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

DNA是生命的关键组成部分，DNA中的异常突变或化学修饰与几种疾病有关，包括癌症、糖尿病、阿尔茨海默病？类风湿性关节炎的治疗科学和工程的最新进展已经导致DNA作为治疗和诊断的令人兴奋的可能性的出现，特别是对于癌症。然而，基于DNA的疗法的生物制造和利用DNA中的化学修饰的疾病诊断的开发仍处于起步阶段。具体而言，缺乏可以小规模和大规模富集修饰的DNA的具有成本效益的材料，这分别对诊断和治疗应用很重要。拟议的研究汇集了计算化学，分子工程和生物技术的最新进展，以产生新的功能材料，用于选择性结合和富集修饰的DNA，从而为疾病诊断和生物制造带来新的，具有成本效益的过程。这个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空白，首先生成一个来自化疗药物的配体的计算（计算机模拟）库，这些配体对DNA甲基化位点具有固有的亲和力。使用DNA像素的DNA的电子结构的新的计算表示，与用于研究相互作用分子的取向的最先进的方法相一致，将用于识别选择性地结合甲基化DNA的配体超过未甲基化的类似物。将这些配体缀合到微珠上，以便实验性地评价它们对甲基化DNA与未甲基化DNA的结合、富集和洗脱的功效。结合数据的甲基化和未甲基化的DNA将进一步用于开发计算的结构-活性关系模型，以阐明物理化学现象，支配配体的选择性。这些新材料将用于富集用于治疗应用的质粒DNA和用于诊断应用的来自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预计更稳定且更便宜，这使得这种方法对于生物分离、生物制造、诊断和治疗具有吸引力。除了两名博士研究生的培训，我们将通过富尔顿本科研究计划和高中学生通过科学和工程经验的研究项目在亚利桑那州州立大学指导本科生。我们将通过伦斯勒化学学会协调对高中的推广，并将与亚利桑那州立大学的教育探索中心合作，以开发在线主动学习模块，更广泛地在线传播和推广到全世界的高中生。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估来支持。

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.