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Biophysically Inspired Rational Design of Structured Chimeric Substrates for DNAzyme Cascade Engineering

机译:生物物理学启发的DNAzyme级联工程结构嵌合底物的合理设计。

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摘要

The development of large-scale molecular computational networks is a promising approach to implementing logical decision making at the nanoscale, analogous to cellular signaling and regulatory cascades. DNA strands with catalytic activity (DNAzymes) are one means of systematically constructing molecular computation networks with inherent signal amplification. Linking multiple DNAzymes into a computational circuit requires the design of substrate molecules that allow a signal to be passed from one DNAzyme to another through programmed biochemical interactions. In this paper, we chronicle an iterative design process guided by biophysical and kinetic constraints on the desired reaction pathways and use the resulting substrate design to implement heterogeneous DNAzyme signaling cascades. A key aspect of our design process is the use of secondary structure in the substrate molecule to sequester a downstream effector sequence prior to cleavage by an upstream DNAzyme. Our goal was to develop a concrete substrate molecule design to achieve efficient signal propagation with maximal activation and minimal leakage. We have previously employed the resulting design to develop high-performance DNAzyme-based signaling systems with applications in pathogen detection and autonomous theranostics.
机译:大规模分子计算网络的发展是一种有前途的方法,类似于细胞信号传导和调控级联,可在纳米级实现逻辑决策。具有催化活性的DNA链(DNA酶)是系统构建具有固有信号放大作用的分子计算网络的一种方法。将多个DNAzyme连接到一个计算电路中,需要设计底物分子,这些分子允许信号通过编程的生化相互作用从一种DNAzyme传递到另一种DNAzyme。在本文中,我们按预期的反应途径,在生物物理和动力学约束的指导下,编入了迭代的设计过程,并使用所得的底物设计来实现异构DNAzyme信号级联。我们设计过程的一个关键方面是在底物分子中使用二级结构在被上游DNA酶切割之前隔离下游效应子序列。我们的目标是开发一种具体的底物分子设计,以实现具有最大活化度和最小泄漏的有效信号传播。我们以前已经采用了所得的设计来开发高性能的基于DNAzyme的信号系统,并将其应用于病原体检测和自主治疗学。

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