Tuning curved DNA origami structures through mechanical design and chemical adducts

Abstract

The bending and twisting of DNA origami structures are important features for controlling the physical properties of DNA nanodevices. It has not been fully explored yet how to finely tune the bending and twisting of curved DNA structures. Traditional tuning of the curved DNA structures was limited to controlling the in-plane-bending angle through varying the numbers of base pairs of deletions and insertions. Here, we developed two tuning strategies of curved DNA origami structures from in silico and in vitro aspects. In silico, the out-of-plane bending and twisting angles of curved structures were introduced, and were tuned through varying the patterns of base pair deletions and insertions. In vitro, a chemical adduct (ethidium bromide) was applied to dynamically tune a curved spiral. The 3D structural conformations, like chirality, of the curved DNA structures were finely tuned through these two strategies. The simulation and TEM results demonstrated that the patterns of base pair insertions and deletions and chemical adducts could effectively tune the bending and twisting of curved DNA origami structures. These strategies expand the programmable accuracy of curved DNA origami structures and have potential in building efficient dynamic functional nanodevices.

Regulating the Polymerization of DNA Structures via Allosteric Control of Monomers

“…EB could bind to DNA double strands, unwinding, lengthening, and stiffening the strands. − It has been demonstrated that EB could increase the left-handed twist in straight DNA bundles. , However, curved DNA structures were designed through applying deletions and insertions in different helices, causing nonuniform local twist and tension, which could influence the binding affinity of intercalators, , complicating the interaction between intercalators with curved DNA structures. We recently observed increasing helical density and decreasing diameter of a polymerized left-handed DNA spiral induced by EB, but the concrete conformation change of curved monomers induced by EB was not explored.…”

“…Different from static assembly of DNA tiles, we utilized the allosteric conformational properties of curved DNA structures induced by EB during the polymerization process to derive allosteric products. We adopted a right-handed monomer structure composed of consecutive curved subunits (colored in yellow, red, blue, and green; Figure a, Figures S3 and S10), which was roughly symmetric to the left-handed structure in refs − . The latter subunit was rotated 30° relative to the former neighboring subunit to form a right-handed shape.…”

Mechanics of Dynamic and Deformable DNA Nanostructures

“…Adjusting the jack edges allows one to change the force distribution in the structures and design conformation patterns with several stages. [93][94][95][96][97][98][99] Another strategy is using chemical adducts to modulate the helicity in DNA-DNA associations, 35 thereby changing the force states and deforming the structures progressively. Deformation of DNA nanostructures may also be induced by external loadings.…”

“…Another study also demonstrated that adding chemical adducts can tune curved structures. 35 Several Cshaped monomers were put together forming a 10-bundle-crosssection left-handed spiral structure. Since dsDNA has right-handed twisting and EtBr can weaken the right-handed twist, the structure would have more left-handed twisting/curvature with the addition of EtBr.…”

“…More precise progressive control may be realized by intercalators and other chemical adducts. [35][36][37][38][39][40][41] This method usually applies on dsDNA helices, thus the structures formed by several closely packed dsDNA helices will be reconfigured or deformed in response to the adducts. There are also other DNA structures which deform due to external loading.…”