Login Register Cart 0
Generic placeholder image

Current Topics in Medicinal Chemistry

Editor-in-Chief

ISSN (Print): 1568-0266
ISSN (Online): 1873-4294

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Mini-Review Article

Structural DNA Nanotechnology: Immobile Holliday Junctions to Artifi

Author(s): Raghu Pradeep Narayanan* and Leeza Abraham

Volume 22, Issue 8, 2022

Published on: 28 March, 2022

Page: [668 - 685] Pages: 18

DOI: 10.2174/1568026622666220112143401

Price: $65

Abstract

DNA nanotechnology marvels the scientific world with its capabilities to design, engineer, and demonstrate nanoscale shapes. This review is a condensed version walking the reader through the structural developments in the field over the past 40 years starting from the basic design rules of the double-stranded building block to the most recent advancements in self-assembled hierarchically achieved structures to date. It builds from the fundamental motivation of building 3-dimensional (3D) lattice structures of tunable cavities going all the way up to artificial nanorobots fighting cancer. The review starts by covering the most important developments from the fundamental bottom-up approach of building structures, which is the ‘tile’ based approach covering 1D, 2D, and 3D building blocks, after which the top-down approach using DNA origami and DNA bricks is also covered. Thereafter, DNA nanostructures assembled using not so commonly used (yet promising) techniques like i-motifs, quadruplexes, and kissing loops are covered. Highlights from the field of dynamic DNA nanostructures have been covered as well, walking the reader through various approaches used within the field to achieve movement. The article finally concludes by giving the authors a view of what the future of the field might look like while suggesting in parallel new directions that fellow/future DNA nanotechnologists could think about.

Keywords: DNA nanotechnology, Self-assembly, Nanorobots, Biomolecule, 3D, 2D.

« Previous Next »
Graphical Abstract

[1]
Watson, J.D.; Crick, F.H.C. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 1953, 171(4356), 737-738.
[http://dx.doi.org/10.1038/171737a0] [PMID: 13054692]
[2]
Seeman, N.C. Nucleic acid junctions and lattices. J. Theor. Biol., 1982, 99(2), 237-247.
[http://dx.doi.org/10.1016/0022-5193(82)90002-9] [PMID: 6188926]
[3]
Hong, F.; Zhang, F.; Liu, Y.; Yan, H. DNA origami: Scaffolds for creating higher order structures. Chem. Rev., 2017, 117(20), 12584-12640.
[http://dx.doi.org/10.1021/acs.chemrev.6b00825] [PMID: 28605177]
[4]
Madsen, M.; Gothelf, K.V. Chemistries for DNA nanotechnology. Chem. Rev., 2019, 119(10), 6384-6458.
[http://dx.doi.org/10.1021/acs.chemrev.8b00570] [PMID: 30714731]
[5]
Hu, Q.; Li, H.; Wang, L.; Gu, H.; Fan, C. DNA nanotechnology-enabled drug delivery systems. Chem. Rev., 2019, 119(10), 6459-6506.
[http://dx.doi.org/10.1021/acs.chemrev.7b00663] [PMID: 29465222]
[6]
Stephanopoulos, N. Hybrid nanostructures from the Self-assembly of proteins and DNA. Chem, 2020, 6(2), 364-405.
[http://dx.doi.org/10.1016/j.chempr.2020.01.012]
[7]
Chandrasekaran, A.R. Nuclease resistance of DNA nanostructures. Nat. Rev. Chem., 2021, 5(4), 1-15.
[http://dx.doi.org/10.1038/s41570-021-00251-y] [PMID: 33585701]
[8]
Lin, C.; Ke, Y.; Li, Z.; Wang, J.H.; Liu, Y.; Yan, H. Mirror image DNA nanostructures for chiral supramolecular assemblies. Nano Lett., 2009, 9(1), 433-436.
[http://dx.doi.org/10.1021/nl803328v] [PMID: 19063615]
[9]
Mao, C.; Sun, W.; Seeman, N.C. Designed two-dimensional DNA holliday junction arrays visualized by atomic force microscopy. J. Am. Chem. Soc., 1999, 121(23), 5437-5443.
[http://dx.doi.org/10.1021/ja9900398]
[10]
Fu, T.J.; Seeman, N.C. DNA double-crossover molecules. Biochemistry, 1993, 32(13), 3211-3220.
[http://dx.doi.org/10.1021/bi00064a003] [PMID: 8461289]
[11]
Wang, X.; Chandrasekaran, A.R.; Shen, Z.; Ohayon, Y.P.; Wang, T.; Kizer, M.E.; Sha, R.; Mao, C.; Yan, H.; Zhang, X.; Liao, S.; Ding, B.; Chakraborty, B.; Jonoska, N.; Niu, D.; Gu, H.; Chao, J.; Gao, X.; Li, Y.; Ciengshin, T.; Seeman, N.C. Paranemic crossover dna: there and back again. Chem. Rev., 2019, 119(10), 6273-6289.
[http://dx.doi.org/10.1021/acs.chemrev.8b00207] [PMID: 29911864]
[12]
Winfree, E.; Liu, F.; Wenzler, L.A.; Seeman, N.C. Design and self-assembly of two-dimensional DNA crystals. Nature, 1998, 394(6693), 539-544.
[http://dx.doi.org/10.1038/28998] [PMID: 9707114]
[13]
Shen, W.; Liu, Q.; Ding, B.; Shen, Z.; Zhu, C.; Mao, C. The study of the paranemic crossover (PX) motif in the context of self-assembly of DNA 2D crystals. Org. Biomol. Chem., 2016, 14(30), 7187-7190.
[http://dx.doi.org/10.1039/C6OB01146B] [PMID: 27404049]
[14]
He, Y.; Chen, Y.; Liu, H.; Ribbe, A.E.; Mao, C. Self-assembly of hexagonal DNA two-dimensional (2D) arrays. J. Am. Chem. Soc., 2005, 127(35), 12202-12203.
[http://dx.doi.org/10.1021/ja0541938] [PMID: 16131180]
[15]
Yan, H.; Park, S.H.; Finkelstein, G.; Reif, J.H.; LaBean, T.H. DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science, 2003, 301(5641), 1882-1884.
[http://dx.doi.org/10.1126/science.1089389] [PMID: 14512621]
[16]
He, Y.; Tian, Y.; Ribbe, A.E.; Mao, C. Highly connected two-dimensional crystals of DNA six-point-stars. J. Am. Chem. Soc., 2006, 128(50), 15978-15979.
[http://dx.doi.org/10.1021/ja0665141] [PMID: 17165718]
[17]
Hamada, S.; Murata, S. Substrate-assisted assembly of interconnected single-duplex DNA nanostructures. Angew. Chem. Int. Ed., 2009, 48(37), 6820-6823.
[http://dx.doi.org/10.1002/anie.200902662]
[18]
LaBean, T.H.; Yan, H.; Kopatsch, J.; Liu, F.; Winfree, E.; Reif, J.H.; Seeman, N.C. Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc., 2000, 122(9), 1848-1860.
[http://dx.doi.org/10.1021/ja993393e]
[19]
Zhang, F.; Liu, Y.; Yan, H. Complex Archimedean tiling self-assembled from DNA nanostructures. J. Am. Chem. Soc., 2013, 135(20), 7458-7461.
[http://dx.doi.org/10.1021/ja4035957] [PMID: 23651321]
[20]
Liu, L.; Li, Z.; Li, Y.; Mao, C. Rational design and self-assembly of two-dimensional, dodecagonal DNA quasicrystals. J. Am. Chem. Soc., 2019, 141(10), 4248-4251.
[http://dx.doi.org/10.1021/jacs.9b00843] [PMID: 30827097]
[21]
He, Y.; Ye, T.; Su, M.; Zhang, C.; Ribbe, A.E.; Jiang, W.; Mao, C. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature, 2008, 452(7184), 198-201.
[http://dx.doi.org/10.1038/nature06597] [PMID: 18337818]
[22]
Chen, J.H.; Seeman, N.C. Synthesis from DNA of a molecule with the connectivity of a cube. Nature, 1991, 350(6319), 631-633.
[http://dx.doi.org/10.1038/350631a0] [PMID: 2017259]
[23]
Goodman, R.P.; Berry, R.M.; Turberfield, A.J. The single-step synthesis of a DNA tetrahedron. Chem. Commun. (Camb.), 2004, (12), 1372-1373.
[http://dx.doi.org/10.1039/b402293a] [PMID: 15179470]
[24]
Kato, T.; Goodman, R.P.; Erben, C.M.; Turberfield, A.J.; Namba, K. High-resolution structural analysis of a DNA nanostructure by cryoEM. Nano Lett., 2009, 9(7), 2747-2750.
[http://dx.doi.org/10.1021/nl901265n] [PMID: 19492821]
[25]
Majumder, U.; Rangnekar, A.; Gothelf, K.V.; Reif, J.H.; LaBean, T.H. Design and construction of double-decker tile as a route to three-dimensional periodic assembly of DNA. J. Am. Chem. Soc., 2011, 133(11), 3843-3845.
[http://dx.doi.org/10.1021/ja1108886] [PMID: 21355587]
[26]
Hong, F.; Jiang, S.; Lan, X.; Narayanan, R.P.; Šulc, P.; Zhang, F.; Liu, Y.; Yan, H. Layered-crossover tiles with precisely tunable angles for 2D and 3D DNA crystal engineering. J. Am. Chem. Soc., 2018, 140(44), 14670-14676.
[http://dx.doi.org/10.1021/jacs.8b07180] [PMID: 30336007]
[27]
Hong, F.; Jiang, S.; Wang, T.; Liu, Y.; Yan, H. 3D framework DNA origami with layered crossovers. Angew. Chem. Int. Ed. Engl., 2016, 55(41), 12832-12835.
[http://dx.doi.org/10.1002/anie.201607050] [PMID: 27628457]
[28]
Zheng, J.; Birktoft, J.J.; Chen, Y.; Wang, T.; Sha, R.; Constantinou, P.E.; Ginell, S.L.; Mao, C.; Seeman, N.C. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature, 2009, 461(7260), 74-77.
[http://dx.doi.org/10.1038/nature08274] [PMID: 19727196]
[29]
Simmons, C.R.; Zhang, F.; Birktoft, J.J.; Qi, X.; Han, D.; Liu, Y.; Sha, R.; Abdallah, H.O.; Hernandez, C.; Ohayon, Y.P.; Seeman, N.C.; Yan, H. Construction and structure determination of a three-dimensional DNA crystal. J. Am. Chem. Soc., 2016, 138(31), 10047-10054.
[http://dx.doi.org/10.1021/jacs.6b06508] [PMID: 27447429]
[30]
Simmons, C.R.; Zhang, F.; MacCulloch, T.; Fahmi, N.; Stephanopoulos, N.; Liu, Y.; Seeman, N.C.; Yan, H. Tuning the cavity size and chirality of self-assembling 3D DNA crystals. J. Am. Chem. Soc., 2017, 139(32), 11254-11260.
[http://dx.doi.org/10.1021/jacs.7b06485] [PMID: 28731332]
[31]
Simmons, C.R.; MacCulloch, T.; Zhang, F.; Liu, Y.; Stephanopoulos, N.; Yan, H. A self-assembled rhombohedral DNA crystal scaffold with tunable cavity sizes and high-resolution structural detail. Angew. Chem. Int. Ed. Engl., 2020, 59(42), 18619-18626.
[http://dx.doi.org/10.1002/anie.202005505] [PMID: 32533629]
[32]
Shih, W.M.; Quispe, J.D.; Joyce, G.F.A. 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature, 2004, 427(6975), 618-621.
[http://dx.doi.org/10.1038/nature02307] [PMID: 14961116]
[33]
Rothemund, P.W.K. Folding DNA to create nanoscale shapes and patterns. Nature, 2006, 440(7082), 297-302.
[http://dx.doi.org/10.1038/nature04586] [PMID: 16541064]
[34]
Dey, S.; Fan, C.; Gothelf, K.V.; Li, J.; Lin, C.; Liu, L.; Liu, N.; Nijenhuis, M.A.D.; Saccà, B.; Simmel, F.C.; Yan, H.; Zhan, P. DNA origami. Nat. Rev. Methods Prim., 2021, 1(1), 13.
[http://dx.doi.org/10.1038/s43586-020-00009-8]
[35]
Douglas, S.M.; Dietz, H.; Liedl, T.; Högberg, B.; Graf, F.; Shih, W.M. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature, 2009, 459(7245), 414-418.
[http://dx.doi.org/10.1038/nature08016] [PMID: 19458720]
[36]
Ke, Y.; Douglas, S.M.; Liu, M.; Sharma, J.; Cheng, A.; Leung, A.; Liu, Y.; Shih, W.M.; Yan, H. Multilayer DNA origami packed on a square lattice. J. Am. Chem. Soc., 2009, 131(43), 15903-15908.
[http://dx.doi.org/10.1021/ja906381y] [PMID: 19807088]
[37]
Dietz, H.; Douglas, S.M.; Shih, W.M. Folding DNA into twisted and curved nanoscale shapes. Science, 2009, 325(5941), 725-730.
[http://dx.doi.org/10.1126/science.1174251] [PMID: 19661424]
[38]
Zhang, F.; Jiang, S.; Wu, S.; Li, Y.; Mao, C.; Liu, Y.; Yan, H. Complex wireframe DNA origami nanostructures with multi-arm junction vertices. Nat. Nanotechnol., 2015, 10(9), 779-784.
[http://dx.doi.org/10.1038/nnano.2015.162] [PMID: 26192207]
[39]
Han, D.; Pal, S.; Yang, Y.; Jiang, S.; Nangreave, J.; Liu, Y.; Yan, H. DNA gridiron nanostructures based on four-arm junctions. Science, 2013, 339(6126), 1412-1415.
[http://dx.doi.org/10.1126/science.1232252] [PMID: 23520107]
[40]
Han, D.; Qi, X.; Myhrvold, C.; Wang, B.; Dai, M.; Jiang, S.; Bates, M.; Liu, Y.; An, B.; Zhang, F.; Yan, H.; Yin, P. Single-stranded DNA and RNA origami. Science, 2017, 358(6369), eaao2648.
[http://dx.doi.org/10.1126/science.aao2648] [PMID: 29242318]
[41]
Tikhomirov, G.; Petersen, P.; Qian, L. Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns. Nature, 2017, 552(7683), 67-71.
[http://dx.doi.org/10.1038/nature24655] [PMID: 29219965]
[42]
Iinuma, R.; Ke, Y.; Jungmann, R.; Schlichthaerle, T.; Woehrstein, J.B.; Yin, P. Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT. Science, 2014, 344(6179), 65-69.
[http://dx.doi.org/10.1126/science.1250944] [PMID: 24625926]
[43]
Wagenbauer, K.F.; Sigl, C.; Dietz, H. Gigadalton-scale shape-programmable DNA assemblies. Nature, 2017, 552(7683), 78-83.
[http://dx.doi.org/10.1038/nature24651] [PMID: 29219966]
[44]
Yao, G.; Zhang, F.; Wang, F.; Peng, T.; Liu, H.; Poppleton, E.; Šulc, P.; Jiang, S.; Liu, L.; Gong, C.; Jing, X.; Liu, X.; Wang, L.; Liu, Y.; Fan, C.; Yan, H. Meta-DNA structures. Nat. Chem., 2020, 12(11), 1067-1075.
[http://dx.doi.org/10.1038/s41557-020-0539-8] [PMID: 32895523]
[45]
Liu, W.; Tagawa, M.; Xin, H.L.; Wang, T.; Emamy, H.; Li, H.; Yager, K.G.; Starr, F.W.; Tkachenko, A.V.; Gang, O. Diamond family of nanoparticle superlattices. Science, 2016, 351(6273), 582-586.
[http://dx.doi.org/10.1126/science.aad2080] [PMID: 26912698]
[46]
Wang, Y.; Dai, L.; Ding, Z.; Ji, M.; Liu, J.; Xing, H.; Liu, X.; Ke, Y.; Fan, C.; Wang, P.; Tian, Y. DNA origami single crystals with Wulff shapes. Nat. Commun., 2021, 12(1), 3011.
[http://dx.doi.org/10.1038/s41467-021-23332-4] [PMID: 34021131]
[47]
Sigl, C.; Willner, E.M.; Engelen, W.; Kretzmann, J.A.; Sachenbacher, K.; Liedl, A.; Kolbe, F.; Wilsch, F.; Aghvami, S.A.; Protzer, U.; Hagan, M.F.; Fraden, S.; Dietz, H. Programmable icosahedral shell system for virus trapping. Nat. Mater., 2021, 20(9), 1281-1289.
[http://dx.doi.org/10.1038/s41563-021-01020-4] [PMID: 34127822]
[48]
Douglas, S.M.; Marblestone, A.H.; Teerapittayanon, S.; Vazquez, A.; Church, G.M.; Shih, W.M. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res., 2009, 37(15), 5001-5006.
[http://dx.doi.org/10.1093/nar/gkp436] [PMID: 19531737]
[49]
Gerling, T.; Wagenbauer, K.F.; Neuner, A.M.; Dietz, H. Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components. Science, 2015, 347(6229), 1446-1452.
[http://dx.doi.org/10.1126/science.aaa5372] [PMID: 25814577]
[50]
Tian, Y.; Zhang, Y.; Wang, T.; Xin, H.L.; Li, H.; Gang, O. Lattice engineering through nanoparticle-DNA frameworks. Nat. Mater., 2016, 15(6), 654-661.
[http://dx.doi.org/10.1038/nmat4571] [PMID: 26901516]
[51]
Tian, Y.; Lhermitte, J.R.; Bai, L.; Vo, T.; Xin, H.L.; Li, H.; Li, R.; Fukuto, M.; Yager, K.G.; Kahn, J.S.; Xiong, Y.; Minevich, B.; Kumar, S.K.; Gang, O. Ordered three-dimensional nanomaterials using DNA-prescribed and valence-controlled material voxels. Nat. Mater., 2020, 19(7), 789-796.
[http://dx.doi.org/10.1038/s41563-019-0550-x] [PMID: 31932669]
[52]
Majewski, P.W.; Michelson, A.; Cordeiro, M.A.L.; Tian, C.; Ma, C.; Kisslinger, K.; Tian, Y.; Liu, W.; Stach, E.A.; Yager, K.G.; Gang, O. Resilient three-dimensional ordered architectures assembled from nanoparticles by DNA. Sci. Adv., 2021, 7(12), eabf0617.
[http://dx.doi.org/10.1126/sciadv.abf0617] [PMID: 33741597]
[53]
Shani, L.; Michelson, A.N.; Minevich, B.; Fleger, Y.; Stern, M.; Shaulov, A.; Yeshurun, Y.; Gang, O. DNA-assembled superconducting 3D nanoscale architectures. Nat. Commun., 2020, 11(1), 5697.
[http://dx.doi.org/10.1038/s41467-020-19439-9] [PMID: 33173061]
[54]
Qi, X.; Zhang, F.; Su, Z.; Jiang, S.; Han, D.; Ding, B.; Liu, Y.; Chiu, W.; Yin, P.; Yan, H. Programming molecular topologies from single-stranded nucleic acids. Nat. Commun., 2018, 9(1), 4579.
[http://dx.doi.org/10.1038/s41467-018-07039-7] [PMID: 30389935]
[55]
Benson, E.; Mohammed, A.; Gardell, J.; Masich, S.; Czeizler, E.; Orponen, P.; Högberg, B. DNA rendering of polyhedral meshes at the nanoscale. Nature, 2015, 523(7561), 441-444.
[http://dx.doi.org/10.1038/nature14586] [PMID: 26201596]
[56]
Veneziano, R.; Ratanalert, S.; Zhang, K.; Zhang, F.; Yan, H.; Chiu, W.; Bathe, M. Designer nanoscale DNA assemblies programmed from the top down. Science, 2016, 352(6293), 1534-1534.
[http://dx.doi.org/10.1126/science.aaf4388] [PMID: 27229143]
[57]
Jun, H.; Shepherd, T.R.; Zhang, K.; Bricker, W.P.; Li, S.; Chiu, W.; Bathe, M. Automated sequence design of 3D polyhedral wireframe DNA origami with honeycomb edges. ACS Nano, 2019, 13(2), 2083-2093.
[http://dx.doi.org/10.1021/acsnano.8b08671] [PMID: 30605605]
[58]
de Llano, E.; Miao, H.; Ahmadi, Y.; Wilson, A.J.; Beeby, M.; Viola, I.; Barisic, I. Adenita: Interactive 3D modelling and visualization of DNA nanostructures. Nucleic Acids Res., 2020, 48(15), 8269-8275.
[http://dx.doi.org/10.1093/nar/gkaa593] [PMID: 32692355]
[59]
Huang, C-M.; Kucinic, A.; Johnson, J.A.; Su, H-J.; Castro, C.E. Integrated computer-aided engineering and design for DNA assemblies. Nat. Mater., 2021, 20(9), 1264-1271.
[http://dx.doi.org/10.1038/s41563-021-00978-5] [PMID: 33875848]
[60]
Wei, B.; Dai, M.; Yin, P. Complex shapes self-assembled from single-stranded DNA tiles. Nature, 2012, 485(7400), 623-626.
[http://dx.doi.org/10.1038/nature11075] [PMID: 22660323]
[61]
Ke, Y.; Ong, L.L.; Shih, W.M.; Yin, P. Three-dimensional structures self-assembled from DNA bricks. Science, 2012, 338(6111), 1177-1183.
[http://dx.doi.org/10.1126/science.1227268] [PMID: 23197527]
[62]
Ke, Y.; Ong, L.L.; Sun, W.; Song, J.; Dong, M.; Shih, W.M.; Yin, P. DNA brick crystals with prescribed depths. Nat. Chem., 2014, 6(11), 994-1002.
[http://dx.doi.org/10.1038/nchem.2083] [PMID: 25343605]
[63]
Ong, L.L.; Hanikel, N.; Yaghi, O.K.; Grun, C.; Strauss, M.T.; Bron, P.; Lai-Kee-Him, J.; Schueder, F.; Wang, B.; Wang, P.; Kishi, J.Y.; Myhrvold, C.; Zhu, A.; Jungmann, R.; Bellot, G.; Ke, Y.; Yin, P. Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components. Nature, 2017, 552(7683), 72-77.
[http://dx.doi.org/10.1038/nature24648] [PMID: 29219968]
[64]
Mergny, J-L.; Sen, D. DNA quadruple helices in nanotechnology. Chem. Rev., 2019, 119(10), 6290-6325.
[http://dx.doi.org/10.1021/acs.chemrev.8b00629] [PMID: 30605316]
[65]
Zeraati, M.; Langley, D.B.; Schofield, P.; Moye, A.L.; Rouet, R.; Hughes, W.E.; Bryan, T.M.; Dinger, M.E.; Christ, D. I-motif DNA structures are formed in the nuclei of human cells. Nat. Chem., 2018, 10(6), 631-637.
[http://dx.doi.org/10.1038/s41557-018-0046-3] [PMID: 29686376]
[66]
Cheng, E.; Xing, Y.; Chen, P.; Yang, Y.; Sun, Y.; Zhou, D.; Xu, L.; Fan, Q.; Liu, D. A pH-triggered, fast-responding DNA hydrogel. Angew. Chem. Int. Ed. Engl., 2009, 48(41), 7660-7663.
[http://dx.doi.org/10.1002/anie.200902538] [PMID: 19739155]
[67]
Leung, K.; Chakraborty, K.; Saminathan, A.; Krishnan, Y. A DNA nanomachine chemically resolves lysosomes in live cells. Nat. Nanotechnol., 2019, 14(2), 176-183.
[http://dx.doi.org/10.1038/s41565-018-0318-5] [PMID: 30510277]
[68]
Kwok, C.K.; Merrick, C.J. G-quadruplexes: Prediction, characterization, and biological application. Trends Biotechnol., 2017, 35(10), 997-1013.
[http://dx.doi.org/10.1016/j.tibtech.2017.06.012] [PMID: 28755976]
[69]
Spiegel, J.; Adhikari, S.; Balasubramanian, S. The structure and function of DNA G-quadruplexes. Trends Chem., 2020, 2(2), 123-136.
[http://dx.doi.org/10.1016/j.trechm.2019.07.002] [PMID: 32923997]
[70]
Li, X.; Sánchez-Ferrer, A.; Bagnani, M.; Adamcik, J.; Azzari, P.; Hao, J.; Song, A.; Liu, H.; Mezzenga, R. Metal ions confinement defines the architecture of G-quartet, G-quadruplex fibrils and their assembly into nematic tactoids. Proc. Natl. Acad. Sci. USA, 2020, 117(18), 9832-9839.
[http://dx.doi.org/10.1073/pnas.1919777117] [PMID: 32317383]
[71]
Mathews, D.H.; Moss, W.N.; Turner, D.H. Folding and finding RNA secondary structure. Cold Spring Harb. Perspect. Biol., 2010, 2(12), a003665-a003665.
[http://dx.doi.org/10.1101/cshperspect.a003665] [PMID: 20685845]
[72]
Hao, C.; Li, X.; Tian, C.; Jiang, W.; Wang, G.; Mao, C. Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage. Nat. Commun., 2014, 5(1), 3890.
[http://dx.doi.org/10.1038/ncomms4890] [PMID: 24835104]
[73]
Geary, C.; Grossi, G.; McRae, E.K.S.; Rothemund, P.W.K.; Andersen, E.S. RNA origami design tools enable cotranscriptional folding of kilobase-sized nanoscaffolds. Nat. Chem., 2021, 13(6), 549-558.
[http://dx.doi.org/10.1038/s41557-021-00679-1] [PMID: 33972754]
[74]
Barth, A.; Kobbe, D.; Focke, M. DNA-DNA kissing complexes as a new tool for the assembly of DNA nanostructures. Nucleic Acids Res., 2016, 44(4), 1502-1513.
[http://dx.doi.org/10.1093/nar/gkw014] [PMID: 26773051]
[75]
Lat, P.K.; Schultz, C.W.; Yu, H-Z.; Sen, D. A long and reversibly self-assembling 1D DNA nanostructure built from triplex and quadruplex hybrid tiles. Angew. Chem. Int. Ed. Engl., 2021, 60(16), 8722-8727.
[http://dx.doi.org/10.1002/anie.202016668] [PMID: 33580565]
[76]
Ryssy, J.; Natarajan, A.K.; Wang, J.; Lehtonen, A.J.; Nguyen, M-K.; Klajn, R.; Kuzyk, A. Light-responsive dynamic DNA-origami-based plasmonic assemblies. Angew. Chem. Int. Ed. Engl., 2021, 60(11), 5859-5863.
[http://dx.doi.org/10.1002/anie.202014963] [PMID: 33320988]
[77]
Avakyan, N.; Greschner, A.A.; Aldaye, F.; Serpell, C.J.; Toader, V.; Petitjean, A.; Sleiman, H.F. Reprogramming the assembly of unmodified DNA with a small molecule. Nat. Chem., 2016, 8(4), 368-376.
[http://dx.doi.org/10.1038/nchem.2451] [PMID: 27001733]
[78]
Hoshika, S.; Leal, N.A.; Kim, M.J.; Kim, M.S.; Karalkar, N.B.; Kim, H.J.; Bates, A.M.; Watkins, N.E., Jr; SantaLucia, H.A.; Meyer, A.J.; DasGupta, S.; Piccirilli, J.A.; Ellington, A.D.; SantaLucia, J., Jr; Georgiadis, M.M.; Benner, S.A. Hachimoji DNA and RNA: A genetic system with eight building blocks. Science, 2019, 363(6429), 884-887.
[http://dx.doi.org/10.1126/science.aat0971] [PMID: 30792304]
[79]
Liu, M.; Fu, J.; Hejesen, C.; Yang, Y.; Woodbury, N.W.; Gothelf, K.; Liu, Y.; Yan, H. A DNA tweezer-actuated enzyme nanoreactor. Nat. Commun., 2013, 4(1), 2127.
[http://dx.doi.org/10.1038/ncomms3127] [PMID: 23820332]
[80]
Zhang, F.; Nangreave, J.; Liu, Y.; Yan, H. Reconfigurable DNA origami to generate quasifractal patterns. Nano Lett., 2012, 12(6), 3290-3295.
[http://dx.doi.org/10.1021/nl301399z] [PMID: 22559073]
[81]
Song, J.; Li, Z.; Wang, P.; Meyer, T.; Mao, C.; Ke, Y. Reconfiguration of DNA molecular arrays driven by information relay. Science, 2017, 357(6349), eaan3377.
[http://dx.doi.org/10.1126/science.aan3377] [PMID: 28642234]
[82]
Andersen, E.S.; Dong, M.; Nielsen, M.M.; Jahn, K.; Subramani, R.; Mamdouh, W.; Golas, M.M.; Sander, B.; Stark, H.; Oliveira, C.L.P.; Pedersen, J.S.; Birkedal, V.; Besenbacher, F.; Gothelf, K.V.; Kjems, J. Self-assembly of a nanoscale DNA box with a controllable lid. Nature, 2009, 459(7243), 73-76.
[http://dx.doi.org/10.1038/nature07971] [PMID: 19424153]
[83]
Kuzyk, A.; Yang, Y.; Duan, X.; Stoll, S.; Govorov, A.O.; Sugiyama, H.; Endo, M.; Liu, N. A light-driven three-dimensional plasmonic nanosystem that translates molecular motion into reversible chiroptical function. Nat. Commun., 2016, 7(1), 10591.
[http://dx.doi.org/10.1038/ncomms10591] [PMID: 26830310]
[84]
Kopperger, E.; List, J.; Madhira, S.; Rothfischer, F.; Lamb, D.C.; Simmel, F.C. A self-assembled nanoscale robotic arm controlled by electric fields. Science, 2018, 359(6373), 296-301.
[http://dx.doi.org/10.1126/science.aao4284] [PMID: 29348232]
[85]
Marras, A.E.; Zhou, L.; Su, H-J.; Castro, C.E. Programmable motion of DNA origami mechanisms. Proc. Natl. Acad. Sci. USA, 2015, 112(3), 713-718.
[http://dx.doi.org/10.1073/pnas.1408869112] [PMID: 25561550]
[86]
List, J.; Falgenhauer, E.; Kopperger, E.; Pardatscher, G.; Simmel, F.C. Long-range movement of large mechanically interlocked DNA nanostructures. Nat. Commun., 2016, 7(1), 12414.
[http://dx.doi.org/10.1038/ncomms12414] [PMID: 27492061]
[87]
Kosuri, P.; Altheimer, B.D.; Dai, M.; Yin, P.; Zhuang, X. Rotation tracking of genome-processing enzymes using DNA origami rotors. Nature, 2019, 572(7767), 136-140.
[http://dx.doi.org/10.1038/s41586-019-1397-7] [PMID: 31316204]
[88]
Thubagere, A.J.; Li, W.; Johnson, R.F.; Chen, Z.; Doroudi, S.; Lee, Y.L.; Izatt, G.; Wittman, S.; Srinivas, N.; Woods, D.; Winfree, E.; Qian, L. A cargo-sorting DNA robot. Science, 2017, 357(6356), eaan6558.
[http://dx.doi.org/10.1126/science.aan6558] [PMID: 28912216]
[89]
Li, S.; Jiang, Q.; Liu, S.; Zhang, Y.; Tian, Y.; Song, C.; Wang, J.; Zou, Y.; Anderson, G.J.; Han, J-Y.; Chang, Y.; Liu, Y.; Zhang, C.; Chen, L.; Zhou, G.; Nie, G.; Yan, H.; Ding, B.; Zhao, Y. A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo. Nat. Biotechnol., 2018, 36(3), 258-264.
[http://dx.doi.org/10.1038/nbt.4071] [PMID: 29431737]
[90]
Kuzuya, A.; Sakai, Y.; Yamazaki, T.; Xu, Y.; Komiyama, M. Nanomechanical DNA origami ‘single-molecule beacons’ directly imaged by atomic force microscopy. Nat. Commun., 2011, 2(1), 449.
[http://dx.doi.org/10.1038/ncomms1452] [PMID: 21863016]
[91]
Shin, J-S.; Pierce, N.A. A synthetic DNA walker for molecular transport. J. Am. Chem. Soc., 2004, 126(35), 10834-10835.
[http://dx.doi.org/10.1021/ja047543j] [PMID: 15339155]
[92]
Yurke, B.; Turberfield, A.J.; Mills, A.P., Jr; Simmel, F.C.; Neumann, J.L. A DNA-fuelled molecular machine made of DNA. Nature, 2000, 406(6796), 605-608.
[http://dx.doi.org/10.1038/35020524] [PMID: 10949296]
[93]
Yin, P.; Choi, H.M.T.; Calvert, C.R.; Pierce, N.A. Programming biomolecular self-assembly pathways. Nature, 2008, 451(7176), 318-322.
[http://dx.doi.org/10.1038/nature06451] [PMID: 18202654]
[94]
Ketterer, P.; Willner, E.M.; Dietz, H. Nanoscale rotary apparatus formed from tight-fitting 3D DNA components. Sci. Adv., 2016, 2(2), e1501209.
[http://dx.doi.org/10.1126/sciadv.1501209] [PMID: 26989778]
[95]
Endo, M.; Sugiyama, H. Single-molecule imaging of dynamic motions of biomolecules in DNA origami nanostructures using high-speed atomic force microscopy. Acc. Chem. Res., 2014, 47(6), 1645-1653.
[http://dx.doi.org/10.1021/ar400299m] [PMID: 24601497]
[96]
Bhatia, D.; Arumugam, S.; Nasilowski, M.; Joshi, H.; Wunder, C.; Chambon, V.; Prakash, V.; Grazon, C.; Nadal, B.; Maiti, P.K.; Johannes, L.; Dubertret, B.; Krishnan, Y. Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways. Nat. Nanotechnol., 2016, 11(12), 1112-1119.
[http://dx.doi.org/10.1038/nnano.2016.150] [PMID: 27548358]
[97]
Jiang, Q.; Song, C.; Nangreave, J.; Liu, X.; Lin, L.; Qiu, D.; Wang, Z-G.; Zou, G.; Liang, X.; Yan, H.; Ding, B. DNA origami as a carrier for circumvention of drug resistance. J. Am. Chem. Soc., 2012, 134(32), 13396-13403.
[http://dx.doi.org/10.1021/ja304263n] [PMID: 22803823]
[98]
Schüller, V.J.; Heidegger, S.; Sandholzer, N.; Nickels, P.C.; Suhartha, N.A.; Endres, S.; Bourquin, C.; Liedl, T. Cellular immunostimulation by CpG-sequence-coated DNA origami structures. ACS Nano, 2011, 5(12), 9696-9702.
[http://dx.doi.org/10.1021/nn203161y] [PMID: 22092186]
[99]
Zhou, C.; Duan, X.; Liu, N. DNA-nanotechnology-enabled chiral plasmonics: From static to dynamic. Acc. Chem. Res., 2017, 50(12), 2906-2914.
[http://dx.doi.org/10.1021/acs.accounts.7b00389] [PMID: 28953361]
[100]
Samanta, A.; Banerjee, S.; Liu, Y. DNA nanotechnology for nanophotonic applications. Nanoscale, 2015, 7(6), 2210-2220.
[http://dx.doi.org/10.1039/C4NR06283C] [PMID: 25592639]
[101]
Hu, Y.; Niemeyer, C.M. From DNA nanotechnology to material systems engineering. Adv. Mater., 2019, 31(26), e1806294.
[http://dx.doi.org/10.1002/adma.201806294] [PMID: 30767279]
[102]
Shen, L.; Wang, P.; Ke, Y. DNA nanotechnology-based biosensors and therapeutics. Adv. Healthcare Mater., 2021, 10(15), 2002205.
[103]
Jiang, S.; Ge, Z.; Mou, S.; Yan, H.; Fan, C. Designer DNA nanostructures for therapeutics. Chem, 2021, 7(5), 1156-1179.
[http://dx.doi.org/10.1016/j.chempr.2020.10.025]
[104]
Pettersen, E.F.; Goddard, T.D.; Huang, C.C.; Meng, E.C.; Couch, G.S.; Croll, T.I.; Morris, J.H.; Ferrin, T.E. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci., 2021, 30(1), 70-82.
[http://dx.doi.org/10.1002/pro.3943] [PMID: 32881101]
[105]
Kuhlman, B.; Dantas, G.; Ireton, G.C.; Varani, G.; Stoddard, B.L.; Baker, D. Design of a novel globular protein fold with atomic-level accuracy. Science, 2003, 302(5649), 1364-1368.
[http://dx.doi.org/10.1126/science.1089427] [PMID: 14631033]
[106]
Leaver-Fay, A.; Tyka, M.; Lewis, S.M.; Lange, O.F.; Thompson, J.; Jacak, R.; Kaufman, K.; Renfrew, P.D.; Smith, C.A.; Sheffler, W.; Davis, I.W.; Cooper, S.; Treuille, A.; Mandell, D.J.; Richter, F.; Ban, Y.E.; Fleishman, S.J.; Corn, J.E.; Kim, D.E.; Lyskov, S.; Berrondo, M.; Mentzer, S.; Popović, Z.; Havranek, J.J.; Karanicolas, J.; Das, R.; Meiler, J.; Kortemme, T.; Gray, J.J.; Kuhlman, B.; Baker, D.; Bradley, P. ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol., 2011, 487, 545-574.
[http://dx.doi.org/10.1016/B978-0-12-381270-4.00019-6] [PMID: 21187238]
[107]
Williams, S. Tiamat: A three-dimensional editing tool for complex DNA structures; Springer: Berlin, Heidelberg, 2009, pp. 90-101.
[108]
Jumper, J.; Evans, R.; Pritzel, A.; Green, T.; Figurnov, M.; Ronneberger, O.; Tunyasuvunakool, K.; Bates, R.; Žídek, A.; Potapenko, A.; Bridgland, A.; Meyer, C.; Kohl, S.A.A.; Ballard, A.J.; Cowie, A.; Romera-Paredes, B.; Nikolov, S.; Jain, R.; Adler, J.; Back, T.; Petersen, S.; Reiman, D.; Clancy, E.; Zielinski, M.; Steinegger, M.; Pacholska, M.; Berghammer, T.; Bodenstein, S.; Silver, D.; Vinyals, O.; Senior, A.W.; Kavukcuoglu, K.; Kohli, P.; Hassabis, D. Highly accurate protein structure prediction with AlphaFold. Nature, 2021, 596(7873), 583-589.
[http://dx.doi.org/10.1038/s41586-021-03819-2] [PMID: 34265844]
[109]
Ponnuswamy, N.; Bastings, M.M.C.; Nathwani, B.; Ryu, J.H.; Chou, L.Y.T.; Vinther, M.; Li, W.A.; Anastassacos, F.M.; Mooney, D.J.; Shih, W.M. Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation. Nat. Commun., 2017, 8(1), 15654.
[http://dx.doi.org/10.1038/ncomms15654] [PMID: 28561045]
[110]
Flory, J.D.; Simmons, C.R.; Lin, S.; Johnson, T.; Andreoni, A.; Zook, J.; Ghirlanda, G.; Liu, Y.; Yan, H.; Fromme, P. Low temperature assembly of functional 3D DNA-PNA-protein complexes. J. Am. Chem. Soc., 2014, 136(23), 8283-8295.
[http://dx.doi.org/10.1021/ja501228c] [PMID: 24871902]
[111]
Kumar, S.; Pearse, A.; Liu, Y.; Taylor, R.E. Modular self-assembly of gamma-modified peptide nucleic acids in organic solvent mixtures. Nat. Commun., 2020, 11(1), 2960.
[http://dx.doi.org/10.1038/s41467-020-16759-8] [PMID: 32528008]
[112]
Gerling, T.; Kube, M.; Kick, B.; Dietz, H. Sequence-programmable covalent bonding of designed DNA assemblies. Sci. Adv., 2018, 4(8), eaau1157.
[http://dx.doi.org/10.1126/sciadv.aau1157] [PMID: 30128357]
[113]
Song, I.H.; Shin, S.W.; Park, K.S.; Lansac, Y.; Jang, Y.H.; Um, S.H. Enzyme-guided DNA sewing architecture. Sci. Rep., 2015, 5(1), 17722.
[http://dx.doi.org/10.1038/srep17722] [PMID: 26634810]
[114]
Feynman, R. There’s plenty of room at the bottom. Eng. Sci., 1960, 23, 22-36.

Rights & Permissions Print Cite
Article Metrics
23
1
© 2024 Bentham Science Publishers | Privacy Policy