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Zou J, Stammers AC, Taladriz-Sender A, Withers JM, Christie I, Santana Vega M, Aekbote BL, Peveler WJ, Rusling DA, Burley GA, Clark AW. Fluorous-Directed Assembly of DNA Origami Nanostructures. ACS NANO 2023; 17:752-759. [PMID: 36537902 PMCID: PMC9835977 DOI: 10.1021/acsnano.2c10727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/15/2022] [Indexed: 05/27/2023]
Abstract
An orthogonal, noncovalent approach to direct the assembly of higher-order DNA origami nanostructures is described. By incorporating perfluorinated tags into the edges of DNA origami tiles we control their hierarchical assembly via fluorous-directed recognition. When we combine this approach with Watson-Crick base-pairing we form discrete dimeric constructs in significantly higher yield (8x) than when either molecular recognition method is used in isolation. This integrated "catch-and-latch" approach, which combines the strength and mobility of the fluorous effect with the specificity of base-pairing, provides an additional toolset for DNA nanotechnology, one that enables increased assembly efficiency while requiring significantly fewer DNA sequences. As a result, our integration of fluorous-directed assembly into origami systems represents a cheap, atom-efficient means to produce discrete superstructures.
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Affiliation(s)
- Jiajia Zou
- James
Watt School of Engineering, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
| | - Ashley C. Stammers
- James
Watt School of Engineering, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
| | - Andrea Taladriz-Sender
- Department
of Pure Applied Chemistry, Thomas Graham Building, 295 Cathedral Street, University of Strathclyde, Glasgow G1 1XL, United Kingdom
| | - Jamie M. Withers
- James
Watt School of Engineering, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
| | - Iain Christie
- James
Watt School of Engineering, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
| | - Marina Santana Vega
- James
Watt School of Engineering, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
| | - Badri L. Aekbote
- James
Watt School of Engineering, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
| | - William J. Peveler
- School
of Chemistry, Joseph Black Building, University
of Glasgow, Glasgow G12 8QQ, United
Kingdom
| | - David A. Rusling
- School
of Pharmacy and Biomedical Sciences, St. Michael’s Building, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
| | - Glenn A. Burley
- Department
of Pure Applied Chemistry, Thomas Graham Building, 295 Cathedral Street, University of Strathclyde, Glasgow G1 1XL, United Kingdom
| | - Alasdair W. Clark
- James
Watt School of Engineering, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, United
Kingdom
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Zhang W, Jiang C, Guo X, Muhammad Faran Ashraf Baig M, Ni C, Xiao SJ. 2D DNA lattices assembled from DX-coupled tiles. J Colloid Interface Sci 2022; 616:499-508. [DOI: 10.1016/j.jcis.2022.02.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
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Gravina NM, Gumbart JC, Kim HD. Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding. J Phys Chem B 2021; 125:4016-4024. [PMID: 33870695 DOI: 10.1021/acs.jpcb.1c00432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Annealing between sticky ends of DNA is an intermediate step in ligation. It can also be utilized to program specific binding sites for DNA tile and origami assembly. This reaction is generally understood as a bimolecular reaction dictated by the local concentration of the sticky ends. Its dependence on the relative orientation between the sticky ends, however, is less understood. Here we report on the interactions between DNA sticky ends using the coarse-grained oxDNA model; specifically, we consider how the orientational alignment of the double-stranded DNA (dsDNA) segments affects the time required for the sticky ends to bind, τb. We specify the orientation of the dsDNA segments with three parameters: θ, which measures the angle between the helical axes, and ϕ1 and ϕ2, which measure rotations of each strand around the helical axis. We find that the binding time depends strongly on both θ and ϕ2: ∼20-fold change with θ and 10-fold change with ϕ2. The binding time is the fastest when the helical axes of duplexes are pointing toward each other and the sticky ends protrude from the farthest two points. Our result is relevant for predicting hybridization efficiency of sticky ends that are rotationally restricted.
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Affiliation(s)
- Nicholas M Gravina
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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