Rodriguez Arlin, Gandavadi Dhanush, Mathivanan Johnsi, Song Tingjie, Madhanagopal Bharath Raj, Talbot Hannah, Sheng Jia, Wang Xing, Chandrasekaran Arun Richard
The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
bioRxiv. 2023 May 4:2023.05.04.539416. doi: 10.1101/2023.05.04.539416.
The programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures, and assembly conditions typically require high concentrations of magnesium ions which restricts their applications. In other solution conditions tested for DNA nanostructure assembly, only a limited set of divalent and monovalent ions have been used so far (typically Mg and Na ). Here, we investigate the assembly of DNA nanostructures in a wide variety of ions using nanostructures of different sizes: a double-crossover motif (76 bp), a three-point-star motif (∼134 bp), a DNA tetrahedron (534 bp) and a DNA origami triangle (7221 bp). We show successful assembly of a majority of these structures in Ca , Ba , Na , K and Li and provide quantified assembly yields using gel electrophoresis and visual confirmation of a DNA origami triangle using atomic force microscopy. We further show that structures assembled in monovalent ions (Na , K and Li ) exhibit up to a 10-fold higher nuclease resistance compared to those assembled in divalent ions (Mg , Ca and Ba ). Our work presents new assembly conditions for a wide range of DNA nanostructures with enhanced biostability.
DNA的可编程特性使得定制设计的静态和动态纳米结构得以构建，而组装条件通常需要高浓度的镁离子，这限制了它们的应用。在其他用于DNA纳米结构组装的测试溶液条件中，到目前为止仅使用了有限的一组二价和一价离子（通常是Mg²⁺和Na⁺）。在此，我们使用不同尺寸的纳米结构研究了多种离子中DNA纳米结构的组装：双交叉基序（76个碱基对）、三点星基序（约134个碱基对）、DNA四面体（534个碱基对）和DNA折纸三角形（7221个碱基对）。我们展示了这些结构中的大多数在Ca²⁺、Ba²⁺、Na⁺、K⁺和Li⁺中成功组装，并使用凝胶电泳提供了定量的组装产率，以及使用原子力显微镜对DNA折纸三角形进行了可视化确认。我们进一步表明，与在二价离子（Mg²⁺、Ca²⁺和Ba²⁺）中组装的结构相比，在一价离子（Na⁺、K⁺和Li⁺）中组装的结构表现出高达10倍的更高核酸酶抗性。我们的工作为具有增强生物稳定性的多种DNA纳米结构提供了新的组装条件。
