Steric Communication between Dynamic Components on DNA Nanodevices,ACS Nano

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Steric Communication between Dynamic Components on DNA Nanodevices
ACS Nano ( IF 15.8 ) Pub Date : 2023-04-18 , DOI: 10.1021/acsnano.2c12455
Yuchen Wang ₁ , Sebastian Sensale _{2,

3} , Miguel Pedrozo ₁ , Chao-Min Huang _{1,

2} , Michael G Poirier _{4,

5,

6} , Gaurav Arya ₂ , Carlos E Castro _{1,

5}

Affiliation

Biomolecular nanotechnology has helped emulate basic robotic capabilities such as defined motion, sensing, and actuation in synthetic nanoscale systems. DNA origami is an attractive approach for nanorobotics, as it enables creation of devices with complex geometry, programmed motion, rapid actuation, force application, and various kinds of sensing modalities. Advanced robotic functions like feedback control, autonomy, or programmed routines also require the ability to transmit signals among subcomponents. Prior work in DNA nanotechnology has established approaches for signal transmission, for example through diffusing strands or structurally coupled motions. However, soluble communication is often slow and structural coupling of motions can limit the function of individual components, for example to respond to the environment. Here, we introduce an approach inspired by protein allostery to transmit signals between two distal dynamic components through steric interactions. These components undergo separate thermal fluctuations where certain conformations of one arm will sterically occlude conformations of the distal arm. We implement this approach in a DNA origami device consisting of two stiff arms each connected to a base platform via a flexible hinge joint. We demonstrate the ability for one arm to sterically regulate both the range of motion and the conformational state (latched or freely fluctuating) of the distal arm, results that are quantitatively captured by mesoscopic simulations using experimentally informed energy landscapes for hinge-angle fluctuations. We further demonstrate the ability to modulate signal transmission by mechanically tuning the range of thermal fluctuations and controlling the conformational states of the arms. Our results establish a communication mechanism well-suited to transmit signals between thermally fluctuating dynamic components and provide a path to transmitting signals where the input is a dynamic response to parameters like force or solution conditions.

中文翻译：

DNA 纳米器件上动态组件之间的空间通信

生物分子纳米技术帮助模拟了基本的机器人功能，例如合成纳米级系统中的定义运动、传感和驱动。DNA 折纸是纳米机器人的一种有吸引力的方法，因为它可以创建具有复杂几何形状、程序化运动、快速驱动、力应用和各种传感模式的设备。反馈控制、自治或程序化例程等高级机器人功能也需要在子组件之间传输信号的能力。DNA 纳米技术的先前工作已经建立了信号传输的方法，例如通过扩散链或结构耦合运动。然而，可溶性交流通常很慢，运动的结构耦合会限制单个组件的功能，例如对环境的响应。这里，我们介绍了一种受蛋白质变构启发的方法，通过空间相互作用在两个远端动态组件之间传输信号。这些组件经历单独的热波动，其中一个臂的某些构象将在空间上阻塞远端臂的构象。我们在 DNA 折纸设备中实施了这种方法，该设备由两个刚性臂组成，每个刚性臂通过一个灵活的铰链接头连接到一个基础平台。我们展示了一只手臂空间调节远端手臂的运动范围和构象状态（锁定或自由波动）的能力，这些结果是通过使用实验信息的能量景观的铰链角度波动的介观模拟定量捕获的结果。我们进一步展示了通过机械调整热波动范围和控制臂的构象状态来调制信号传输的能力。我们的结果建立了一种非常适合在热波动动态组件之间传输信号的通信机制，并提供了一种传输信号的路径，其中输入是对力或溶液条件等参数的动态响应。

更新日期：2023-04-18

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