SemiSynBio: An On-Chip Nanoscale Storage System Using Chimeric DNA

SemiSynBio：使用嵌合 DNA 的片上纳米级存储系统

• 批准号: 1807526
• 负责人: Olgica Milenkovic
• 金额: $ 200万
• 依托单位: University of Illinois at Urbana-Champaign
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-10-01 至 2023-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1807526&HistoricalAwards=false
• 关键词: SemiSynBio; Chip; Nanoscale; Storage; System

DNA-based data storage is an emerging recording paradigm that has received significant attention from the scientific community due to several recent demonstrations of the viability of storing information in macro-molecules. Unlike classical optical and magnetic storage technologies, DNA-based storage platforms offer extremely high recording densities, and they do not require electrical supply to maintain data integrity. Furthermore, under mild maintenance conditions, DNA retains its information content for centuries while still allowing users to retrieve the information independent of the specific reading technology. Still, despite the promises of DNA-based archival systems, several problems remain that prevent wide-scale deployment of the technology. These include the high cost of DNA synthesis, the lack of structural and distributed organization of data encoded in DNA, and the nonexistence of an integrated random access and readout mechanism. To address these issues, this collaborative project aims to test and implement a new molecular storage paradigm that combines unique ideas in polymer chemistry, coding theory and molecular dynamics modeling, as well as new nano-material and solid state nano-pore technologies. The accompanying interdisciplinary research and educational programs involve experts in chemistry, biophysics, electrical engineering and theoretical computer science and aim to train a new cadre of students able to address future scientific challenges in molecular storage and computing systems. The technical goal of the proposed program is to reduce the cost-integration barrier between classical recorders and DNA-based data storage devices by developing a new system centered around chimeric DNA, comprising cheap native DNA and chemically modified nucleotides. Chemically-modified nucleotides extend the coding alphabet from four symbols to more than twenty. Chimeric DNA is stored and accessed using a novel implementation of self-rolled semiconductor micro-tubular grids, controlled by three-dimensional arrays of electrodes. Random access in such systems is achieved via voltage modulation, with selected DNA guided into a sample preparation and specialized nano-pore sequencing device. The implementation of such systems is aided by new software tools for molecular dynamics simulations. Additional system support is provided via new coding methods that combat the effects of chimeric DNA integration and nano-pore sensing errors. Particular research challenges include identifying chemical modifications in nucleotides amenable for detection via nano-pore sequencers, calculating electrostatic forces within the tubes and within the pores in the presence of chimeric DNA, and integrating the micro tubular chip with an on-chip sample preparation and sensing device. Supporting work on bioinformatics and coding theoretic algorithmic development are expected to ensure additional robustness and operational stability of the proposed system.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.

基于DNA的数据存储是一种新兴的记录范式，由于最近几次证明了在大分子中存储信息的可行性，该范式受到了科学界的极大关注。与传统的光和磁存储技术不同，基于DNA的存储平台提供极高的记录密度，并且不需要电力供应来保持数据完整性。此外，在温和的维护条件下，DNA保留其信息内容几个世纪，同时仍然允许用户独立于特定的阅读技术检索信息。尽管基于DNA的档案系统前景看好，但仍存在一些问题，阻碍了该技术的大规模部署。这些问题包括DNA合成的高成本，缺乏DNA编码数据的结构和分布式组织，以及不存在集成的随机访问和读出机制。为了解决这些问题，该合作项目旨在测试和实施一种新的分子存储范式，该范式结合了聚合物化学，编码理论和分子动力学建模以及新的纳米材料和固态纳米孔技术的独特思想。伴随的跨学科研究和教育计划涉及化学，生物物理学，电气工程和理论计算机科学的专家，旨在培养一批能够应对分子存储和计算系统未来科学挑战的新学生。该计划的技术目标是通过开发一种以嵌合DNA为中心的新系统，包括廉价的天然DNA和化学修饰的核苷酸，来减少传统记录器和基于DNA的数据存储设备之间的成本整合障碍。化学修饰的核苷酸将编码字母表从四个符号扩展到二十多个。嵌合DNA的存储和访问使用一种新的实施方式的自卷半导体微管网格，由三维阵列的电极控制。在这样的系统中的随机访问是通过电压调制实现的，其中选择的DNA被引导到样品制备和专用纳米孔测序装置中。这种系统的实施是由分子动力学模拟的新软件工具辅助的。通过新的编码方法提供了额外的系统支持，这些方法可以对抗嵌合DNA整合和纳米孔传感错误的影响。具体的研究挑战包括识别适合通过纳米孔测序仪检测的核苷酸中的化学修饰，在嵌合DNA存在下计算管内和孔内的静电力，以及将微管芯片与芯片上样品制备和传感装置集成。生物信息学和编码理论算法开发的支持工作预计将确保拟议系统的额外鲁棒性和操作稳定性。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Electrically Controlled Nanofluidic DNA Sluice for Data Storage Applications

• DOI: 10.1021/acsanm.1c02519
• 发表时间: 2021-10-12
• 期刊: ACS APPLIED NANO MATERIALS
• 影响因子: 5.9
• 作者: Athreya, Nagendra;Khandelwal, Apratim;Leburton, Jean-Pierre
• 通讯作者: Leburton, Jean-Pierre

Coded Trace Reconstruction

• DOI: 10.1109/tit.2020.2996377
• 发表时间: 2020-10-01
• 期刊: IEEE TRANSACTIONS ON INFORMATION THEORY
• 影响因子: 2.5
• 作者: Cheraghchi, Mahdi;Gabrys, Ryan;Ribeiro, Joao
• 通讯作者: Ribeiro, Joao