Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability.

Charlotte Kielar,Adrian Keller,Christin Möser,Siqi Zhu,Xiaodan Xu,David M Smith,Yang Xin,Nelli Gorin,Guido Grundmeier

doi:10.3390/molecules24142577

Abstract

DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at −20 °C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability.

Highlights

DNA origami has become a widely employed technique for the rapid high-yield synthesis of arbitrary, yet well-defined, nanoscale shapes [1]
DNA origami nanostructures are currently employed as drug delivery vehicles [4,5,6,7,8], sensors [9,10,11,12], templates for the fabrication of nanoelectronic [13,14,15,16] and plasmonic devices [17,18,19,20,21], substrates for single-molecule studies [22,23,24,25,26,27], and masks in molecular lithography [28,29,30,31,32]
While all these applications crucially rely on an intact DNA origami shape, many of them subject the employed DNA origami nanostructures to rather harsh treatments

Summary

Introduction

DNA origami has become a widely employed technique for the rapid high-yield synthesis of arbitrary, yet well-defined, nanoscale shapes [1]. DNA origami nanostructures are currently employed as drug delivery vehicles [4,5,6,7,8], sensors [9,10,11,12], templates for the fabrication of nanoelectronic [13,14,15,16] and plasmonic devices [17,18,19,20,21], substrates for single-molecule studies [22,23,24,25,26,27], and masks in molecular lithography [28,29,30,31,32]. Molecules 2019, 24, 2577 interest in the effects that environmental and processing conditions exert on DNA origami structural integrity has spiked in the last few years [33,34,35,36,37,38,39,40,41,42,43,44,45].

Methods

Results

Conclusion