Conformational Control of DNA Origami by DNA Oligomers, Intercalators and UV Light

Abstract

DNA origami has garnered great attention due to its excellent programmability and precision. It offers a powerful means to create complex nanostructures which may not be possible by other methods. The macromolecular structures may be used as static templates for arranging proteins and other molecules. They are also capable of undergoing structural transformation in response to external signals, which may be exploited for sensing and actuation at the nanoscale. Such on-demand reconfigurations are executed mostly by DNA oligomers through base-pairing and/or strand displacement, demonstrating drastic shape changes between two different states, for example, open and close. Recent studies have developed new mechanisms to modulate the origami conformation in a controllable, progressive manner. Here we present several methods for conformational control of DNA origami nanostructures including chemical adducts and UV light as well as widely applied DNA oligomers. The detailed methods should be useful for beginners in the field of DNA nanotechnology.

Controlling Chiroptical Responses via Chemo-Mechanical Deformation of DNA Origami Structures

“…The achiral zigzag form was observed around the helical pitch of 10.9 bp per turn, and the RH helical form appeared at the helical pitch of approximately 11.4 bp per turn. These results indicated that various chiral properties of AuNP arrangements would be possible by adding intercalators to change the effective helical pitch of dsDNA. , …”

“…DNA intercalators change the equilibrium configuration of dsDNA when bound. For example, ethidium bromide (EtBr) is known to unwind unconstrained dsDNA so that its helical pitch increases from 10.5 base pairs (bp) per turn for B-form DNA. , These chemicals may induce mechanical stresses into structured DNA assemblies because DNA helices on them are cross-linked and constrained by Holliday junctions (crossovers), thereby deforming the structure into bent and/or twisted shapes. , …”

“…These results indicated that various chiral properties of AuNP arrangements would be possible by adding intercalators to change the effective helical pitch of dsDNA. 35,36 For experimental verification, AuNPs of 5 nm diameters were attached to five binding sites on 6HB. The yield of attaching five AuNPs to the 6HB was roughly ∼80% when we counted the number of AuNPs from the atomic force microscopy (AFM) images (Figure S3).…”

Salt-induced conformational switching of a flat rectangular DNA origami structure

“…10,11 Mechanical flexibility can also be designed by creating flexible elements such as joints, [12][13][14][15] hinges, 16 catenanes/interlocked systems, 17 and could be transiently adapted using tools of dynamic DNA nanotechnology such as strand displacement reactions. 18 Generally, the dynamic flexibility of DNA origami structures is difficult to access as structural tools usually yield average values and dynamic, little invasive tools are required including optical 10,[12][13][14][15] and mechanical singlemolecule methods [19][20][21] as well as computational tools such as molecular dynamics simulations. 22 The rectangular DNA origami structure of the original Rothemund publication 1 and its torsion-reduced variants such as the so-called new rectangular origami (NRO) 23 have emerged as model systems to interrogate the stiffness and dynamics of a 2D nucleic acid structure.…”

“…10,11 Mechanical flexibility can also be designed by creating flexible elements such as joints, 12–15 hinges, 16 catenanes/interlocked systems, 17 and could be transiently adapted using tools of dynamic DNA nanotechnology such as strand displacement reactions. 18 Generally, the dynamic flexibility of DNA origami structures is difficult to access as structural tools usually yield average values and dynamic, little invasive tools are required including optical 10,12–15 and mechanical single-molecule methods 19–21 as well as computational tools such as molecular dynamics simulations. 22…”