AI Chat Paper
Note: Please note that the following content is generated by AMiner AI. SciOpen does not take any responsibility related to this content.
{{lang === 'zh_CN' ? '文章概述' : 'Summary'}}
{{lang === 'en_US' ? '中' : 'Eng'}}
Chat more with AI
PDF (41 MB)
Collect
Submit Manuscript AI Chat Paper
Show Outline
Outline
Show full outline
Hide outline
Outline
Show full outline
Hide outline
Review Article | Open Access | Online First

Design, regulation, and functionalization of self-assembled DNA crystals

Ziyu Li1Mingqiang Li1Xiaoguo Liu1 ( )Jielin Chen1,2 ( )
School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
Interdisciplinary Institute for Medical Engineering, Fuzhou University, Fuzhou 350108, China
Show Author Information

Graphical Abstract

Self-assembled DNA crystals are crystalline nanomaterials formed by complementary base pairing of DNA molecules. They have atomic-level high precision and are highly programmable. This article reviews the history and recent developments of this rising filed.

Abstract

Crystals are materials in which atoms, ions, or molecules are arranged in a periodic and ordered three-dimensional structure. Among novel crystalline nanomaterials, self-assembled DNA crystals form via the base-pair complementarity of DNA molecules. Unlike traditional ionic or metallic crystals, self-assembled DNA crystals offer high programmability, enabling the design of addressable frameworks with tunable pore sizes for host-guest interactions and further functionalization through interfacial chemical modifications. Over the past 15 years, research interest in DNA nanotechnology and DNA self-assembled nanomaterials has surged. This review provides a comprehensive overview of the design principles, regulation, and functionalization of self-assembled DNA crystals for applications in molecular recognition, catalysis, and photonic crystals, while also addressing their emerging challenges within the broader context of nucleic acid chemistry and structural DNA nanotechnology.

References

[1]

Cramer, P. Rosalind Franklin and the advent of molecular biology. Cell 2020, 182, 787–789.

[2]

Franklin, R. E.; Gosling, R. G. Molecular configuration in sodium thymonucleate. Nature 1953, 171, 740–741.

[3]

Kim, S. H.; Sussman, J. L.; Suddath, F. L.; Quigley, G. J.; Mcpherson, A.; Wang, A. H. J.; Seeman, N. C.; Rich, A. The general structure of transfer RNA molecules. Proc. Natl. Acad. Sci. USA 1974, 71, 4970–4974.

[4]

Wang, A. H. J.; Quigley, G. J.; Kolpak, F. J.; Crawford, J. L.; Van Boom, J. H.; Van Der Marel, G.; Rich, A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 1979, 282, 680–686.

[5]

Wing, R.; Drew, H.; Takano, T.; Broka, C.; Tanaka, S.; Itakura, K.; Dickerson, R. E. Crystal structure analysis of a complete turn of B-DNA. Nature 1980, 287, 755–758.

[6]

Lu, D.; Alexandra Searles, M.; Klug, A. Crystal structure of a zinc-finger-RNA complex reveals two modes of molecular recognition. Nature 2003, 426, 96–100.

[7]

Ponce-Salvatierra, A.; Wawrzyniak-Turek, K.; Steuerwald, U.; Höbartner, C.; Pena, V. Crystal structure of a DNA catalyst. Nature 2016, 529, 231–234.

[8]

Kelly, J. A.; Feigon, J.; Yeates, T. O. Reconciliation of the X-ray and NMR Structures of the Thrombin-Binding Aptamer d(GGTTGGTGTGGTTGG). J. Mol. Biol. 1996, 256, 417–422.

[9]

Ortiz-Lombardía, M.; González, A.; Eritja, R.; Aymamí, J.; Azorín, F.; Coll, M. Crystal structure of a DNA Holliday junction. Nat. Struct. Biol. 1999, 6, 913–917.

[10]

Seeman, N. C. Nucleic acid junctions and lattices. J. Theor. Biol. 1982, 99, 237–247.

[11]

Seeman, N. C.; Sleiman, H. F. DNA nanotechnology. Nat. Rev. Mater. 2017, 3, 17068.

[12]

Cutler, J. I.; Auyeung, E.; Mirkin, C. A. Spherical Nucleic Acids. J. Am. Chem. Soc. 2012, 134, 1376–1391.

[13]

Park, D. J.; Zhang, C.; Ku, J. C.; Zhou, Y.; Schatz, G. C.; Mirkin, C. A. Plasmonic photonic crystals realized through DNA-programmable assembly. Proc. Natl. Acad. Sci. USA 2015, 112, 977–981

[14]

Winfree, E.; Liu, F. R.; Wenzler, L. A.; Seeman, N. C. Design and self-assembly of two-dimensional DNA crystals. Nature 1998, 394, 539–544.

[15]

Mao, C. D.; Sun, W. Q.; Seeman, N. C. Designed two-dimensional DNA Holliday junction arrays visualized by atomic force microscopy. J. Am. Chem. Soc. 1999, 121, 5437–5443.

[16]

Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 2006, 440, 297–302.

[17]

Dey, S.; Fan, C. H.; Gothelf, K. V.; Li, J.; Lin, C. X.; Liu, L. F.; Liu, N.; Nijenhuis, M. A. D.; Saccà, B.; Simmel, F. C. et al. DNA origami. Nat. Rev. Methods Primers 2021, 1, 13.

[18]

Ke, Y. G.; Ong, L. L.; Shih, W. M.; Yin, P. Three-dimensional structures self-assembled from DNA bricks. Science 2012, 338, 1177–1183.

[19]

Ke, Y. G.; Ong, L. L.; Sun, W.; Song, J.; Dong, M. D.; Shih, W. M.; Yin, P. DNA brick crystals with prescribed depths. Nat. Chem. 2014, 6, 994–1002.

[20]

Chen, Y. H.; Yang, C. Y.; Zhu, Z.; Sun, W. Suppressing high-dimensional crystallographic defects for ultra-scaled DNA arrays. Nat. Commun. 2022, 13, 2707.

[21]

Zhao, M. Y.; Chen, Y. H.; Wang, K. X.; Zhang, Z. X.; Streit, J. K.; Fagan, J. A.; Tang, J. S.; Zheng, M.; Yang, C. Y.; Zhu, Z. et al. DNA-directed nanofabrication of high-performance carbon nanotube field-effect transistors. Science 2020, 368, 878–881.

[22]

Mathieu, F.; Liao, S. P.; Kopatsch, J.; Wang, T.; Mao, C. D.; Seeman, N. C. Six-helix bundles designed from DNA. Nano Lett. 2005, 5, 661–665.

[23]

Han, D. R.; Pal, S.; Nangreave, J.; Deng, Z. T.; Liu, Y.; Yan, H. DNA origami with complex curvatures in three-dimensional space. Science 2011, 332, 342–346.

[24]

Han, D. R.; Pal, S.; Liu, Y.; Yan, H. Folding and cutting DNA into reconfigurable topological nanostructures. Nat. Nanotechnol. 2010, 5, 712–717.

[25]

Tikhomirov, G.; Petersen, P.; Qian, L. L. Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns. Nature 2017, 552, 67–71.

[26]

Mao, C. D.; Sun, W. Q.; Shen, Z. Y.; Seeman, N. C. A nanomechanical device based on the B-Z transition of DNA. Nature 1999, 397, 144–146.

[27]

Jiang, Q.; Song, C.; Nangreave, J.; Liu, X. W.; Lin, L.; Qiu, D. L.; Wang, Z. G.; Zou, G. Z.; Liang, X. J.; Yan, H. et al. DNA origami as a carrier for circumvention of drug resistance. J. Am. Chem. Soc. 2012, 134, 13396–13403.

[28]

Mao, C. D.; Labean, T. H.; Reif, J. H.; Seeman, N. C. Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 2000, 407, 493–496.

[29]

Lv, H.; Xie, N. L.; Li, M. Q.; Dong, M. K.; Sun, C. Y.; Zhang, Q.; Zhao, L.; Li, J.; Zuo, X. L.; Chen, H. B. et al. DNA-based programmable gate arrays for general-purpose DNA computing. Nature 2023, 622, 292–300.

[30]

Li, L.; Yin, J.; Ma, W.; Tang, L. G.; Zou, J. H.; Yang, L. Z.; Du, T.; Zhao, Y.; Wang, L. H.; Yang, Z. et al. A DNA origami device spatially controls CD95 signalling to induce immune tolerance in rheumatoid arthritis. Nat. Mater. 2024, 23, 993–1001.

[31]

Hu, Y. S.; Rogers, J.; Duan, Y. X.; Velusamy, A.; Narum, S.; Al Abdullatif, S.; Salaita, K. Quantifying T cell receptor mechanics at membrane junctions using DNA origami tension sensors. Nat. Nanotechnol. 2024, 19, 1674–1685.

[32]

Liu, S. L.; Jiang, Q.; Zhao, X.; Zhao, R. F.; Wang, Y. N.; Wang, Y. M.; Liu, J. B.; Shang, Y. X.; Zhao, S.; Wu, T. T. et al. A DNA nanodevice-based vaccine for cancer immunotherapy. Nat. Mater. 2021, 20, 421–430.

[33]

Liu, X. G.; Zhang, F.; Jing, X. X.; Pan, M. C.; Liu, P.; Li, W.; Zhu, B. W.; Li, J.; Chen, H.; Wang, L. H. et al. Complex silica composite nanomaterials templated with DNA origami. Nature 2018, 559, 593–598.

[34]

Zhou, W. J.; Lim, Y.; Lin, H. X.; Lee, S.; Li, Y. W.; Huang, Z. Y.; Du, J. S.; Lee, B.; Wang, S. Z.; Sánchez-Iglesias, A. et al. Colloidal quasicrystals engineered with DNA. Nat. Mater. 2024, 23, 424–428.

[35]

Schnitzbauer, J.; Strauss, M. T.; Schlichthaerle, T.; Schueder, F.; Jungmann, R. Super-resolution microscopy with DNA-PAINT. Nat. Protoc. 2017, 12, 1198–1228.

[36]

Garibotti, A. V.; Knudsen, S. M.; Ellington, A. D.; Seeman, N. C. Functional DNAzymes organized into two-dimensional arrays. Nano Lett. 2006, 6, 1505–1507.

[37]

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, 1882–1884.

[38]

Hong, F.; Jiang, S. X.; 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, 14670–14676.

[39]

Zhang, T. Q.; Wei, B. Design of orthogonal DNA sticky-end cohesion based on configuration-specific molecular recognition. J. Am. Chem. Soc. 2022, 144, 18479–18484.

[40]

Zheng, J. P.; Birktoft, J. J.; Chen, Y.; Wang, T.; Sha, R. J.; Constantinou, P. E.; Ginell, S. L.; Mao, C. D.; Seeman, N. C. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 2009, 461, 74–77.

[41]

Paukstelis, P. J.; Nowakowski, J.; Birktoft, J. J.; Seeman, N. C. Crystal structure of a continuous three-dimensional DNA lattice. Chem. Biol. 2004, 11, 1119–1126.

[42]

Zhang, T.; Hartl, C.; Frank, K.; Heuer-jungemann, A.; Fischer, S.; Nickels, P. C.; Nickel, B.; Liedl, T. 3D DNA origami crystals. Adv. Mater. 2018, 30, 1800273.

[43]

Walczak, M.; Brady, R. A.; Leathers, A.; Kotar, J.; Di Michele, L. Influence of hydrophobic moieties on the crystallization of amphiphilic DNA nanostructures. J. Chem. Phys. 2023, 158, 084501.

[44]

Brady, R. A.; Brooks, N. J.; Foderà, V.; Cicuta, P.; Di Michele, L. Amphiphilic-DNA platform for the design of crystalline frameworks with programmable structure and functionality. J. Am. Chem. Soc. 2018, 140, 15384–15392.

[45]

Mcneil, R. Jr.; Paukstelis, P. J. JrCore-shell and layer-by-layer assembly of 3D DNA crystals. Adv. Mater. 2017, 29, 1701019.

[46]

Zhang, D. N.; Paukstelis, P. J. Enhancing DNA crystal durability through chemical crosslinking. Chembiochem 2016, 17, 1163–1170.

[47]

Muser, S. E.; Paukstelis, P. J. Three-dimensional DNA crystals with pH-responsive noncanonical junctions. J. Am. Chem. Soc. 2012, 134, 12557–12564.

[48]

Janowski, J.; Pham, V. A. B.; Vecchioni, S.; Woloszyn, K.; Lu, B.; Zou, Y. J.; Erkalo, B.; Perren, L.; Rueb, J.; Madnick, J. et al. Engineering tertiary chirality in helical biopolymers. Proc. Natl. Acad. Sci. USA 2024, 121, e2321992121.

[49]

Woloszyn, K.; Vecchioni, S.; Ohayon, Y. P.; Lu, B.; Ma, Y. L.; Huang, Q. Y.; Zhu, E.; Chernovolenko, D.; Markus, T.; Jonoska, N. Augmented DNA nanoarchitectures: A structural library of 3D self-assembling tensegrity triangle variants. Adv. Mater. 2022, 34, 2206876.

[50]

Vecchioni, S.; Lu, B.; Janowski, J.; Woloszyn, K.; Jonoska, N.; Seeman, N. C.; Mao, C. D.; Ohayon, Y. P.; Sha, R. J. The rule of thirds: Controlling junction chirality and polarity in 3D DNA tiles. Small 2023, 19, 2206511.

[51]

Simmons, C. R.; Macculloch, T.; Krepl, M.; Matthies, M.; Buchberger, A.; Crawford, I.; Šponer, J.; Šulc, P.; Stephanopoulos, N.; Yan, H. The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly. Nat. Commun. 2022, 13, 3112.

[52]

Haider, S.; Li, P. F.; Khiali, S.; Munnur, D.; Ramanathan, A.; Parkinson, G. N. Holliday junctions formed from human telomeric DNA. J. Am. Chem. Soc. 2018, 140, 15366–15374.

[53]

Simmons, C. R.; Zhang, F.; Birktoft, J. J.; Qi, X. D.; Han, D. R.; Liu, Y.; Sha, R. J.; Abdallah, H. O.; Hernandez, C.; Ohayon, Y. P. et al. Construction and structure determination of a three-dimensional DNA crystal. J. Am. Chem. Soc. 2016, 138, 10047–10054.

[54]

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, 11254–11260.

[55]

Zhang, F.; Simmons, C. R.; Gates, J.; Liu, Y.; Yan, H. Self-assembly of a 3D DNA crystal structure with rationally designed six-fold symmetry. Angew. Chem., Int. Ed. 2018, 57, 12504–12507.

[56]

Wang, T. Q.; Bai, T. X.; Tan, Z. Y.; Ohayon, Y. P.; Sha, R. J.; Vecchioni, S.; Seeman, N. C.; Wei, B. Mesojunction-based design paradigm of structural DNA nanotechnology. J. Am. Chem. Soc. 2023, 145, 2455–2460.

[57]

Lu, B.; Vecchioni, S.; Ohayon, Y. P.; Woloszyn, K.; Markus, T.; Mao, C. D.; Seeman, N. C.; Canary, J. W.; Sha, R. J. Highly symmetric, self-assembling 3D DNA crystals with cubic and trigonal lattices. Small 2023, 19, 2205830.

[58]

Yao, G. B.; Zhang, F.; Wang, F.; Peng, T. H.; Liu, H.; Poppleton, E.; Šulc, P.; Jiang, S. X.; Liu, L.; Gong, C. et al. Meta-DNA structures. Nat. Chem. 2020, 12, 1067–1075.

[59]

Qi, M. Y.; Ma, W. H.; Xu, Q.; Wang, F.; Song, P.; Jia, S. S.; Zuo, X. L.; Li, M. Q.; Yao, G. B.; Fan, C. H. Meta-DNA strand displacement for sub-micron-scale autonomous reconfiguration. J. Am. Chem. Soc. 2023, 145, 16812–16820.

[60]

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, 414–418.

[61]

Wang, Y.; Dai, L. Z.; Ding, Z. Y.; Ji, M.; Liu, J. L.; Xing, H.; Liu, X. G.; Ke, Y. G.; Fan, C. H.; Wang, P. et al. DNA origami single crystals with Wulff shapes. Nat. Commun. 2021, 12, 3011.

[62]

Tian, Y.; Lhermitte, J. R.; Bai, L.; Vo, T.; Xin, H. L.; Li, H. L.; Li, R. P.; Fukuto, M.; Yager, K. G.; Kahn, J. S. et al. Ordered three-dimensional nanomaterials using DNA-prescribed and valence-controlled material voxels. Nat. Mater. 2020, 19, 789–796.

[63]

Tian, Y.; Zhang, Y. G.; Wang, T.; Xin, H. L.; Li, H. L.; Gang, O. Lattice engineering through nanoparticle-DNA frameworks. Nat. Mater. 2016, 15, 654–661.

[64]

Xie, X. L.; Ji, M.; Yan, X. H.; Yu, Y. F.; Wang, Y.; Ma, N. N.; Xing, H.; Tian, Y. Layer-controllable “2.5D” DNA origami crystals synthesized by a hierarchical assembly strategy. Angew. Chem., Int. Ed. 2024, 63, e202402312.

[65]

Brady, R. A.; Brooks, N. J.; Cicuta, P.; Di Michele, L. Crystallization of amphiphilic DNA C-stars. Nano Lett. 2017, 17, 3276–3281.

[66]

Ji, M.; Liu, J. L.; Dai, L. Z.; Wang, L.; Tian, Y. Programmable cocrystallization of DNA origami shapes. J. Am. Chem. Soc. 2020, 142, 21336–21343.

[67]

Stiakakis, E.; Jung, N.; Adžić, N.; Balandin, T.; Kentzinger, E.; Rücker, U.; Biehl, R.; Dhont, J. K. G.; Jonas, U.; Likos, C. N. Self assembling cluster crystals from DNA based dendritic nanostructures. Nat. Commun. 2021, 12, 7167.

[68]

Heuer-Jungemann, A.; Liedl, T. From DNA tiles to functional DNA materials. Trends Chem. 2019, 1, 799–814.

[69]

Lu, B.; Vecchioni, S.; Ohayon, Y. P.; Canary, J. W.; Sha, R. J. The wending rhombus: Self-assembling 3D DNA crystals. Biophys. J. 2022, 121, 4759–4765.

[70]

Kong, H. T.; Sun, B.; Yu, F.; Wang, Q. S.; Xia, K.; Jiang, D. W. Exploring the potential of three-dimensional DNA crystals in nanotechnology: Design, optimization, and applications. Adv. Sci. 2023, 10, 2302021.

[71]

Paukstelis, P. J.; Seeman, N. C. 3D DNA crystals and nanotechnology. Crystals 2016, 6, 97.

[72]

Sha, R. J.; Birktoft, J. J.; Nguyen, N.; Chandrasekaran, A. R.; Zheng, J. P.; Zhao, X. S.; Mao, C. D.; Seeman, N. C. Self-assembled DNA crystals: The impact on resolution of 5'-phosphates and the DNA source. Nano Lett. 2013, 13, 793–797.

[73]

Ohayon, Y. P.; Hernandez, C.; Chandrasekaran, A. R.; Wang, X. Y.; Abdallah, H. O.; Jong, M. A.; Mohsen, M. G.; Sha, R. J.; Birktoft, J. J.; Lukeman, P. S. et al. Designing higher resolution self-assembled 3D DNA crystals via strand terminus modifications. ACS Nano 2019, 13, 7957–7965.

[74]

Stahl, E.; Praetorius, F.; De Oliveira Mann, C. C.; Hopfner, K. P.; Dietz, H. Impact of heterogeneity and lattice bond strength on DNA triangle crystal Growth. ACS Nano 2016, 10, 9156–9164.

[75]

Zhao, J. M.; Zhao, Y.; Li, Z.; Wang, Y.; Sha, R. J.; Seeman, N. C.; Mao, C. D. Modulating self-assembly of DNA crystals with rationally designed agents. Angew. Chem., Int. Ed. 2018, 57, 16529–16532.

[76]

Zhao, J. M.; Zhang, C. Z.; Lu, B.; Sha, R. J.; Noinaj, N.; Mao, C. D. Divergence and convergence: Complexity emerges in crystal engineering from an 8-mer DNA. J. Am. Chem. Soc. 2023, 145, 10475–10479.

[77]

Jing, X. X.; Zhang, F.; Pan, M. C.; Dai, X. P.; Li, J.; Wang, L. H.; Liu, X. G.; Yan, H.; Fan, C. H. Solidifying framework nucleic acids with silica. Nat. Protoc. 2019, 14, 2416–2436.

[78]

Kulikowski, J.; Wang, S.; Aitken, Z.; Grimm, J.; Gao, B. S.; Wang, M. M.; Doan, D.; Lee, A. C.; Shen, L. Y.; Huang, W. et al. DNA-silica nanolattices as mechanical metamaterials. Matter 2024, 7, 2144–2160.

[79]

Michelson, A.; Flanagan, T. J.; Lee, S. W.; Gang, O. High-strength, lightweight nano-architected silica. Cell Rep. Phys. Sci. 2023, 4, 101475.

[80]

Zhao, J.; Chandrasekaran, A. R.; Li, Q.; Li, X.; Sha, R.; Seeman, N. C.; Mao, C. Post-assembly stabilization of rationally designed DNA crystals. Angew. Chem., Int. Ed. 2015, 54, 9936–9939.

[81]

Zhao, Y.; Chandrasekaran, A. R.; Rusling, D. A.; Woloszyn, K.; Hao, Y. D.; Hernandez, C.; Vecchioni, S.; Ohayon, Y. P.; Mao, C. D.; Seeman, N. C. et al. The formation and displacement of ordered DNA triplexes in self-assembled three-dimensional DNA crystals. J. Am. Chem. Soc. 2023, 145, 3599–3605.

[82]

Hao, Y. D.; Kristiansen, M.; Sha, R. J.; Birktoft, J. J.; Hernandez, C.; Mao, C. D.; Seeman, N. C. A device that operates within a self-assembled 3D DNA crystal. Nat. Chem. 2017, 9, 824–827.

[83]

Li, Z.; Liu, L. F.; Zheng, M. X.; Zhao, J. M.; Seeman, N. C.; Mao, C. D. Making engineered 3D DNA crystals robust. J. Am. Chem. Soc. 2019, 141, 15850–15855.

[84]

Zheng, M. X.; Li, Z.; Zhang, C. Z.; Seeman, N. C.; Mao, C. D. Powering ≈50 µm motion by a molecular event in DNA crystals. Adv. Mater. 2022, 34, 2200441.

[85]

Lu, B.; Vecchioni, S.; Ohayon, Y. P.; Sha, R. J.; Woloszyn, K.; Yang, B.; Mao, C. D.; Seeman, N. C. 3D hexagonal arrangement of DNA tensegrity triangles. ACS Nano 2021, 15, 16788–16793.

[86]

Conn, F. W.; Jong, M. A.; Tan, A.; Tseng, R.; Park, E.; Ohayon, Y. P.; Sha, R. J.; Mao, C. D.; Seeman, N. C. Time lapse microscopy of temperature control during self-assembly of 3D DNA crystals. J. Cryst. Growth 2017, 476, 1–5.

[87]

Li, Z.; Zheng, M. X.; Liu, L. F.; Seeman, N. C.; Mao, C. D. 5′-phosphorylation strengthens sticky-end cohesions. J. Am. Chem. Soc. 2021, 143, 14987–14991.

[88]

Chen, J. L.; Dai, Z. Z.; Lv, H.; Jin, Z. C.; Tang, Y. Q.; Xie, X. D.; Shi, J. Y.; Wang, F.; Li, Q.; Liu, X. G. et al. Programming crystallization kinetics of self-assembled DNA crystals with 5-methylcytosine modification. Proc. Natl. Acad. Sci. USA 2024, 121, e2312596121.

[89]

Yan, X. H.; Wang, Y.; Ma, N. N.; Yu, Y. F.; Dai, L. Z.; Tian, Y. Dynamically reconfigurable DNA origami crystals driven by a designated path diagram. J. Am. Chem. Soc. 2023, 145, 3978–3986.

[90]

Dai, L. Z.; Hu, X. X.; Ji, M.; Ma, N. N.; Xing, H.; Zhu, J. J.; Min, Q. H.; Tian, Y. Programming the morphology of DNA origami crystals by magnesium ion strength. Proc. Natl. Acad. Sci. USA 2023, 120, e2302142120.

[91]

Melinger, J. S.; Sha, R. J.; Mao, C. D.; Seeman, N. C.; Ancona, M. G. Fluorescence and energy transfer in dye-labeled DNA crystals. J. Phys. Chem. B 2016, 120, 12287–12292.

[92]

Geng, C.; Paukstelis, P. J. DNA crystals as vehicles for biocatalysis. J. Am. Chem. Soc. 2014, 136, 7817–7820.

[93]

Zhang, C. Z.; Zhao, J. M.; Lu, B.; Seeman, N. C.; Sha, R. J.; Noinaj, N.; Mao, C. D. Engineering DNA crystals toward studying DNA-guest molecule interactions. J. Am. Chem. Soc. 2023, 145, 4853–4859.

[94]

Simmons, C. R.; Buchberger, A.; Henry, S. J. W.; Novacek, A.; Fahmi, N. E.; Macculloch, T.; Stephanopoulos, N.; Yan, H. Site-specific arrangement and structure determination of minor groove binding molecules in self-assembled three-dimensional DNA crystals. J. Am. Chem. Soc. 2023, 145, 26075–26085.

[95]

Wang, X.; Sha, R. J.; Kristiansen, M.; Hernandez, C.; Hao, Y. D.; Mao, C. D.; Canary, J. W.; Seeman, N. C. An organic semiconductor organized into 3D DNA arrays by “bottom-up” rational design. Angew. Chem., Int. Ed. 2017, 56, 6445–6448.

[96]

Wang, X.; Deshmukh, R.; Sha, R. J.; Birktoft, J. J.; Menon, V.; Seeman, N. C.; Canary, J. W. Orienting an organic semiconductor into DNA 3D arrays by covalent bonds. Angew. Chem., Int. Ed. 2022, 61, e202115155.

[97]

Posnjak, G.; Yin, X.; Butler, P.; Bienek, O.; Dass, M.; Lee, S.; Sharp, I. D.; Liedl, T. Diamond-lattice photonic crystals assembled from DNA origami. Science 2024, 384, 781–785.

[98]

Liu, H.; Matthies, M.; Russo, J.; Rovigatti, L.; Narayanan, R. P.; Diep, T.; Mckeen, D.; Gang, O.; Stephanopoulos, N.; Sciortino, F. et al. Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments. Science 2024, 384, 776–781.

[99]

Park, S. H.; Park, H.; Nam, J. M.; Ke, Y. G.; Liedl, T.; Tian, Y.; Lee, S. DNA origami-designed 3D phononic crystals. Nanophotonics 2023, 12, 2611–2621.

[100]

Castells-Graells, R.; Meador, K.; Arbing, M. A.; Sawaya, M. R.; Gee, M.; Cascio, D.; Gleave, E.; Debreczeni, J. É.; Breed, J.; Leopold, K. et al. Cryo-EM structure determination of small therapeutic protein targets at 3 Å-resolution using a rigid imaging scaffold. Proc. Natl. Acad. Sci. USA 2023, 120, e2305494120.

[101]

Herzik, M. A. Jr. ; Wu, M. Y.; Lander, G. C. High-resolution structure determination of sub-100 kDa complexes using conventional cryo-EM. Nat. Commun. 2019, 10, 1032.

[102]

Dai, X. P.; Chen, X. L.; Jing, X. X.; Zhang, Y. N.; Pan, M. C.; Li, M. Q.; Li, Q.; Liu, P.; Fan, C. H.; Liu, X. G. DNA origami-encoded integration of heterostructures. Angew. Chem., Int. Ed. 2022, 61, e202114190.

[103]

Shang, Y. X.; Li, N.; Liu, S. B.; Wang, L.; Wang, Z. G.; Zhang, Z.; Ding, B. Q. Site-specific synthesis of silica nanostructures on DNA origami templates. Adv. Mater. 2020, 32, e2000294.

[104]

Canossa, S.; Ji, Z.; Gropp, C.; Rong, Z. C.; Ploetz, E.; Wuttke, S.; Yaghi, O. M. System of sequences in multivariate reticular structures. Nat. Rev. Mater. 2022, 8, 331–340.

[105]

Zang, S. H.; Hauser, A. W.; Paul, S.; Hocky, G. M.; Sacanna, S. Enabling three-dimensional real-space analysis of ionic colloidal crystallization. Nat. Mater. 2024, 23, 1131–1137.

[106]

Wang, D.; Cui, J. H.; Gan, M. Z.; Xue, Z. H.; Wang, J.; Liu, P. F.; Hu, Y.; Pardo, Y.; Hamada, S.; Yang, D. Y. et al. Transformation of biomass DNA into biodegradable materials from gels to plastics for reducing petrochemical consumption. J. Am. Chem. Soc. 2020, 142, 10114–10124.

[107]

Han, J. P.; Cui, Y. C.; Gu, Z.; Yang, D. Y. Controllable assembly/disassembly of polyphenol-DNA nanocomplex for cascade-responsive drug release in cancer cells. Biomaterials 2021, 273, 120846.

[108]

Han, J. P.; Guo, Y. F.; Wang, H.; Zhang, K. Y.; Yang, D. Y. Sustainable bioplastic made from biomass DNA and ionomers. J. Am. Chem. Soc. 2021, 143, 19486–19497.

[109]

Arnon, Z. A.; Piperno, S.; Redeker, D. C.; Randall, E.; Tkachenko, A. V.; Shpaisman, H.; Gang, O. Acoustically shaped DNA-programmable materials. Nat. Commun. 2024, 15, 6875.

[110]

Hensley, A.; Jacobs, W. M.; Rogers, W. B. Self-assembly of photonic crystals by controlling the nucleation and growth of DNA-coated colloids. Proc. Natl. Acad. Sci. USA 2022, 119, e2114050118.

[111]

Kretzmann, J. A.; Liedl, A.; Monferrer, A.; Mykhailiuk, V.; Beerkens, S.; Dietz, H. Gene-encoding DNA origami for mammalian cell expression. Nat. Commun. 2023, 14, 1017.

Nano Research
Cite this article:
Li Z, Li M, Liu X, et al. Design, regulation, and functionalization of self-assembled DNA crystals. Nano Research, 2025, https://doi.org/10.26599/NR.2025.94907250

570

Views

154

Downloads

0

Crossref

0

Web of Science

0

Scopus

0

CSCD

Altmetrics

Received: 19 September 2024
Revised: 28 November 2024
Accepted: 11 January 2025
Published: 14 March 2025
© The Author(s) 2025. Published by Tsinghua University Press.

This is an open access article under the terms of the Creative Commons Attribution 4.0 International License (CC BY 4.0, https://creativecommons.org/licenses/by/4.0/).

Return