Hairygami：可功能化悬突驱动的DNA纳米结构构象变化分析
Hairygami: Analysis of DNA Nanostructures' Conformational Change Driven by Functionalizable Overhangs
AI总结：
本研究针对DNA origami结构成像无法捕捉完整构象、易引发客体分子虚假相互作用的问题，通过模拟与实验发现功能化单链悬突会熵驱动二维DNA origami片产生曲率，还开源了相关增强采样模拟代码。
摘要：
DNA origami（DNA折纸术）是一种通过设计DNA链自组装构建纳米结构的常用方法。这类结构常被用作“钉板”，用于模板化组装蛋白质、金纳米颗粒、适体及其他分子，应用范围涵盖治疗、诊断、等离子体光子学与光子学等领域。\n 利用原子力显微镜（AFM）或透射电子显微镜（TEM）对这些结构成像无法捕捉其完整构象系综，因为这类成像仅能显示它们平铺在表面的形状。然而，纳米结构的某些构象可能会将客体分子定位到设计预期之外的距离，进而导致本应分离的客体分子之间产生虚假相互作用。本研究采用分子动力学模拟捕捉二维DNA origami片的构象系综，发现引入通常用于将客体分子功能化到折纸结构上的单链悬突，会在本体中诱导片层结构产生曲率。研究表明这种形状变形源于熵效应，这对设计稳定的DNA origami面包板具有重要意义，同时也提供了一种通过引入悬突调控结构形状的潜在方法。我们随后通过实验验证，在二价盐和一价盐缓冲液条件下，DNA悬突均会使DNA origami片产生曲率。我们还通过实验进一步验证，连接了蛋白质的功能化DNA origami也会出现这种诱导曲率。我们将开发的、采用增强采样技术表征DNA origami构象空间的模拟代码作为开源软件发布。
英文摘要：
DNA origami is a widely used method to construct nanostructures by self-assembling designed DNA strands. These structures are often used as "pegboards" for templated assembly of proteins, gold nanoparticles, aptamers, and other molecules, with applications ranging from therapeutics and diagnostics to plasmonics and photonics. Imaging these structures using AFM or TEM does not capture their full conformation ensemble as they only show their shape flattened on a surface. However, certain conformations of the nanostructure can position guest molecules into distances unaccounted for in their intended design, thus leading to spurious interactions between guest molecules that are designed to be separated. Here, we use molecular dynamics simulations to capture conformational ensemble of 2D DNA origami tiles and show that introducing single-stranded overhangs, which are typically used for functionalization of the origami with guest molecules, induces a curvature of the tile structure in the bulk. We show that the shape deformation is of entropic origin, with implications for design of robust DNA origami breadboards as well as potential approach to modulate structure shape by introducing overhangs. We then verify experimentally that the DNA overhangs introduce curvature into the DNA origami tiles in divalent as well as monovalent salt buffer conditions. We further experimentally verify that DNA origami functionalized with attached proteins also experience such induced curvature. We provide the developed simulation code implementing the enhanced sampling to characterize conformational space of DNA origami as open source software.
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