Block Copolymer Aided Controllable Design of Colloidal Molecules by DNA-programmable Assembly

Xian-Deng Qiu; Hao Tang; Rong Wang

doi:10.1007/s10118-025-3424-5

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Block Copolymer Aided Controllable Design of Colloidal Molecules by DNA-programmable Assembly

RESEARCH ARTICLE | Updated：2025-12-03

- Block Copolymer Aided Controllable Design of Colloidal Molecules by DNA-programmable Assembly
- Chinese Journal of Polymer Science Vol. 43, Issue 12, Pages: 2213-2221(2025)
- Affiliations：
  
  Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Author bio：
  
  wangrong@nju.edu.cn
- Funds：
- DOI：10.1007/s10118-025-3424-5
  CLC：
- Received：25 June 2025，
  
  Accepted：02 August 2025，
  
  Online First：03 November 2025，
  
  Published：15 December 2025
- Accepted：
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Qiu, X. D.; Tang, H.; Wang, R. Block copolymer aided controllable design of colloidal molecules by DNA-programmable assembly. Chinese J. Polym. Sci. 2025, 43, 2213–2221

Xian-Deng Qiu, Hao Tang, Rong Wang. Block Copolymer Aided Controllable Design of Colloidal Molecules by DNA-programmable Assembly[J]. Chinese Journal of Polymer Science, 2025, 43(12): 2213-2221.
Qiu, X. D.; Tang, H.; Wang, R. Block copolymer aided controllable design of colloidal molecules by DNA-programmable assembly. Chinese J. Polym. Sci. 2025, 43, 2213–2221 DOI： 10.1007/s10118-025-3424-5.

Xian-Deng Qiu, Hao Tang, Rong Wang. Block Copolymer Aided Controllable Design of Colloidal Molecules by DNA-programmable Assembly[J]. Chinese Journal of Polymer Science, 2025, 43(12): 2213-2221. DOI： 10.1007/s10118-025-3424-5.

摘要

The synergistic strategy that integrates molecular dynamics simulations and interpretable machine learning was used to program the assembly of block-copolymer and DNA-functionalized nanoparticles into stable colloidal molecules

achieving precise

high-yield assembly. SHAP analysis was used to identify key structural descriptors and clarifies mechanisms governing ordered coassembly.

Abstract

Colloidal molecules exhibit unique electronic

optical

and magnetic properties owing to their molecular-like configurations and coupling effects

making them promising building blocks for multifunctional materials. However

achieving precise and controllable assembly of isotropic nanoparticles with high yields remains a great challenge. In this study

we present a synergistic strategy that integrates molecular dynamics simulations with interpretable machine learning to develop a programmable assembly system based on block copolymers and DNA-functionalized nanoparticles. Our simulation results reveal that block copolymer modification facilitates stepwise control over surface phase separation and nanoparticle coassembly

thereby enhancing structural stability and efficiently suppressing disordered aggregation of atom-like nanoparticles. Furthermore

we demonstrated that precise

controllable

and programmable assembly of colloidal molecules can be achieved through rational DNA sequence design. SHapley Additive exPlanations (SHAP) analysis identified key structural descriptors that govern assembly outcomes and elucidated their underlying mechanistic roles. This work not only deepens the understanding of colloidal molecule assembly mechanisms but also lays a theoretical foundation for the rational design of functional colloidal architectures in nanomaterial science.

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Keywords

references

Wu, X.; Hao, C.; Kumar, J.; Kuang, H.; Kotov, N. A.; Liz-Marzán, L. M.; Xu, C. Environmentally responsive plasmonic nanoassemblies for biosensing. Chem. Soc. Rev. 2018 , 47 , 4677−4696..

Yi, C.; Liu, H.; Zhang, S.; Yang, Y.; Zhang, Y.; Lu, Z.; Kumacheva, E.; Nie, Z. Self-limiting directional nanoparticle bonding governed by reaction stoichiometry. Science 2020 , 369 , 1369−1374..

Rouet, P. E.; Chomette, C.; Duguet, E.; Ravaine, S. Colloidal molecules from valence-endowed nanoparticles by covalent chemistry. Angew. Chem., Int. Ed. 2018 , 57 , 15754−15757..

Chen, X.; Ding, L.; Wang, Y.; Gao, Z.; Li, J.; Liu, X.; Wang, L.; Zhu, Y.; Fan, C.; Jia, S.; Yao, G. Welded gold nanoparticle assemblies defined plasmonic coupling. Nano Lett. 2024 , 24 , 8956−8963..

Fan, J. A.; Wu, C.; Bao, K.; Bao, J.; Bardhan, R.; Halas, N. J.; Manoharan, V. N.; Nordlander, P.; Shvets, G.; Capasso, F. Self-assembled plasmonic nanoparticle clusters. Science 2010 , 328 , 1135−1138..

Lin, M.-H.; Chen, H.-Y.; Gwo, S. Layer-by-layer assembly of three-dimensional colloidal supercrystals with tunable plasmonic properties. J. Am. Chem. Soc. 2010 , 132 , 11259−11263..

Urban, A. S.; Shen, X.;Wang, Y.; Large, N.; Wang, H.; Knight, M. W.; Nordlander, P.; Chen, H.; Halas, N. J. Three-dimensional plasmonic nanoclusters. Nano Lett. 2013 , 13 , 4399−4403..

Zhao, Y.; Shang, L.; Cheng, Y.; Gu, Z. Spherical colloidal photonic crystals. Acc. Chem. Res. 2014 , 47 , 3632−3642..

Fang, W.; Jia, S.; Chao, J.; Wang, L.; Duan, X.; Liu, H.; Li, Q.; Zuo, X.; Wang, L.; Wang, L.; Liu, N.; Fan, C. Quantizing single-molecule surface-enhanced raman scattering with DNA origami metamolecules. Sci. Adv. 2019 , 5 , eaau4506..

Li, W.; Palis, H.; Mérindol, R.; Majimel, J.; Ravaine, S.; Duguet, E. Colloidal molecules and patchy particles: Complementary concepts, synthesis and self-assembly. Chem. Soc. Rev. 2020 , 49 , 1955−1976..

Hueckel, T.; Hocky, G. M.; Sacanna, S. Total synthesis of colloidal matter. Nat. Rev. Mater. 2021 , 6 , 1053−1069..

Wang, Y.; Wang, Y.; Breed, D. R.; Manoharan, V. N.; Feng, L.; Hollingsworth, A. D.; Weck, M.; Pine, D. J. Colloids with valence and specific directional bonding. Nature 2012 , 491 , 51−55..

Dong, W.; Zhang, Y.; Yi, C.; Chang, J. J.; Ye, S.; Nie, Z. Halogen bonding-driven reversible self-assembly of plasmonic colloidal molecules. ACS Nano 2023 , 17 , 3047−3054..

Chen, G.; Gibson, K. J.; Liu, D.; Rees, H. C.; Lee, J.-H.; Xia, W.; Lin, R.; Xin, H. L.; Gang, O.; Weizmann, Y. Regioselective surface encoding of nanoparticles for programmable self-assembly. Nat. Mater. 2019 , 18 , 169−174..

Groschel, A. H.; Walther, A.; Lobling, T. I.; Schacher, F. H.; Schmalz, H.; Muller, A. H. Guided hierarchical coassembly of soft patchy nanoparticles. Nature 2013 , 503 , 247−251..

Zhang, Y.; Tang, H.; Wang, R. Controlling the two components modified on nanoparticles to construct nanomaterials. Soft Matter 2022 , 18 , 8213−8222..

Elacqua, E.; Zheng, X.; Shillingford, C.; L iu, M.; Weck, M. Molecular recognition in the colloidal world. Acc. Chem. Res. 2017 , 50 , 2756−2766..

Cui, Y.; Wang, J.; Liang, J.; Qiu, H. Molecular engineering of colloidal atoms. Small 2023 , 19 , 2207609..

Huang, Z.; Gong, J.; Nie, Z. Symmetry-breaking synthesis of multicomponentnanoparticles. Acc. Chem. Res. 2019 , 52 , 1125−1133..

Xiao, R.; Jia, J.; Wang, R.; Feng, Y.; Chen, H. Strong ligand control for noble metal nanostructures. Acc. Chem. Res. 2023 , 56 , 1539−1552..

Choueiri, R. M.; Galati, E.; Therien-Aubin, H.; Klinkova, A.; Larin, E. M.; Querejeta-Fernandez, A.; Han, L.; Xin, H. L.; Gang, O.; Zhulina, E. B.; Rubinstein, M.; Kumacheva, E. Surface patterning of nanoparticles with polymer patches. Nature 2016 , 538 , 79−83..

Rossner, C.; Zhulina, E. B.; Kumacheva, E. Staged surface patterning and self-assembly of nanoparticles functionalized with end-grafted block copolymer ligands. Angew. Chem., Int. Ed. 2019 , 58 , 9269−9274 ..

Duan, H.; Luo, Q.; Wei, Z.; Lin, Y.; He, J. Symmetry-broken patches on gold nanoparticles through deficient ligand exchange. ACS Macro Lett. 2021 , 10 , 786−790..

Manoharan, V. N.; Elsesser, M. T.; Pine, D. J. Dense packing and symmetry in small clusters of microspheres. Science 2003 , 301 , 483−487..

Kraft, D. J.; Vlug, W. S.; van Kats, C. M.; van Blaaderen, A.; Imhof, A.; Kegel, W. K. Self-assembly of colloids with liquid protrusions. J. Am. Chem. Soc. 2009 , 131 , 1182−1186..

Li, Z. W.; Sun, Y.W.; Wang, Y. H.; Zhu, Y. L.; Lu, Z. Y.; Sun, Z. Y. Softness-enhanced self-assembly of pyrochlore- and perovskite-like colloidal photonic crystals from triblock janus particles. J. Phys. Chem. Lett. 2021 , 12 , 7159−7165..

Tian, Y.; Wang, T.; Liu, W.; Xin, H. L.; Li, H.; Ke, Y.; Shih, W. M.; Gang, O. Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames. Nat. Nanotechnol. 2015 , 10 , 637−644..

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 , 789−796..

Martynenko, I. V.; Erber, E.; Ruider, V.; Dass, M.; Posnjak, G.; Yin, X.; Altpeter, P.; Liedl, T. Site-directed placement of three-dimensional DNA origami. Nat. Nanotechnol. 2023 , 18 , 1456−1462..

Edwardson, T. G. W.; Lau, K. L.; Bousmail, D.; Serpell, C. J.; Sleiman, H. F. Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles. Nat. Chem. 2016 , 8 , 162−170..

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

Zhu, G.; Xu, Z.; Yang, Y.; Dai, X.; Yan, L. T. Hierarchical crystals formed from DNA-functionalized Janus nanoparticles. ACS Nano 2018 , 12 , 9467−9475..

Zhu, G.; Gao, L.; Wang, Y.; Tlusty, T.; Yan, L. T. Programmable potentials choreograph defects in a colloidal crystal shell. Phys. Rev. Lett. 2024 , 132 , 048201..

Zhou, X.; Yao, D.; Hua, W.; Huang, N.; Chen, X.; Li, L.; He, M.; Zhang, Y.; Guo, Y.; Xiao, S.; Bian, F.; Liang, H. Programming colloidal bonding using DNA strand-displacement circuitry. Proc. Natl. Acad. Sci. U.S.A 2020 , 117 , 5617−5623..

Mirkin, C. A.; Letsinger, R. L.; Mucic, R. C.; Storhoff, J. J. A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 1996 , 382 , 607−609..

Macfarlane, R. J.; Lee, B.; Jones, M. R.; Harris, N.; Schatz, G. C.; Mirkin, C. A. Nanoparticle superlattice engineering with DNA. Science 2011 , 334 , 204−208..

Wang, S.; Lee, S.; Du, J. S.; Partridge, B. E.; Cheng, H. F.; Zhou, W.; Dravid, V. P.; Lee, B.; Glotzer, S. C.; Mirkin, C. A. The emergence of valency in colloidal crys tals through electron equivalents. Nat. Mater. 2022 , 21 , 580−587..

Liang, L.; Wu, L.; Zheng, P.; Ding, T.; Ray, K.; Barman, I. DNA-patched nanoparticles for the self-assembly of colloidal metamaterials. JACS Au 2023 , 3 , 1176−1184..

Ding, L.; Chen, X.; Ma, W.; Li, J.; Liu, X.; Fan, C.; Yao, G. DNA-mediated regioselective encoding of colloids for programmableself-assembly. Chem. Soc. Rev. 2023 , 52 , 5684−5705..

Rogers, W. B.; Shih, W. M.; Manoharan, V. N. Using DNA to program the self-assembly of colloidal nanoparticles and microparticles. Nat. Rev. Mater. 2016 , 1 , 16008..

Kyriazi, M.-E.; Giust, D.; El-Sagheer, A. H.; Lackie, P. M.; Muskens, O. L.; Brown, T.; Kanaras, A. G. Multiplexed mRNA sensing and combinatorial-targeted drug delivery using DNA-gold nanoparticle dimers. ACS Nano 2018 , 12 , 3333−3340..

Qiu, X.; Tang, H.; Zhang, L.; Wang, R. Directional self-assembly of programmable atom-like nanoparticles into colloidal molecules. J. Phys. Chem. Lett. 2025 , 16 , 3141−3148..

Knorowski, C.; Burleigh, S.; Travesset, A. Dynamics and statics of DNA-programmable nanoparticle self-assembly and crystallization. Phys. Rev. Lett. 2011 , 106 , 215501..

Yu, Q.; Zhang, X.; Hu, Y.; Zhang, Z.; Wang, R. Dynamic properties of DNA-programmable nanoparticle crystallization. ACS Nano 2016 , 10 , 7485−7492..

Yu, Q.; Hu, J.; Hu, Y.; Wang, R. Significance of DNA bond strength in programmable nanoparticle thermodynamics and dynamics. Soft Matter 2018 , 14 , 2665−2670..

Zhang, Y.; Xiao, S.; Liang, H. Avoiding kinetic trapping in the self-assembly of DNA-functionalized gold nanoparticles by using an enthalpy-mediated strategy. Macromolecules 2023 , 56 , 3454−3463..

Bai, J. L.; Liu, D.; Wang, R. Self-assembly of amphiphilic diblock copolymers induced by liquid-liquid phase separation. Chinese J. Polym. Sci. 2021 , 39 , 1217−1224..

Zhang, Y.; Tang, H.; Wang, R.; Zhang, L. Enhancing crystallization of DNA-functionalized nanoparticles by polymer chains. Macromolecules 2023 , 56 , 1189−1198..

Zhang, Y.; Tang, H.; Zhou, J.; Zhang, L.; Wang, R. Designing multimodal ON-OFF nanoswitches of DNA-functionalized nanoparticles by stimuli-responsive polymers. J. Phys. Chem. B 2023 , 127 , 8049−8056..

Yang, Y.; Yi, C.; Duan, X.; Wu, Q.; Zhang, Y.; Tao, J.; Dong, W.; Nie, Z. Block-random copolymer-micellization-mediated formation of polymeric patches on gold nanoparticles. J. Am. Chem. Soc. 2021 , 143 , 5060−5070..

Percebom, A. M.; Giner-Casares, J. J.; Claes, N.; Bals, S.; Loh, W.; Liz-Marzán, L. M. Janus gold nanoparticles obtained via spontaneous binary polymer shell segregation. Chem. Commun. 2016 , 52 , 4278−4281..

Rossner, C.; Tang, Q.; Müller, M.; Kothleitner, G. Phase separation in mixed polymer brushes on nanoparticle surfaces enables the generation of anisotropic nanoarchitectures. Soft Matter 2018 , 14 , 4551−4557..

Gu, M.; Ma, X.; Zhang, L.; Lin, J. Reversible polymerization-like kinetics for programmable self-assembly of DNA-encoded nanoparticles with limited valence. J. Am. Chem. Soc. 2019 , 141 , 16408−16415..

Cai, T.; Zhao, S.; Lin, J.; Zhang, L. Kinetically programming copolymerization-like coassembly of multicomponent nanoparticles with DNA. ACS Nano 2022 , 16 , 15907−15916..

Tang, H.; Qiu, X.; Xie, D.; Wang, R. Templated fabrication of DNA-programmable vesicles via amphiphile-functionalized nanoparticles. Macromolecules 2025 , 58 , 3082−3091..

Li, X.; Dai, X.; Pan, Y.; Sun, Y.; Yang, B.; Chen, K.; Wang, Y.; Xu, J.-F.; Dong, Y.; Yang, Y. R.; Yan, L. T.; Liu, D. Studies on the synergistic effect of tandem semi-stable complementary domains on sequence-defined DNA block copolymers. J. Am. Chem. Soc. 2022 , 144 , 21267−21277..

Yu, Q. Y.; Wang, R. Effect of chain rigidity on the crystallization of DNA-directed nanoparticle system. Macromolecules 2018 , 51 , 8372−8376..

Plimpton, S. Fast parallel algorithms for short-range molecular dynamics. J. Comput. Phys. 1995 , 117 , 1−19..

Zhang, S.; He, X.; Xiao, P.; Xia, X.; Zheng, F.; Xiang, S.; Lu, Q. Interpretable machine learning for investigating the molecular mechanisms governing the transparency of colorless transparent polyimide for oled cover windows. Adv. Funct. Mater. 2024 , 34 , 2409143..

Zhou, Y.; Wen, J.; Nie, Y. Microscopic mechanisms of self-healing in polymers revealed by molecular simulations and machine learning. Macromolecules 2024 , 57 , 3258−3270..

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

Dalal, R. J.; Oviedo, F.; Leyden, M. C.; Reineke, T.M. Polymer design via SHAP and Bayesian machine learning optimizes pDNA and CRISPR ribonucleoprotein delivery. Chem. Sci. 2024 , 15 , 7219−7228..

Lundberg, S. M.; Nair, B.; Vavilala, M. S.; Horibe, M.; Eisses, M. J.; Adams, T.; Liston, D. E.; Low, D. K.; Newman, S. F.; Kim, J.; Lee, S. I. Explainable machine-learning predictions for the prevention of hypoxaemia during surgery. Nat. Biomed. Eng. 2018 , 2 , 749−760..

Lundberg, S. M.; Erion, G.; Chen, H.; DeGrave, A.; Prutkin, J. M.; Nair, B.; Katz, R.; Himmelfarb, J.; Bansal, N.; Lee, S. I. From local explanations to global understanding with explainable AI for trees. Nat. Mach. Intell. 2020 , 2 , 56−67..

Wan, Z. L.; Zhao, W. C.; Qiu, H. K.; Zhou, S. S.; Chen, S. Y.; Fu, C. L.; Feng, X. Y.; Pan, L. J.; Wang, K.; He, T. C.; Wang, Y. G.; Sun, Z. Y. Data-driven exploration of polymer processing effects on the mechanical properties in carbon black-reinforced rubber composites. Chinese J. Polym. Sci. 2024 , 42 , 2038−2047..

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