Reconfigurable pH-Responsive DNA Origami Lattices

Abstract

DNA nanotechnology enables straightforward fabrication of user-defined and nanometer-precise templates for a cornucopia of different uses. To date, most of these DNA assemblies have been static, but dynamic structures are increasingly coming into view. The programmability of DNA not only allows for encoding of the DNA object shape but also it may be equally used in defining the mechanism of action and the type of stimuli-responsiveness of the dynamic structures. However, these “robotic” features of DNA nanostructures are usually demonstrated for only small, discrete, and device-like objects rather than for collectively behaving higher-order systems. Here, we show how a large-scale, two-dimensional (2D) and pH-responsive DNA origami-based lattice can be assembled into two different configurations (“open” and “closed” states) on a mica substrate and further switched from one to the other distinct state upon a pH change of the surrounding solution. The control over these two configurations is achieved by equipping the arms of the lattice-forming DNA origami units with “pH-latches” that form Hoogsteen-type triplexes at low pH. In short, we demonstrate how the electrostatic control over the adhesion and mobility of the DNA origami units on the surface can be used both in the large lattice formation (with the help of directed polymerization) and in the conformational switching of the whole lattice. To further emphasize the feasibility of the method, we also demonstrate the formation of pH-responsive 2D gold nanoparticle lattices. We believe this work can bridge the nanometer-precise DNA origami templates and higher-order large-scale systems with the stimuli-induced dynamicity.

The motive forces in DNA-enabled nanomachinery

“…Such origami unit can be further assembled into one-dimensional and two-dimensional lattices which still possess pH responsiveness. 25 Moreover, several groups recently 26 , 27 have explored using triplex formation to fold duplex scaffold into defined nanostructures. In comparison to standard Watson-Crick-mediated duplex origami, triplex origami is based on Hoogsteen binding to align neighboring duplex.…”

Divergent Polymer Superstructures from Protonated Poly(adenine) DNA and RNA

“…pH-responsive nucleic acid sequences are found throughout natural DNA structuresthe i -motif may bind proteins during transcription, and triplex DNA regulates nucleic acid metabolism and gene function . The predictability and sensitivity of these structures have underscored their use in dynamic nanotechnology applications, − for example, in molecular machinery, − synthetic biology, , switchable structures, − and plasmonic DNA devices . In contrast, the use of the A-motif (self-associated adenines that are protonated at the N7 position) has lagged, potentially due to the low pH at which it is activated for assembly as well as the limited/contradictory knowledge of its scope and applicability. − Recently, we demonstrated the use of this protonated adenine motif in the reversible fibrillization of DNA origami .…”

Modulating Lipid Membrane Morphology by Dynamic DNA Origami Networks

“…More specifically, the DOCs can be polymerized into reconfigurable 1D filament-like chains or 2D lattices by DNA hybridization. 20,21 The reconfiguration of the microscale DNA architectures is driven by strand displacement reactions. 22−24 1a), we show that their polymerization can result in membrane deformation to different extents depending on the degree of polymerization of the DOC networks.…”

“…In this work, we demonstrate a membrane-bound DNA origami cross (DOC) chiral structure that is capable of both polymerization and reconfiguration to engineer the membrane morphology of giant unilamellar vesicles (GUVs). More specifically, the DOCs can be polymerized into reconfigurable 1D filament-like chains or 2D lattices by DNA hybridization. , The reconfiguration of the microscale DNA architectures is driven by strand displacement reactions. − After anchoring the DOCs onto GUVs (Figure a), we show that their polymerization can result in membrane deformation to different extents depending on the degree of polymerization of the DOC networks.…”