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Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges.

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Title: Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges.
Authors: Lolaico M; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden., Blokhuizen S; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden., Shen B; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.; Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University School of Chemical Engineering, P.O. Box 16100, 00076 Aalto, Finland., Wang Y; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden., Högberg B; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.
Source: ACS nano [ACS Nano] 2023 Apr 11; Vol. 17 (7), pp. 6565-6574. Date of Electronic Publication: 2023 Mar 23.
Publication Type: Journal Article; Research Support, Non-U.S. Gov't
Language: English
Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101313589 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1936-086X (Electronic) Linking ISSN: 19360851 NLM ISO Abbreviation: ACS Nano Subsets: MEDLINE
Imprint Name(s): Original Publication: Washington D.C. : American Chemical Society
MeSH Terms: Nanotechnology*/methods , Nanostructures*/chemistry, Nucleic Acid Conformation ; DNA/chemistry ; Computer-Aided Design
Abstract: In recent years, interest in wireframe DNA origami has increased, with different designs, software, and applications emerging at a fast pace. It is now possible to design a wide variety of shapes by starting with a 2D or 3D mesh and using different scaffold routing strategies. The design choices of the edges in wireframe structures can be important in some applications and have already been shown to influence the interactions between nanostructures and cells. In this work, we increase the alternatives for the design of A-trail routed wireframe DNA structures by using four-helix bundles (4HB). Our approach is based on the incorporation of additional helices to the edges of the wireframe structure to create a 4HB on a square lattice. We first developed the software for the design of these structures, followed by a demonstration of the successful design and folding of a library of structures, and then, finally, we investigated the higher mechanical rigidity of the reinforced structures. In addition, the routing of the scaffold allows us to easily incorporate these reinforced edges together with more flexible, single helix edges, thereby allowing the user to customize the desired stiffness of the structure. We demonstrated the successful folding of this type of hybrid structure and the different stiffnesses of the different parts of the nanostructures using a combination of computational and experimental techniques.
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Contributed Indexing: Keywords: DNA nanotechnology; coarse-grained molecular dynamics; four-helix bundle; scaffolded DNA origami; wireframe origami
Substance Nomenclature: 9007-49-2 (DNA)
Entry Date(s): Date Created: 20230323 Date Completed: 20230412 Latest Revision: 20230417
Update Code: 20230417
PubMed Central ID: PMC10100577
DOI: 10.1021/acsnano.2c11982
PMID: 36951760
Database: MEDLINE
Description
ISSN:1936-086X
DOI:10.1021/acsnano.2c11982