Structural DNA Nanotechnology: from Design to Applications

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2012 Jul 28

PMID 22837684

Citations 14

Authors

Reza M Zadegan

Michael L Norton

Affiliations

Soon will be listed here.

Abstract

The exploitation of DNA for the production of nanoscale architectures presents a young yet paradigm breaking approach, which addresses many of the barriers to the self-assembly of small molecules into highly-ordered nanostructures via construct addressability. There are two major methods to construct DNA nanostructures, and in the current review we will discuss the principles and some examples of applications of both the tile-based and DNA origami methods. The tile-based approach is an older method that provides a good tool to construct small and simple structures, usually with multiply repeated domains. In contrast, the origami method, at this time, would appear to be more appropriate for the construction of bigger, more sophisticated and exactly defined structures.

Citing Articles

Applications of Nanotechnology for Spatial Omics: Biological Structures and Functions at Nanoscale Resolution.

Wang R, Hastings W, Saliba J, Bao D, Huang Y, Maity S ACS Nano. 2024; 19(1):73-100.

PMID: 39704725 PMC: 11752498. DOI: 10.1021/acsnano.4c11505.

Review of the Role of Nanotechnology in Overcoming the Challenges Faced in Oral Cancer Diagnosis and Treatment.

Umapathy V, Natarajan P, Swamikannu B Molecules. 2023; 28(14).

PMID: 37513267 PMC: 10385509. DOI: 10.3390/molecules28145395.

Predicting accurate ab initio DNA electron densities with equivariant neural networks.

Lee A, Rackers J, Bricker W Biophys J. 2022; 121(20):3883-3895.

PMID: 36057785 PMC: 9674991. DOI: 10.1016/j.bpj.2022.08.045.

Constructing Large 2D Lattices Out of DNA-Tiles.

Parikka J, Sokolowska K, Markesevic N, Toppari J Molecules. 2021; 26(6).

PMID: 33801952 PMC: 8000633. DOI: 10.3390/molecules26061502.

DNA Transformations for Diagnosis and Therapy.

Ahn S, Liu J, Vellampatti S, Wu Y, Um S Adv Funct Mater. 2021; 31(12):2008279.

PMID: 33613148 PMC: 7883235. DOI: 10.1002/adfm.202008279.

References

Fujibayashi K, Hariadi R, Park S, Winfree E, Murata S . Toward reliable algorithmic self-assembly of DNA tiles: a fixed-width cellular automaton pattern. Nano Lett. 2007; 8(7):1791-7. DOI: 10.1021/nl0722830. View

Andersen E, Dong M, Nielsen M, Jahn K, Lind-Thomsen A, Mamdouh W . DNA origami design of dolphin-shaped structures with flexible tails. ACS Nano. 2009; 2(6):1213-8. DOI: 10.1021/nn800215j. View

Andersen E, Dong M, Nielsen M, Jahn K, Subramani R, Mamdouh W . Self-assembly of a nanoscale DNA box with a controllable lid. Nature. 2009; 459(7243):73-6. DOI: 10.1038/nature07971. View

Castro C, Kilchherr F, Kim D, Lin Shiao E, Wauer T, Wortmann P . A primer to scaffolded DNA origami. Nat Methods. 2011; 8(3):221-9. DOI: 10.1038/nmeth.1570. View

Endo M, Sugiyama H . Chemical approaches to DNA nanotechnology. Chembiochem. 2009; 10(15):2420-43. DOI: 10.1002/cbic.200900286. View

Douglas S, Marblestone A, Teerapittayanon S, Vazquez A, Church G, Shih W . Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 2009; 37(15):5001-6. PMC: 2731887. DOI: 10.1093/nar/gkp436. View

Dietz H, Douglas S, Shih W . Folding DNA into twisted and curved nanoscale shapes. Science. 2009; 325(5941):725-30. PMC: 2737683. DOI: 10.1126/science.1174251. View

Subramani R, Juul S, Rotaru A, Andersen F, Gothelf K, Mamdouh W . A novel secondary DNA binding site in human topoisomerase I unravelled by using a 2D DNA origami platform. ACS Nano. 2010; 4(10):5969-77. DOI: 10.1021/nn101662a. View

Kershner R, Bozano L, Micheel C, Hung A, Fornof A, Cha J . Placement and orientation of individual DNA shapes on lithographically patterned surfaces. Nat Nanotechnol. 2009; 4(9):557-61. DOI: 10.1038/nnano.2009.220. View

10.

Bath J, Green S, Turberfield A . A free-running DNA motor powered by a nicking enzyme. Angew Chem Int Ed Engl. 2005; 44(28):4358-61. DOI: 10.1002/anie.200501262. View

11.

Barish R, Schulman R, Rothemund P, Winfree E . An information-bearing seed for nucleating algorithmic self-assembly. Proc Natl Acad Sci U S A. 2009; 106(15):6054-9. PMC: 2660060. DOI: 10.1073/pnas.0808736106. View

12.

Tian Y, He Y, Chen Y, Yin P, Mao C . A DNAzyme that walks processively and autonomously along a one-dimensional track. Angew Chem Int Ed Engl. 2005; 44(28):4355-8. DOI: 10.1002/anie.200500703. View

13.

Seeman N . Construction of three-dimensional stick figures from branched DNA. DNA Cell Biol. 1991; 10(7):475-86. DOI: 10.1089/dna.1991.10.475. View

14.

Kim D, Kilchherr F, Dietz H, Bathe M . Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Res. 2011; 40(7):2862-8. PMC: 3326316. DOI: 10.1093/nar/gkr1173. View

15.

Eskelinen A, Kuzyk A, Kaltiaisenaho T, Timmermans M, Nasibulin A, Kauppinen E . Assembly of single-walled carbon nanotubes on DNA-origami templates through streptavidin-biotin interaction. Small. 2011; 7(6):746-50. DOI: 10.1002/smll.201001750. View

16.

Kuzyk A, Laitinen K, Torma P . DNA origami as a nanoscale template for protein assembly. Nanotechnology. 2009; 20(23):235305. DOI: 10.1088/0957-4484/20/23/235305. View

17.

Han D, Pal S, Liu Y, Yan H . Folding and cutting DNA into reconfigurable topological nanostructures. Nat Nanotechnol. 2010; 5(10):712-7. PMC: 3071358. DOI: 10.1038/nnano.2010.193. View

18.

Shih W, Quispe J, Joyce G . A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature. 2004; 427(6975):618-21. DOI: 10.1038/nature02307. View

19.

Li Z, Liu M, Wang L, Nangreave J, Yan H, Liu Y . Molecular behavior of DNA origami in higher-order self-assembly. J Am Chem Soc. 2010; 132(38):13545-52. PMC: 3071357. DOI: 10.1021/ja106292x. View

20.

Hung A, Micheel C, Bozano L, Osterbur L, Wallraff G, Cha J . Large-area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami. Nat Nanotechnol. 2009; 5(2):121-6. DOI: 10.1038/nnano.2009.450. View