Mathematical Modeling of a Self-Assembled Probe for Non Intercalator Type Real-Time Monitoring of PCR

用于非嵌入剂型 PCR 实时监测的自组装探针的数学建模

• 批准号: 9813297
• 负责人: Fereshteh Emami
• 金额: $ 34.66万
• 依托单位: SOUTHEASTERN LOUISIANA UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2023-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9813297
• 关键词: Acids; Address; Algorithms; Attention; Behavior; Binding; Biochemistry; Biological; Biosensing Techniques; Buffers; Catechols; Chemicals; Clinical Research; Complex; Computer Simulation; Consumption; DNA; DNA Probes; DNA Sequence; DNA amplification; Data; Detection; Diagnostics Research; Diphosphates; Drug Screening; Dyes; Equilibrium; Experimental Designs; Fluorescence; GC Rich Sequence; Goals; Growth; Imagery; Intercalating Agents; Ionic Strengths; Knowledge; Laws; Measurement; Medical; Methods; Modeling; Molecular; Monitor; Organism; Outcome; Pathway interactions; Pharmacologic Substance; Polymerase Chain Reaction; Process; Reaction; Research; Resolution; Ribonucleotides; Salts; Scheme; Science; Screening procedure; Signal Transduction; Structure; System; Technology; Temperature; Testing; Thermodynamics; Time; Vertebral column; aptamer; aqueous; base; chemical reaction; computational basis; innovation; inorganic phosphate; insight; mathematical algorithm; mathematical model; melting; molecular diagnostics; molecular modeling; novel; polymerization; real time monitoring; self assembly; sensor; simulation; time use; tool; tripolyphosphate

PROJECT SUMMARY/ABSTRACT Real-time PCR has become a crucial tool in many fields of molecular diagnostics, and many methods have been developed to monitor PCR as the reaction proceeds. The objective of this application is to examine sensing molecules such as the assembles of ZnII–DPA-attached phenylboronic acid (1.Zn) and catechol-type dyes like alizarin red S (ARS) for non-intercalator type real-time monitoring of PCR using mathematical modeling and experimental observation. The central hypothesis, which was formulated based on preliminary data, is that the 1.Zn–ARS sensor is selective towards pyrophosphate (PPi), the byproduct of DNA amplification, over the other phosphates. Different analytical evidence displayed existence multiple intertwined equilibria for the self- assembled 1.Zn-dyes sensors, yet the molecular mechanisms that underlie the phosphate sensing processes are not well understood. The long-term goal is to understand the molecular details of such very complicated self- assembly combinations that are not only limited to these examples through mathematical modeling, and to broaden this knowledge by developing novel biosensing strategies. The rationale for the proposed research is to identify unknown influences on ribonucleotide detection processes, to advance our understanding of self- assembled supramolecular host-guest thermodynamics, and to generate testable hypotheses for aptamer and drug screening procedures. To address these goals, we aim to develop a mathematical algorithm that can model the entire twenty-seven molecular intertwined interactions and reactions among the supramolecular probe, 1.Zn- ARS, and biological phosphates. We will determine the thermodynamic parameters of the interactions and reactions using the developed mathematical model, experimental design, and data fitting of the potentiometric measurements. We will then introduce optimum experimental conditions for the best real-time oligophosphate monitoring based on mathematical modeling and computer simulations. In addition, as a proof of principle, we will validate the simulated results with the experimental real-time PCR observations. This study is innovative because a sophisticated mathematical model and computer simulations will be used to investigate the reaction pathways for the formation of different guest-host bindings of 1.Zn-ARS-PPi. The computer simulations will enable the visualization of the effects of different values of binding constants, temperatures, ionic strengths, concentrations, starting pHs, etc. for any possible experimental conditions and provide appropriate directions for real-time biomolecular sensing. The proposed project is significant because, by combining the power of supramolecular self-assemblies with mathematical modeling, a better understanding of 1.Zn-ARS-PPi molecular interactions within their complex chemical networks will be achieved that can be generalized to many other complex chemical processes in pharmaceutical and biochemistry sciences to help detect and monitor analytes of medical importance.

项目总结/摘要 实时PCR已经成为分子诊断的许多领域中的关键工具，并且已经研究了许多方法。 用于在反应进行时监测PCR。本申请的目的是检查感知 分子如ZnII-DPA-连接的苯基硼酸（1.Zn）和儿茶酚型染料如 茜素红S（ARS）用于使用数学建模的PCR的非嵌入剂型实时监测， 实验观察根据初步数据提出的中心假设是， 1.Zn-ARS传感器对DNA扩增的副产物焦磷酸盐（PPi）具有较强的选择性， 磷酸盐不同的分析证据显示，自我存在多重交织的平衡， 组装1.锌染料传感器，但磷酸盐传感过程的分子机制 并没有得到很好的理解。长期目标是了解这种非常复杂的自我- 装配组合不仅限于通过数学建模的这些示例， 通过开发新的生物传感策略来拓宽这方面的知识。拟议研究的基本原理是 以确定对核糖核苷酸检测过程的未知影响，以促进我们对自我的理解， 组装的超分子主客体热力学，并产生适体和 药物筛选程序。为了实现这些目标，我们的目标是开发一种数学算法， 整个27个分子之间的相互作用和反应的超分子探针，1.Zn- ARS和生物磷酸盐。我们将确定相互作用的热力学参数， 反应使用开发的数学模型，实验设计，和数据拟合的电位 测量.然后，我们将介绍最佳的实验条件，最佳的实时寡磷酸盐 基于数学建模和计算机模拟的监测。此外，作为原则证明，我们 将验证模拟结果与实验实时PCR观察。本研究具有创新性 因为将使用复杂的数学模型和计算机模拟来研究反应， 1.Zn-ARS-PPi不同客体-主体结合形成的途径。计算机模拟将 使得能够可视化结合常数、温度、离子强度 浓度，起始pH值等任何可能的实验条件，并提供适当的指导， 实时生物分子传感。该项目之所以重要，是因为它结合了 超分子自组装与数学建模，更好地了解1.Zn-ARS-PPi分子 将实现其复杂化学网络内的相互作用，可以推广到许多其他 制药和生物化学科学中的复杂化学过程，以帮助检测和监测分析物 医学上的重要性