Thermodynamic Cycles and Relaxation Timescales in Surface Hybridization

ID：MPS/DMR/BMAT（7623）1206754 PI：Levicky，Rastislav ORG：NYU Polytechnic Institute职位：表面杂交中的热力学循环和弛豫时间尺度智力优势：核酸分析越来越多地被整合到医疗保健和临床诊断中。 一种特别擅长将通量与可负担性相结合的技术是多重表面杂交（SH）。 临床SH测试可用于包括癌症诊断、囊性纤维化预筛选、病原体检测和药物代谢评估在内的应用。 这些测试通过监测两条核酸链之间的杂交或缔合程度来起作用，一条核酸链是固定在固体材料表面上的“探针”，另一条核酸链是存在于溶液中的样品“靶”序列。 SH技术在临床诊断中的到来大大加强了对基本理解的需求，从而可以优化诊断性能。 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）表面上的杂交热力学与溶液中的杂交热力学之间的联系，以及（2）当许多靶序列竞争探针时接近平衡的时间尺度。 第一个主题是必不可少的，使几十年的溶液杂交研究应用到SH应用，例如，优化的探针序列的设计和交叉杂交的校正算法的发展。 第二个主题集中在竞争性SH中的限速瓶颈的识别上，当许多靶序列竞争探针时，其目标是推进用于最小化动力学偏差和用于增强对较低拷贝靶序列的灵敏度的策略。 作为这些研究的一部分，将获得关于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，这些相互作用影响密集改性材料表面上的杂交反应。 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紧急临床技术中使用的材料表面的核心设计原则。更广泛的重要性：SH的复杂分子现象长期以来阻碍了诊断应用的通用指南的发展。 因此，该项目的结果将立即用于探针改性材料表面的设计，以及用于解释数百个研究和越来越多的临床实验室中进行的实验。 研究工作将与教育游戏软件开发的教育计划相结合，该软件将通过直接集成到游戏机制中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，在学生在正式课程中遇到相关概念之前，提高他们对STEM概念的定性熟悉程度。 该软件将与纽约大学理工学院的游戏创新实验室合作开发，中学生可以使用。 游戏软件的最初概念是使用童话人物通过依赖分子概念来解决问题。 该软件将引入分子的概念，分子之间的选择性相互作用（例如超分子结构的组装），以及通过使用“分子砖”来构建具有不同能量分数的防御工事的热力学概念的简单再现，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.