Foundational Aspects of Biomolecular Information and Computation

生物分子信息和计算的基础方面

• 批准号: 203140-2012
• 负责人: Kari, Lila
• 金额: $ 2.48万
• 依托单位: University of Western Ontario
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2015
• 资助国家: 加拿大
• 起止时间: 2015-01-01 至 2016-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=569875
• 关键词: Foundational; Aspects; Biomolecular; Information; Computation

In the same way we use the letters of the alphabet to write text, and the bits 0 and 1 to write computer machine code, the four basic DNA units (Adenine, Guanine, Cytosine, Thymine) are used by Nature to write genetic information as DNA strands. The possibility of encoding symbolic information on DNA, and the fact that biochemical processes such as cut-and-paste of DNA strands have been proved to be able to perform arithmetic and logic operations, led to the development of the field of DNA computing. The primary goal of my research is to analyze this new way of storing and manipulating data on DNA strands, as bioinformation and biocomputation are fundamentally different from their electronic counterparts in several aspects. Most importantly, DNA-encoded information is not associated with a memory location but consists of infinitesimal free-floating DNA strands that interact with each other due to their Watson-Crick complementarity. This proposal aims to develop the foundations for a "theory of bioinformation and biocomputation", by defining and investigating formal-language-theoretic models of DNA-based information and bio-operations, that take into account the intrinsic characteristics of their biological substrates. Besides expanding the traditional notions of information and computation to account for computation taking place in nature, the results of this research could provide insights into the computational properties of biomolecular information and consequently have potential implications for their practical applications in, e.g., multi-input RNA-based logic circuits for medical diagnosis, or building DNA nanostructures for nanoelectronic and nano-optical devices. Another aspect of the proposed research is an exploration of the paradigm of nanocomputation by self-assembly by investigating the power and limitations of models of computational self-assembly systems with DNA tiles. The results of this research could have potential implications for the design, evaluation, and analysis of DNA architectures for bionanotechnology.

同样，我们使用字母表中的字母来写文本，使用0和1位来写计算机机器代码，自然界使用四个基本的DNA单元（腺嘌呤，鸟嘌呤，胞嘧啶，胸腺嘧啶）来写DNA链的遗传信息。在DNA上编码符号信息的可能性，以及DNA链的剪切和粘贴等生物化学过程已被证明能够执行算术和逻辑运算的事实，导致了DNA计算领域的发展。我研究的主要目标是分析这种在DNA链上存储和操作数据的新方法，因为生物信息和生物计算在几个方面与电子对应物有着根本的不同。最重要的是，DNA编码的信息与记忆位置无关，而是由无限小的自由浮动的DNA链组成，由于它们的沃森-克里克互补性，它们相互作用。 该提案旨在通过定义和研究基于DNA的信息和生物操作的形式语言理论模型，考虑到其生物基质的内在特征，为“生物信息和生物计算理论”奠定基础。除了扩展信息和计算的传统概念以解释自然界中发生的计算之外，这项研究的结果还可以提供对生物分子信息的计算特性的见解，因此对它们的实际应用具有潜在的影响，例如，用于医疗诊断的多输入RNA逻辑电路，或用于纳米电子和纳米光学器件的DNA纳米结构。 所提出的研究的另一个方面是通过研究具有DNA瓦片的计算自组装系统的模型的能力和局限性来探索通过自组装的纳米计算的范例。这项研究的结果可能对生物纳米技术的DNA结构的设计，评估和分析具有潜在的影响。