Structure-based molecular regulations have been widely adopted to modulate protein networks in cells and recently developed to control allosteric DNA operations in vitro. However, current examples of programmable allosteric signal transmission through integrated DNA networks are stringently constrained by specific design requirements. Developing a new, more general, and programmable scheme for establishing allosteric DNA networks remains challenging. Here, we developed a general strategy for programmable allosteric DNA regulations that can be finely tuned by varying the dimensions, positions, and number of conformational signals. By programming the allosteric signals, we realized fan-out/fan-in DNA gates and multiple-layer DNA cascading networks, as well as expanding the approach to long-range allosteric signal transmission through tunable DNA origami nanomachines ~100 nm in size. This strategy will enable programmable and complex allosteric DNA networks and nanodevices for nanoengineering, chemical, and biomedical applications displaying sense-compute-actuate molecular functionalities.
The precursors of functional biomolecules in living cells are synthesized in a bottom‐up manner and subsequently activated by modification into a delicate structure with near‐atomic precision. DNA origami technology provides a promising way to mimic the synthesis of precursors, although mimicking the modification process is a challenge. Herein, a DNA paper‐cutting (DNA kirigami) method to trim origami into designer nanostructures is proposed, where the modification is implemented by a polymerase‐triggered DNA strand displacement reaction. Six geometric shapes are created by cutting rectangular DNA origami. Gel electrophoresis and atomic force microscopy results demonstrate the feasibility and capability of the DNA paper‐cutting method. The proposed DNA paper‐cutting strategy can enrich the toolbox for dynamically transforming DNA origami and has potential applications in biomimetics.
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.
Regulation of self-assembly is crucial in constructing structural biomaterials, such as tunable DNA nanostructures. Traditional tuning of self-assembled DNA nanostructures was mainly conducted by introducing external stimuli after the assembly process. Here, we explored the allosteric assembly of DNA structures via introducing external stimuli during the assembly process to produce structurally heterogeneous polymerization products. We demonstrated that ethidium bromide (EB), a DNA intercalator, could increase the left-handed out-of-plane chirality of curved DNA structures. Then, EB and double strands were introduced as competing stimuli to transform monomers into allosteric conformations, leading to three different polymerization products. The steric trap between different polymerization products promoted the polymerized structures to keep their geometric properties, like chirality, under varying intensity of external stimuli. Our strategy harnesses allosteric effects for assembly of DNA-based materials and is expected to expand the design space for advanced control in synthetic materials.
Owing to their capacity for accurate structural control and complex programmability, DNA molecules have been extensively studied in relation to the construction of nanodevices. However, the existing logic gate sections based on DNA self-assembly were independent of each other, which hampered the development of large-scale integrated DNA circuits. Herein, we have explored a logic operation device with excellent scalability based on assembling and selectively releasing AuNPs on DNA origami, and have performed YES gate, OR gate, AND gate, and three-input composite gate. In the experiment, the logic operation result is detected by gel analysis and TEM image. The resolution of the output signals was greatly improved by determining the releasing of AuNPs from two-layer honeycomb origami. Our study provides a promising approach for building more complex large-scale DNA logic circuits.
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