Lattice-free prediction of three-dimensional structure of programmed DNA assemblies

Abstract

DNA can be programmed to self-assemble into high molecular weight 3D assemblies with precise nanometer-scale structural features. Although numerous sequence design strategies exist to realize these assemblies in solution, there is currently no computational framework to predict their 3D structures on the basis of programmed underlying multi-way junction topologies constrained by DNA duplexes. Here, we introduce such an approach and apply it to assemblies designed using the canonical immobile four-way junction. The procedure is used to predict the 3D structure of high molecular weight planar and spherical ring-like origami objects, a tile-based sheet-like ribbon, and a 3D crystalline tensegrity motif, in quantitative agreement with experiments. Our framework provides a new approach to predict programmed nucleic acid 3D structure on the basis of prescribed secondary structure motifs, with possible application to the design of such assemblies for use in biomolecular and materials science.

A multifunctional DNA origami as carrier of metal complexes to achieve enhanced tumoral delivery and nullified systemic toxicity

“…Researchers have developed the technique of tile and origami-based DNA hybridization to fabricate nanoscale projects with desired size and shapes, such as capital letters [10], dolphin [11], Chinese characters and 3 dimensional (3D) shapes including crystal lattices [12], spheres and screws [13]. With the development of DNA technology, DNA origami is considered as prospective candidate for drug delivery because it has unique advantages including (1) predictable and well-defined structure [14], (2) high efficacy of drug loading [15], (3) chemically modifiable for drug design [16], (4) stability in physiological M A N U S C R I P T A C C E P T E D ACCEPTED MANUSCRIPT 5 conditions [17] and (5) superior biocompatibility [18].…”

DNA Nanostructures as Smart Drug-Delivery Vehicles and Molecular Devices

“…Very recently, techniques for modular scaffold-free fabrication [13,14], 3D meshing and wireframe-based approaches [15][16][17], as well as shape-complementarity-based construction [18] of DNA objects have been introduced. In addition, powerful computational tools for designing and analyzing DNA nanostructures have been developed [19][20][21], which appreciably help researchers to create their own DNA nanoarchitectures for any conceivable application. Table 1 lists and 2 describes the novel design strategies that can be used for fabricating diverse DNA origami nanostructures and other complex DNA-based shapes for various nanotechnological purposes.…”

Automated design of DNA origami

“…For example, researchers routinely use the design software caDNAno and the finite-element-based simulation software CanDo for prototyping and predicting the shape of multilayer DNA structures in honeycomb and square lattice geometries 5 . In addition, computational frameworks for making lattice-free DNA structures are available 6 .…”

“…After designing the shape and obtaining the sequences, researchers fabricate the structures using standard annealing routines. The DAEDALUS software (http://daedalus-dna-origami.org/) not only generates a list of staple strands but also produces atomistic models of the designed structures, whereas the CanDo software (http://cando-dnaorigami.org/) 5,6 can be used to simulate shapes of the objects in aqueous solution.…”