A primordial DNA store and compute engine

IF 38.1 1区 材料科学 Q1 MATERIALS SCIENCE, MULTIDISCIPLINARY Nature nanotechnology Pub Date : 2024-08-22 DOI:10.1038/s41565-024-01771-6
Kevin N. Lin, Kevin Volkel, Cyrus Cao, Paul W. Hook, Rachel E. Polak, Andrew S. Clark, Adriana San Miguel, Winston Timp, James M. Tuck, Orlin D. Velev, Albert J. Keung
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Abstract

Any modern information system is expected to feature a set of primordial features and functions: a substrate stably carrying data; the ability to repeatedly write, read, erase, reload and compute on specific data from that substrate; and the overall ability to execute such functions in a seamless and programmable manner. For nascent molecular information technologies, proof-of-principle realization of this set of primordial capabilities would advance the vision for their continued development. Here we present a DNA-based store and compute engine that captures these primordial capabilities. This system comprises multiple image files encoded into DNA and adsorbed onto ~50-μm-diameter, highly porous, hierarchically branched, colloidal substrate particles comprised of naturally abundant cellulose acetate. Their surface areas are over 200 cm2 mg−1 with binding capacities of over 1012 DNA oligos mg−1, 10 TB mg−1 or 104 TB cm−3. This ‘dendricolloid’ stably holds DNA files better than bare DNA with an extrapolated ability to be repeatedly lyophilized and rehydrated over 170 times compared with 60 times, respectively. Accelerated ageing studies project half-lives of ~6,000 and 2 million years at 4 °C and −18 °C, respectively. The data can also be erased and replaced, and non-destructive file access is achieved through transcribing from distinct synthetic promoters. The resultant RNA molecules can be directly read via nanopore sequencing and can also be enzymatically computed to solve simplified 3 × 3 chess and sudoku problems. Our study establishes a feasible route for utilizing the high information density and parallel computational advantages of nucleic acids. Here, the authors present a data storage and computation engine comprised of DNA adsorbed to soft dendricolloids, demonstrating end-to-end capabilities from archival storage to non-destructive file access for reading, erasing, rewriting and computing.

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原始 DNA 存储和计算引擎
任何现代信息系统都应具备一系列基本特征和功能:稳定承载数据的基底;对该基底的特定数据进行反复写入、读取、擦除、重新加载和计算的能力;以及以无缝和可编程方式执行这些功能的整体能力。对于新生的分子信息技术来说,实现这一系列原始能力的原理性证明将推动它们的持续发展。在这里,我们展示了一个基于 DNA 的存储和计算引擎,它捕捉到了这些原始能力。该系统由多个图像文件组成,这些图像文件被编码到 DNA 中,并吸附在直径约 50 微米、多孔、分层支化、胶体基质颗粒上,这些颗粒由天然丰富的醋酸纤维素组成。它们的表面积超过 200 cm2 mg-1,结合能力超过 1012 DNA 寡聚 mg-1、10 TB mg-1 或 104 TB cm-3。这种 "树枝状胶体 "比裸 DNA 更能稳定地保存 DNA 文件,其反复冻干和再水化的推断能力分别超过 170 次和 60 次。加速老化研究预测,在 4 °C 和 -18 °C 温度下,半衰期分别为 6000 年和 200 万年。数据还可以擦除和替换,并通过从不同的合成启动子转录实现非破坏性文件访问。由此产生的 RNA 分子可以通过纳米孔测序直接读取,也可以通过酶计算来解决简化的 3 × 3 国际象棋和数独问题。我们的研究为利用核酸的高信息密度和并行计算优势确立了一条可行的途径。
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来源期刊
Nature nanotechnology
Nature nanotechnology 工程技术-材料科学:综合
CiteScore
59.70
自引率
0.80%
发文量
196
审稿时长
4-8 weeks
期刊介绍: Nature Nanotechnology is a prestigious journal that publishes high-quality papers in various areas of nanoscience and nanotechnology. The journal focuses on the design, characterization, and production of structures, devices, and systems that manipulate and control materials at atomic, molecular, and macromolecular scales. It encompasses both bottom-up and top-down approaches, as well as their combinations. Furthermore, Nature Nanotechnology fosters the exchange of ideas among researchers from diverse disciplines such as chemistry, physics, material science, biomedical research, engineering, and more. It promotes collaboration at the forefront of this multidisciplinary field. The journal covers a wide range of topics, from fundamental research in physics, chemistry, and biology, including computational work and simulations, to the development of innovative devices and technologies for various industrial sectors such as information technology, medicine, manufacturing, high-performance materials, energy, and environmental technologies. It includes coverage of organic, inorganic, and hybrid materials.
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