Toward a DNA Nanoprocessor: Optimization of Tile-Associated DNA Circuits

迈向 DNA 纳米处理器：Tile 相关 DNA 电路的优化

• 批准号: 1423219
• 负责人: Dmitry Kolpashchikov
• 金额: $ 29.35万
• 依托单位: The University of Central Florida Board of Trustees
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-07-01 至 2018-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1423219&HistoricalAwards=false
• 关键词: Toward; DNA; Nanoprocessor; Optimization; Tile

A nano-scale processor that uses individual molecules as operational units is a promising alternative to the modern computers that use semiconductor microprocessors. A computer built from molecules is potentially smaller and consumes less energy than its electronic counterpart. A long-term goal of this project is to construct a molecular scale processor from biological molecules, called DNA oligonucleotides. An additional advantage of such DNA-based computers is their biocompatibility, which is the ability to interact with biological molecules, cells and even organs in a controlled fashion. This property is crucial in application of molecular devices in living organisms for the control and corrections of metabolic functions, or in clinical tests for diagnosis of human genetic and infectious diseases. Recently, connectable logic units made of DNA oligonucleotides have been developed by implementing an original design that supports communication between logic gates made of DNA oligonucleotides. In the prior studies, a set of communicating AND, NOT and OR logic gates was designed and characterized. It was demonstrated that such logic gates have advantages over conventional technologies in the analysis of nucleic acid sequences of pathogenic bacteria, such as Mycobacterium tuberculosis. The communicating gates were attached to the DNA tiles to produce simple logic circuits, a counterpart of logic circuit used in modern computers. This project makes next three steps in the development of a DNA nanoprocessor. First, DNA circuits will be powered by chemical reactions to provide energy for continuous operation of the DNA computer. Next step is to achieve re-settable and re-usable mode of operation, such that the DNA computer can be used multiple times for logic operations. This will be achieved by using biocatalysts, such as enzymes and deoxyribozymes which digest DNA inputs, thus resetting the molecular devise in its original state. Third, larger-scale integration of DNA logic units will be achieved. More complex integrated circuits can solve more complex computational tasks. This will be achieved using most recent developments in DNA nanotechnology - controllable self-association of DNA strands in predesigned structures. To sum up, this project will solve three important problems of molecular computation on the way to the production of a first DNA nanoprocessor. This will lay a foundation for the future DNA nanoprocessors, a key component of smart medical molecular nanodevices of the future. The research will be integrated with education through introducing research topics into undergraduate teaching, research training of students at undergraduate and graduate levels, and the outreach program through partnerships with Central Florida high schools.

使用单个分子作为操作单元的纳米级处理器是使用半导体微处理器的现代计算机的一个有前途的替代品。由分子构成的计算机可能比电子计算机更小，消耗的能量更少。该项目的长期目标是从生物分子（称为DNA寡核苷酸）构建分子级处理器。这种基于DNA的计算机的另一个优点是它们的生物相容性，即能够以受控的方式与生物分子，细胞甚至器官相互作用。该性质在生物体中用于控制和校正代谢功能的分子装置的应用中，或在用于诊断人类遗传和传染病的临床测试中是至关重要的。最近，通过实现支持由DNA寡核苷酸制成的逻辑门之间的通信的原始设计，已经开发了由DNA寡核苷酸制成的可连接逻辑单元。在先前的研究中，设计和表征了一组通信AND、NOT和OR逻辑门。结果表明，这种逻辑门在病原菌（如结核分枝杆菌）的核酸序列分析中具有优于传统技术的优势。通信门被连接到DNA瓦片上，以产生简单的逻辑电路，这是现代计算机中使用的逻辑电路的对应物。该项目在DNA纳米处理器的开发中进行了接下来的三个步骤。首先，DNA电路将由化学反应提供动力，为DNA计算机的持续运行提供能量。下一步是实现可重新设置和可重复使用的操作模式，使得DNA计算机可以多次用于逻辑运算。这将通过使用生物催化剂来实现，例如消化DNA输入的酶和脱氧核酶，从而将分子设计重置在其原始状态。第三，将实现DNA逻辑单元的更大规模集成。更复杂的集成电路可以解决更复杂的计算任务。这将通过使用DNA纳米技术的最新发展来实现-在预先设计的结构中DNA链的可控自缔合。 总而言之，该项目将解决分子计算的三个重要问题，以生产第一个DNA纳米处理器。这将为未来的DNA纳米处理器奠定基础，DNA纳米处理器是未来智能医学分子纳米器件的关键组成部分。该研究将通过将研究课题引入本科教学，对本科和研究生水平的学生进行研究培训，以及通过与中央佛罗里达高中的合作伙伴关系开展外展计划，与教育相结合。