SemiSynBio-II: Engineering Write, Access, Read, and Protect (WARP) Drives for DNA-based Data Storage Systems.

数字数据正在以越来越惊人的速度生成，无论是经济上还是环境方面，数据存储材料和能源的使用接近达到当前技术所能提供的物理极限。二十多年来，尽管 DNA 具有高密度、稳定性和低能耗等显着优势，但人们对 DNA 作为潜在的下一代数据存储介质的热情却很有限。这是因为使用DNA执行数据存储系统的核心操作（包括写入、访问、读取和保护）目前需要连续执行多个复杂步骤。此外，它们通常需要在每个操作步骤之间进行专门的处理和纯化。这导致了速度、成本、可扩展性和可重用性方面的实际障碍。该提案的中心假设是，跨学科合作可以通过不同学科的知识和技术的创造性整合，彻底重新构想和重新设计这些核心业务，使其具有连续性、高度实用性和经济可行性。具体来说，生物科学的分子生物学技术将通过计算机科学和工程学科的模型和模拟来了解和设计，而这些生物成分将受到物理控制，并与材料科学和纳米科学专业知识开发的纳米材料相连接。这种混合信息存储系统由 DNA 设计而成，直接与新型纳米纤丝基底连接，将利用生物分子操作的动态处理，并通过基于半导体的纳米孔技术解锁信息的直接和快速读取。基于生物分子的计算模型将告知系统设计及其操作的各个方面，从分子到系统级尺度。该项目的跨学科性质还将提供强大的机会，通过多种途径促进科学技术工程数学（STEM）劳动力的教育和多样性。这项跨学科研究为本科生研究人员提供了直接与来自不同学科的同行和博士生合作解决常见问题的机会。将创建连接合成生物学、纳米科学、材料科学、计算机科学和工程学的本科课程模块，并提供应用跨学科示例，包括 DNA 存储作为案例研究。还将开发实践工具包，以促进通过与接触和支持 STEM 领域代表性不足的小学生的组织合作管理的面对面和虚拟活动。该项目旨在将 DNA 存储系统从批量架构转变为连续架构。每个目标针对一个单元进程（写入、访问、读取、保护）。写：快速、可扩展且廉价的 DNA 合成将通过树算法和酶驱动的 DNA 组装的组合来设计。访问：通过将 DNA 数据库固定在具有易于访问的高表面积的树突状胶体颗粒上，可以实现对信息和文件的连续且可重复使用的访问。这种新颖的支架允许该团队先前开发的基于转录的文件访问系统通过 DNA 数据库的简单层流快速提取转录 RNA 形式的信息。阅读：ACCESS 技术生成的 RNA 将通过纳米孔测序直接读取，并将进行基础实验和机器学习研究，以告知 DNA 数据库的编码算法并优化实时碱基调用。保护：DNA 和前三个混合单元过程的独特物理和热力学属性将被用来加密和混淆信息。虽然每个目标中产生的基本热力学发现、计算模型和物理技术在相互告知其他目标方面具有强大而具体的好处，但这些单元过程将通过两个正在进行的显式伞任务进一步集成在一起。存储受保护数据的端到端微流体设备将通过集成所有单元流程进行设计，并通过系统级建模来识别作为速度、成本、稳健性和寿命瓶颈的单元流程。这项工作还将产生重要的基础知识和模型，这些知识和模型将可推广到其他类型的基于生物分子的信息存储系统，并适用于每个不同学科中有关 DNA 组装和相互作用特异性、纳米颗粒工程和核酸测序的问题。该奖项反映了 NSF 的法定使命，并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，被认为值得支持。

Digital data are being generated at increasingly overwhelming rates both economically and for the environment, with data storage material and energy usages close to reaching the physical limits of what current technologies can provide. For over two decades DNA has been considered with only limited enthusiasm as a potential next generation medium for data storage, despite holding pronounced advantages of high density, stability, and low energy requirements. This is because executing the core operations of a data storage system including write, access, read, and protect using DNA currently requires multiple complex steps carried out in succession. Furthermore, they often require specialized processing and purification in between each operational step. This leads to practical barriers in speed, cost, scalability, and reusability. The central hypothesis of this proposal is that an interdisciplinary collaboration can completely reimagine and reengineer these core operations to be continuous, highly practical, and economically viable through creative integration of knowledge and technologies from disparate disciplines. Specifically, molecular biology techniques from the Biological Sciences will be informed and designed by models and simulations derived from the discipline of Computer Science and Engineering, while these biological components will be physically controlled and interfaced with nanomaterials developed with expertise in Materials Science and Nanoscience. This hybrid information storage system engineered from DNA directly interfaced with novel nanofibrillar substrates, will leverage dynamic processing by biomolecular manipulations, and will unlock direct and rapid readout of information with semiconductor-based nanopore technology. Biomolecular-based computational modeling will inform all aspects of both the design of the system and its operation, from molecular to systems level scales. The interdisciplinary nature of this project will also provide strong opportunities to advance education and diversity in the Science-Technology-Engineering-Math (STEM) workforce through several avenues. This interdisciplinary research provides opportunities for undergraduate researchers to experience directly working with peers and PhD students from very different disciplines on common problems. Undergraduate course modules will be created that bridge synthetic biology, nanoscience, materials science, computer science and engineering that present applied interdisciplinary examples including DNA storage as case studies. Hands-on kits will also be developed to facilitate in-person and virtual activities administered through partnerships with organizations that reach and support underrepresented grade-school students in STEM. This project aims to transform DNA storage systems from batch to continuous architectures. Each Aim addresses a unit process (WRITE, ACCESS, READ, PROTECT). WRITE: Rapid, scalable, and cheap DNA synthesis will be engineered by a combination of tree algorithms and enzyme-driven DNA assembly. ACCESS: Continuous and reusable access of information and files will be achieved by immobilization of a DNA database on dendritic colloidal particles with easily accessible high surface areas. This novel scaffold allows a transcription-based file access system previously developed by the team to rapidly extract information in the form of transcribed RNA through simple laminar flow through the DNA database. READ: RNA generated by the ACCESS technology will be directly read by nanopore sequencing, and fundamental experimental and machine learning studies will be engaged to inform the encoding algorithms of DNA databases and to optimize real-time base-calling. PROTECT: The unique physical and thermodynamic attributes of DNA and of these first three hybrid unit processes will be exploited to encrypt and obfuscate information. While fundamental thermodynamic findings, computational models, and physical technologies generated in each aim have strong and specific benefits in mutually informing the other aims, these unit processes will further be integrated together by two ongoing explicit Umbrella Tasks. End-to-end microfluidic devices storing protected data will be engineered by integrating all unit processes, informed by systems-level modeling to identify unit processes that are the bottlenecks for speed, cost, robustness, and longevity. This work will also generate important fundamental knowledge and models that will be generalizable to other types of biomolecular-based information storage systems as well as applicable to problems in each distinct discipline regarding DNA assembly and interaction specificity, nanoparticle engineering, and nucleic acid sequencing.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.