Idili Andrea, Ricci Francesco, Vallée-Bélisle Alexis
Chemistry Department, University of Rome Tor Vergata, Rome 00133, Italy.
Laboratory of Biosensors and Nanomachines, Département de Chimie, Université de Montréal, Montreal, Québec H3T-1J4, Canada.
Nucleic Acids Res. 2017 Jul 27;45(13):7571-7580. doi: 10.1093/nar/gkx498.
DNA nanotechnology takes advantage of the predictability of DNA interactions to build complex DNA-based functional nanoscale structures. However, when DNA functional and responsive units that are based on non-canonical DNA interactions are employed it becomes quite challenging to predict, understand and control their thermodynamics. In response to this limitation, here we demonstrate the use of isothermal urea titration experiments to estimate the free energy involved in a set of DNA-based systems ranging from unimolecular DNA-based nanoswitches to more complex DNA folds (e.g. aptamers) and nanodevices. We propose here a set of fitting equations that allow to analyze the urea titration curves of these DNA responsive units based on Watson-Crick and non-canonical interactions (stem-loop, G-quadruplex, triplex structures) and to correctly estimate their relative folding and binding free energy values under different experimental conditions. The results described herein will pave the way toward the use of urea titration experiments in the field of DNA nanotechnology to achieve easier and more reliable thermodynamic characterization of DNA-based functional responsive units. More generally, our results will be of general utility to characterize other complex supramolecular systems based on different biopolymers.
DNA纳米技术利用DNA相互作用的可预测性来构建基于DNA的复杂功能性纳米级结构。然而，当采用基于非经典DNA相互作用的DNA功能和响应单元时，预测、理解和控制其热力学变得极具挑战性。针对这一局限性，我们在此展示了使用等温尿素滴定实验来估算一系列基于DNA的系统中涉及的自由能，这些系统涵盖了从单分子DNA纳米开关到更复杂的DNA折叠结构（如适体）和纳米器件。我们在此提出了一组拟合方程，可用于分析这些基于DNA的响应单元的尿素滴定曲线，这些响应单元基于沃森-克里克相互作用和非经典相互作用（茎环结构、G-四链体、三链结构），并能在不同实验条件下正确估算其相对折叠和结合自由能值。本文所述结果将为在DNA纳米技术领域使用尿素滴定实验铺平道路，以实现对基于DNA的功能性响应单元更简便、更可靠的热力学表征。更一般地说，我们的结果对于表征基于不同生物聚合物的其他复杂超分子系统具有普遍适用性。
