Versatile DNA Origami Nanostructures in Simplified and Modular Designing Framework

Abstract

We introduce a simplified and modular architecture for design and construction of complex origami nanostructures. A series of basic two-dimensional and three-dimensional structures are presented. As the resulting structures can be virtually divided into blocks, modular remodeling such as translocation, contraction/extension, and bending is carried out. Structures under such a designing framework are morphable. Local conformational changes can propagate to the entire structure to reshape the global conformation.

Polymorphic design of DNA origami structures through mechanical control of modular components

“…Therefore, modular design approaches, successfully employed in small-sized tiles or brick-based origami 25 , 26 , have not yet been widely introduced in scaffolded DNA origami despite its usefulness for programming a wide range of variations in the bent shape and mechanical stiffness of the structure. A modular design method using two-dimensional repeating scaffold pathway to create two- and three-dimensional structures was only recently reported 27 , though it excludes conventional lattice-packing designs 5 and has limited ability to control mechanical stiffness of the module. Such limitation puts a significant burden in terms of cost and time in the laboratory-scale synthesis, design modification and optimization of various DNA origami structures, acting as a major obstacle to their widespread use in many related research fields.…”

Allostery of DNA nanostructures controlled by enzymatic modifications

“…When DNA polymerase-based elongation was applied to fill the void allosteric sites, the local conformational preference cascaded from the vertical boundary junctions to the entire origami structure, resulting in an allosteric transition from a fat rectangle (10 B × 25 H ) to a thin rectangle (10 H × 25 B ), which was measured at 37 ± 4 nm × 222 ± 11 nm ( N = 30) under AFM (Figure 1A and B , right; details in Supplementary Figures S2 and S4 ). Besides the two typical rectangular configurations, a broom-like configuration was presented as an intermediate allosteric state, which was also identifiable under AFM ( 14 , 15 ). Before polymerase treatment, the distribution of three allosteric states (fat rectangle, broom and thin rectangle) was 92%, 6% and 2%, and after DNA polymerase treatment at 37°C for 5 h, the distribution became 1%, 26% and 73%, respectively (Figure 1C ; Supplementary Figures S4 and S5 ).…”

“…We have already shown in an earlier study that the controllable allosteric transitions by hybridizing effector staples are reversible ( 15 ). The exclusion of effector staples can turn allosteric transition back to the original state.…”

“…As a case study, a DNA nanostructure adapted from an earlier work was used ( 15 ). Folded without allosteric effector staples, the origami structure took a fat rectangle configuration (10 B × 25 H containing 10 blocks with 25 parallel helices in each block), which was measured at 76 ± 7 nm × 92 ± 8 nm ( N = 30) under AFM (Figure 1A and B , left; details in Supplementary Figures S1 and S2 ).…”

“…According to several recent studies, allostery can be designed in synthetic DNA systems ( 12–16 ). Especially, the inclusion or exclusion of effector strands at allosteric sites leads to a controllable allostery for DNA nanostructures ( 14 , 15 ).…”