杂交之间的热力学联系，并确定平衡的动力学瓶颈，该项目将制定基于表面杂交的研究和新兴临床技术中使用的材料表面的核心设计原则。 更广泛的影响：SH 背后的复杂分子现象长期以来阻碍了诊断应用通用指南的制定。 因此，该项目的结果将立即用于探针改性材料表面的设计以及数百个研究实验室和越来越多的临床实验室中进行的实验的解释。 该研究工作将与开发教育游戏软件的教育计划相结合，该软件将通过直接融入游戏机制来引入科学和工程的一般概念。 该软件的教学策略是通过愉快的游戏体验培养对 STEM 概念的定性熟悉，这可以在学生在正式课程中遇到相关概念之前提高他们的兴趣。 该软件将与纽约大学理工学院游戏创新实验室合作开发，其水平适合中学生。 该游戏软件的最初概念是利用童话人物，依靠分子概念来解决问题。 该软件将引入分子的概念、分子之间选择性相互作用的概念（例如超分子结构的组装），以及通过使用“分子砖”构建具有不同能量分数的防御工事的热力学概念的简单演绎，所有这些都是游戏机制的组成部分。

ID: MPS/DMR/BMAT(7623) 1206754 PI: Levicky, Rastislav ORG: NYU Polytechnic InstituteTitle: Thermodynamic Cycles and Relaxation Timescales in Surface HybridizationINTELLECTUAL MERIT: Analysis of nucleic acids is becoming increasingly integrated into health care and clinical diagnostics. A technology that especially excels in combining throughput with affordability is multiplexed surface hybridization (SH). Clinical SH tests are becoming available for applications that include cancer diagnostics, cystic fibrosis prescreening, pathogen detection, and assessment of drug metabolism. These tests function by monitoring the extent of hybridization, or association, between two nucleic acid strands, one a "probe" immobilized on a solid material surface and the other a sample "target" sequence present in solution. Arrival of SH technologies in clinical diagnostics greatly intensifies the need for fundamental understanding, so that diagnostic performance can be optimized. This project addresses two outstanding challenges about the material surfaces used in SH applications: (1) the link between hybridization thermodynamics at the surface with those in solution, and (2) the timescales for approaching equilibrium when many target sequences compete for the probes. The first topic is essential for enabling decades of solution hybridization research to be applied to SH applications, for example, to the design of optimized probe sequences and the development of corrective algorithms for cross-hybridization. The second topic centers on identification of rate-limiting bottlenecks in competitive SH, when many target sequences compete for the probes, with the goal to advance strategies for minimizing kinetic biases and for enhancing sensitivity to lower copy target sequences. As part of these studies, benchmark thermodynamic data will be obtained on molecular interactions, including between probes, that affect hybridization reactions on densely modified material surfaces. By elucidating the thermodynamic connection between surface and solution hybridization, and identifying kinetic bottlenecks to equilibration, this project will formulate design principles central to material surfaces used in research and emergent clinical technologies based on surface hybridization.BROADER IMPACTS: The complex molecular phenomena underlying SH have long hindered development of universal guidelines for diagnostic applications. Results from this project will therefore be immediately useful for design of probe-modified material surfaces as well as for interpretation of experiments performed in hundreds of research and, increasingly, clinical laboratories. The research effort will be integrated with an educational initiative on development of educational gaming software that will introduce general concepts from science and engineering through direct integration into game mechanics. The pedagogical strategy of the software is to develop qualitative familiarity with STEM concepts through an enjoyable gaming experience that can heighten interest in students before they encounter related concepts in formal coursework. The software will be developed in collaboration with the Game Innovation Laboratory at the Polytechnic Institute of NYU, at a level accessible to middle school students. The initial concept for the gaming software is to use fairy tale characters to solve problems through relying on molecular concepts. The software will introduce notions of molecules, of selective interactions between molecules (e.g. assembly of supramolecular structures), and of simple renditions of thermodynamic concepts through use of "molecular bricks" to build fortifications with different energy scores, all as an integral part of game mechanics.