Design Approaches and Computational Tools for DNA Nanostructures

Overview

Journal IEEE Open J Nanotechnol

Publisher IEEE

Date 2022 Jun 27

PMID 35756857

Authors

Heeyuen Koh

Jae Gyung Lee

Jae Young Lee

Ryan Kim

Osamu Tabata

Kim Jin-Woo

Do-Nyun Kim

Affiliations

Soon will be listed here.

Abstract

Designing a structure in nanoscale with desired shape and properties has been enabled by structural DNA nanotechnology. Design strategies in this research field have evolved to interpret various aspects of increasingly more complex nanoscale assembly and to realize molecular-level functionality by exploring static to dynamic characteristics of the target structure. Computational tools have naturally been of significant interest as they are essential to achieve a fine control over both shape and physicochemical properties of the structure. Here, we review the basic design principles of structural DNA nanotechnology together with its computational analysis and design tools.

Citing Articles

Improving DNA nanostructure stability: A review of the biomedical applications and approaches.

Nasiri M, Bahadorani M, Dellinger K, Aravamudhan S, Vivero-Escoto J, Zadegan R Int J Biol Macromol. 2024; 260(Pt 1):129495.

PMID: 38228209 PMC: 11060068. DOI: 10.1016/j.ijbiomac.2024.129495.

Nucleic acid nanostructures for applications: The influence of morphology on biological fate.

Langlois N, Ma K, Clark H Appl Phys Rev. 2023; 10(1):011304.

PMID: 36874908 PMC: 9869343. DOI: 10.1063/5.0121820.

References

Engelen W, Dietz H . Advancing Biophysics Using DNA Origami. Annu Rev Biophys. 2021; 50:469-492. DOI: 10.1146/annurev-biophys-110520-125739. View

Zhan P, Urban M, Both S, Duan X, Kuzyk A, Weiss T . DNA-assembled nanoarchitectures with multiple components in regulated and coordinated motion. Sci Adv. 2019; 5(11):eaax6023. PMC: 6884410. DOI: 10.1126/sciadv.aax6023. 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

SantaLucia Jr J, Hicks D . The thermodynamics of DNA structural motifs. Annu Rev Biophys Biomol Struct. 2004; 33:415-40. DOI: 10.1146/annurev.biophys.32.110601.141800. View

Jun H, Wang X, Parsons M, Bricker W, John T, Li S . Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami. Nucleic Acids Res. 2021; 49(18):10265-10274. PMC: 8501967. DOI: 10.1093/nar/gkab762. View

Nomidis S, Kriegel F, Vanderlinden W, Lipfert J, Carlon E . Twist-Bend Coupling and the Torsional Response of Double-Stranded DNA. Phys Rev Lett. 2017; 118(21):217801. DOI: 10.1103/PhysRevLett.118.217801. View

Wamhoff E, Banal J, Bricker W, Shepherd T, Parsons M, Veneziano R . Programming Structured DNA Assemblies to Probe Biophysical Processes. Annu Rev Biophys. 2019; 48:395-419. PMC: 7035826. DOI: 10.1146/annurev-biophys-052118-115259. View

Jabbari H, Aminpour M, Montemagno C . Computational Approaches to Nucleic Acid Origami. ACS Comb Sci. 2015; 17(10):535-47. DOI: 10.1021/acscombsci.5b00079. View

Lu X, Liu J, Wu X, Ding B . Multifunctional DNA Origami Nanoplatforms for Drug Delivery. Chem Asian J. 2019; 14(13):2193-2202. DOI: 10.1002/asia.201900574. View

10.

Wang W, Arias D, Deserno M, Ren X, Taylor R . Emerging applications at the interface of DNA nanotechnology and cellular membranes: Perspectives from biology, engineering, and physics. APL Bioeng. 2020; 4(4):041507. PMC: 7725538. DOI: 10.1063/5.0027022. View

11.

Simmel F, Yurke B, Singh H . Principles and Applications of Nucleic Acid Strand Displacement Reactions. Chem Rev. 2019; 119(10):6326-6369. DOI: 10.1021/acs.chemrev.8b00580. View

12.

Gu H, Chao J, Xiao S, Seeman N . Dynamic patterning programmed by DNA tiles captured on a DNA origami substrate. Nat Nanotechnol. 2009; 4(4):245-8. PMC: 2836238. DOI: 10.1038/nnano.2009.5. View

13.

Ijas H, Nummelin S, Shen B, Kostiainen M, Linko V . Dynamic DNA Origami Devices: from Strand-Displacement Reactions to External-Stimuli Responsive Systems. Int J Mol Sci. 2018; 19(7). PMC: 6073283. DOI: 10.3390/ijms19072114. View

14.

Sulc P, Romano F, Ouldridge T, Doye J, Louis A . A nucleotide-level coarse-grained model of RNA. J Chem Phys. 2014; 140(23):235102. DOI: 10.1063/1.4881424. View

15.

Yoo J, Aksimentiev A . In situ structure and dynamics of DNA origami determined through molecular dynamics simulations. Proc Natl Acad Sci U S A. 2013; 110(50):20099-104. PMC: 3864285. DOI: 10.1073/pnas.1316521110. View

16.

Ouldridge T, Louis A, Doye J . Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J Chem Phys. 2011; 134(8):085101. DOI: 10.1063/1.3552946. View

17.

Ouldridge T, Louis A, Doye J . DNA nanotweezers studied with a coarse-grained model of DNA. Phys Rev Lett. 2010; 104(17):178101. DOI: 10.1103/PhysRevLett.104.178101. View

18.

Qi H, Ghodousi M, Du Y, Grun C, Bae H, Yin P . DNA-directed self-assembly of shape-controlled hydrogels. Nat Commun. 2013; 4:2275. PMC: 3768014. DOI: 10.1038/ncomms3275. View

19.

Dans P, Walther J, Gomez H, Orozco M . Multiscale simulation of DNA. Curr Opin Struct Biol. 2015; 37:29-45. DOI: 10.1016/j.sbi.2015.11.011. View

20.

Wang D, Song J, Wang P, Pan V, Zhang Y, Cui D . Design and operation of reconfigurable two-dimensional DNA molecular arrays. Nat Protoc. 2018; 13(10):2312-2329. DOI: 10.1038/s41596-018-0039-0. View