<br>通过单链 DNA 成分十字带的生长和断裂实现无酶指数扩增,Journal of the American Chemical Society

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通过单链 DNA 成分十字带的生长和断裂实现无酶指数扩增
Journal of the American Chemical Society ( IF 14.4 ) Pub Date : 2023-12-22 , DOI: 10.1021/jacs.3c08205
Anastasia Ershova _{1,

2,

3} , Dionis Minev _{1,

2,

3} , F Eduardo Corea-Dilbert ₁ , Devon Yu ₁ , Jie Deng _{1,

2,

3} , Walter Fontana ₄ , William M Shih _{1,

2,

3}

Affiliation

基于DNA的单体自组装成高阶结构具有实现各种仿生行为的巨大潜力，包括算法组装、超灵敏检测和自我复制。对于这些行为，需要对不期望的假成核实现高能量势垒，其中可以通过种子引发的组装绕过这些势垒。联合邻居捕获是一种能够构建此类屏障的机制，同时允许算法行为，例如位复制。因此，聚合与分裂的循环可用于实现自我复制材料的指数增长。此前，我们演示了十字交叉聚合，这是一种通过联合邻居捕获实现单链 DNA 和 DNA 折纸单体的强大的种子依赖性自组装的策略。在这里，我们扩展了十字交叉组装，通过立足点介导的链位移同时生长和断裂，实现带的自主等温指数扩增。我们演示了如何通过耦合单链和双链核酸靶标将这种十字链反应（3CR）用作检测策略，并引入基于规则的随机建模方法来模拟分子自组装行为，例如十字链反应丝带断裂。

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Enzyme-Free Exponential Amplification via Growth and Scission of Crisscross Ribbons from Single-Stranded DNA Components

The self-assembly of DNA-based monomers into higher-order structures has significant potential for realizing various biomimetic behaviors including algorithmic assembly, ultrasensitive detection, and self-replication. For these behaviors, it is desirable to implement high energetic barriers to undesired spurious nucleation, where such barriers can be bypassed via seed-initiated assembly. Joint-neighbor capture is a mechanism enabling the construction of such barriers while allowing for algorithmic behaviors, such as bit-copying. Cycles of polymerization with division could accordingly be used for implementing exponential growth in self-replicating materials. Previously, we demonstrated crisscross polymerization, a strategy that attains robust seed-dependent self-assembly of single-stranded DNA and DNA-origami monomers via joint-neighbor capture. Here, we expand the crisscross assembly to achieve autonomous, isothermal exponential amplification of ribbons through their concurrent growth and scission via toehold-mediated strand displacement. We demonstrate how this crisscross chain reaction, or 3CR, can be used as a detection strategy through coupling to single- and double-stranded nucleic acid targets and introduce a rule-based stochastic modeling approach for simulating molecular self-assembly behaviors such as crisscross-ribbon scission.

更新日期：2023-12-22

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