Collaborative Research: Molecular engineering of Methylation-Specific Binding Agents for DNA Purification

脱氧核糖核酸是生命的关键组成部分，脱氧核糖核酸的异常突变或化学修饰与多种疾病有关，包括癌症、糖尿病、阿尔茨海默病、S病和类风湿性关节炎。最近科学和工程的进步导致了DNA作为治疗和诊断的令人兴奋的可能性的出现，特别是对癌症的治疗。然而，基于DNA的疗法的生物制造和利用DNA化学修饰的疾病诊断的发展仍处于初级阶段。具体地说，缺乏能够在小范围和大范围内浓缩分别对诊断和治疗应用非常重要的修饰DNA的成本效益材料。这项拟议的研究结合了计算化学、分子工程和生物技术的最新进展，以产生选择性结合和丰富修饰DNA的新功能材料，从而为疾病诊断和生物制造带来新的、成本效益高的过程。这一合作研究项目解决了涉及甲基化DNA的生物分离中的一个关键缺口，方法是首先生成一个来自化疗药物的计算(电子)配体文库，这些配体与DNA甲基化位点具有内在的亲和力。使用DNA像素对DNA电子结构的新颖计算表示，结合最先进的相互作用分子取向研究方法，将被用于识别选择性地与未甲基化类似物结合甲基化DNA的配体。这些配体将被连接到微球上，以实验评估它们对甲基化和未甲基化DNA的结合、浓缩和洗脱的效果。甲基化和非甲基化DNA的结合数据将被进一步用于开发计算结构-活性关系模型，以阐明支配配体选择性的物理化学现象。这些新材料将被用于浓缩用于治疗的质粒DNA和用于诊断应用的膀胱癌细胞的甲基化基因组DNA。与基于蛋白质的配体相比，所提出的小分子配体有望更稳定、更便宜，这使得这种方法在生物分离、生物制造、诊断和治疗方面具有吸引力。除了培养两名博士研究生外，我们还将通过富尔顿本科生研究计划指导本科生，并通过亚利桑那州立大学的科学和工程经验指导高中生。我们将通过伦斯勒化学学会协调扩展到高中，并将与亚利桑那州立大学的探索教育中心合作，开发在线主动学习模块，以便更广泛地在线传播和扩展到世界各地的高中生。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

DNA is a key building block of life and abnormal mutations or chemical modifications in DNA are associated with several diseases including cancer, diabetes, Alzheimer?s disease and rheumatoid arthritis. Recent advances in science and engineering have led to the emergence of exciting possibilities for DNA as therapeutics and diagnostics, particularly for cancer. However, biomanufacturing of DNA-based therapeutics and development of disease diagnostics that exploit chemical modifications in DNA are still in their infancy. Specifically, cost-effective materials that can enrich modified DNA at small and large scales, which are important for diagnostic and therapeutic applications, respectively, are lacking. The proposed research brings together state-of-the-art advances in computational chemistry, molecular engineering, and biotechnology in order to generate new functional materials for selectively binding and enriching modified DNA, leading to novel, cost-effective processes for disease diagnostics and biomanufacturing. This collaborative research project addresses a key gap in bioseparations involving methylated DNA by first generating a computational (in silico) library of ligands derived from chemotherapeutics that have inherent affinity to sites of DNA methylation. Novel computational representation of the electronic structure of DNA using DNA pixels, in concert with state-of-the-art methods for studying orientations of interacting molecules, will be employed to identify ligands that selectively bind methylated DNA over unmethylated analogs. These ligands will be conjugated onto microbeads in order to experimentally evaluate their efficacy for binding, enrichment, and elution of methylated vs. unmethylated DNA. Binding data of methylated and unmethylated DNA will be further used to develop computational structure-activity relationship models in order to elucidate physicochemical phenomena that govern ligand selectivity. These novel materials will be employed to enrich plasmid DNA for therapeutic applications and methylated genomic DNA from bladder cancer cells for diagnostic applications. The proposed small-molecule ligands are anticipated to be more stable and less expensive compared to protein-based ligands, which makes this approach attractive for bioseparations, biomanufacturing, diagnostics, and therapeutics. In addition to the training of two doctoral graduate students, we will mentor undergraduate students via the Fulton Undergraduate Research Initiative and high school students via the SCience and ENgineering Experience on research projects at Arizona State University. We will coordinate outreach to high schools via the Rensselaer Chemistry Society and will collaborate with the Education Through eXploration Center at ASU in order to develop online active learning modules for broader online dissemination and outreach to high-school students worldwide.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.