Aptamer-Integrated Scaffolds for Biologically Functional DNA Origami Structures

Abstract

The manufacture of DNA origami nanostructures with highly ordered functional motifs is of great significance for biomedical applications. Here, we present a robust strategy to produce customized scaffolds with integrated aptamer sequences, which enables direct construction of functional DNA origami structures. As we demonstrated, aptamers of various numbers and types were efficiently and stably integrated in userdefined positions of the scaffolds. Specifically, two different thrombin aptamer sequences were simultaneously inserted into the M13mp18 phage genome. The assembled functional DNA origami structures from this aptamer-integrated scaffold exhibited increased binding efficiency to thrombin and displayed more than 10-fold stronger resistance to exonuclease degradation than that produced using the traditional staple extension method. Additionally, a scaffold integrated with the platelet-derived growth factor aptamer was produced, and the assembled DNA origami structures showed significant inhibitory effect on breast cancer cells MDA-MB-231. This scalable method of creating design-specific scaffolds opens up a new way to construct more stable and functionally robust DNA origami structures and thus provides an important basis for their broader applications.

Versatile Computer Aided Design of Freeform DNA Nanostructures and Assemblies

“…Furthermore, a semi-automatic software allows the user to examine the design status at several stages, modify details from default settings, and seamlessly move forward and backward through the design steps, all of which is facilitated by rapid feedback in GUIs to visualize results of design choices. Furthermore, the new design paradigm introduced here can fully leverage the growing library of scaffold sources (40)(41)(42)(43), removing restrictions in spatial dimensions and allowing users to realize even more diverse structures. For example, we used the multi-scaffold feature of MagicDNA to achieve large structures, such as the "FNANO" script (Fig.…”

Controllable protein network based on DNA‐origami and biomedical applications

“…[87][88][89] Through varying covalent bonding methods, shape and size, DNA-protein reactions and nucleic acid pairing, there is an interaction between DNA nanostructures and various functional molecules which help established its foundation in cellular drug delivery. 90 For example, Chen et al 91 successfully constructed some DNA scaffolds that binding to PDGF inducers and investigating their suppressor effect on MDA-MB-231 in the breast cancer cells. The result showed DNA origami product designated a strong inhibitory effect, and further inspired people with a new thought of building more stable and functional DNA origami structures.…”

Customized Scaffolds for Direct Assembly of Functionalized DNA Origami

“…34−36 Recently, a study by Chen et al used bacteriophage genome modifications to introduce multiple aptamers at specific locations on folded structures. 37 Although this method can generate a large amount of scaffold (greater than milligram quantity) and is highly efficient for the introduction of aptamers via sequence modification, bacteriophage production of ssDNA does not allow chemical functionalization and still requires the use of modified oligonucleotides to further functionalize the folded DNA-NPs. 37−39 As an alternative, polymerase chain reaction (PCR)-based strategies, particularly the asymmetric PCR (aPCR) method, offer a higher flexibility in sequence design and sequence length and can be used for direct incorporation of functional groups into the scaffold during synthesis.…”

“…In recent years, only a few studies have demonstrated the production of functional DNA origami scaffolds, but these approaches are mainly focused on tuning the size and sequence of scaffolds to overcome the length limitation inherent to commercially available versions of M13mp18. − Recently, a study by Chen et al. used bacteriophage genome modifications to introduce multiple aptamers at specific locations on folded structures . Although this method can generate a large amount of scaffold (greater than milligram quantity) and is highly efficient for the introduction of aptamers via sequence modification, bacteriophage production of ssDNA does not allow chemical functionalization and still requires the use of modified oligonucleotides to further functionalize the folded DNA-NPs. − …”