Biochemical Computing: Experimental and Theoretical Development of Error Correction and Digitalization Concepts

NSF 0726698 ？生化计算：纠错和数字化概念的实验和理论发展[ei: Evgeny Katz， co-PI: Vladimir Privman]摘要本研究旨在发展生化计算中的新概念。生物计算显示出提供更好地将普通电子与生物有机体的信号相结合的机制的希望。在概念层面上，它将进一步理解生物体如何控制极其复杂和耦合的生化反应，即用信息论的语言解释代谢途径。即使是中等复杂性的生物计算系统也将允许在复杂的生理过程和植入式生物医学设备之间进行有效的接口，并将能够在纳米生物机器人和传感系统中运行。近年来，生物计算研究取得了很大进展。然而，为了实用，以及与普通电子兼容，生物计算应该研究最小化/纠正错误和发展“数字化”概念的方法。目前的研究计划接受了这一挑战。基于编码DNA序列、酶和DNAzymes的新系统进行了实验探索、理论建模和优化，这些系统显示出数字生化计算的希望，包括实验实现纠错的第一次尝试。实验方法包括使用编码DNA序列、dnazyme生物催化反应和使用DNA功能化磁性纳米颗粒进行信息处理。使用DNA功能化磁性纳米颗粒的杂交程序纯化无错误DNA序列，通过PCR技术扩增，并用作基于dnazyme的逻辑门的输入信号。演示了数字异或和非与逻辑门、复制（扇出）、利用冗余进行错误校正和信号整流。使用编码DNA序列的电子和光电探针读出结果。

NSF 0726698 ? Biochemical Computing: Experimental and Theoretical Development of Error Correction and Digitalization ConceptsPI: Evgeny Katz, co-PI: Vladimir Privman AbstractThis research is directed towards the developments of new concepts in biochemical computing. Biocomputing shows promise of providing the mechanisms to better couple ordinary electronics with the signaling of biological organisms. On the conceptual level, it will further understanding of how living organisms manage to control extremely complex and coupled biochemical reactions, i.e., interpret metabolic pathways in the language of information theory. Biocomputing systems of even moderate complexity will allow effective interfacing between complex physiological processes and implantable biomedical devices and will be able to operate in nanobiorobotic and sensing systems. Great advances have been made in biocomputing research in recent years. However, to be practical, as well as compatible with ordinary electronics, biocomputing should be researched for ways to minimize/correct errors and develop "digitalization" concepts. This challenge is taken up in the present research program. Experimental exploration as well as theoretical modeling and optimization are performed for new systems based on encoded DNA sequences, enzymes and DNAzymes that show promise for digital biochemical computing, including the first attempt for an experimental realization of error correction. The experimental approach includes information processing using encoded DNA sequences, DNAzyme-biocatalyzed reactions and the use of DNA-functionalized magnetic nanoparticles. The error-free DNA sequences are purified using the hybridization procedure with the DNA-functionalized magnetic nanoparticles, amplified by a PCR technique and used as input signals for DNAzyme-based logic gates. Digital XOR and NAND logic gates, copying (fanout), error correction by utilizing redundancy, and signal rectification, are demonstrated. Electronic and optoelectronic probes of the encoded DNA sequences are used to read out the results.