Molecular tuning of DNA framework–programmed silicification by cationic silica cluster attachment

X Xinxin Jing (State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhang Jiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University) H Haozhi Wang (State Key Laboratory of Synergistic Chem-Bio Synthesis, 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) J Jianxiang Huang Y Yingying Liu (Institute of Intelligent Machines, Hefei Institutes of Physical Science) Z Zimu Li J Jielin Chen (State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhang Jiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University) Y Yiqun Xu (State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhang Jiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University) L Lingyun Li (State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhang Jiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University) Y Yunxiao Lin (State Key Laboratory of Synergistic Chem-Bio Synthesis, 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) D Damiano Buratto (Institute of Quantitative Biology, College of Life Sciences, and Department of Physics, Zhejiang University) Q Qinglin Xia (Division of Physical Biology, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences) M Muchen Pan (Division of Physical Biology, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences) Y Yue Wang M Mingqiang Li (State Key Laboratory of Synergistic Chem-Bio Synthesis, State Key Laboratory of Micro-Nano Engineering Science, 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) R Ruhong Zhou S Stephen Mann C Chunhai Fan (State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhang Jiang Institute for Advanced Study and National Center for Translational Medicine) X Xiaoguo Liu (State Key Laboratory of Synergistic Chem-Bio Synthesis, 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)

Abstract

The organizational complexity of biominerals has long fascinated scientists seeking to understand biological programming and implement new developments in biomimetic materials chemistry. Nonclassical crystallization pathways have been observed and analyzed in typical crystalline biominerals, such as calcium phosphate, calcium carbonate, and ferric oxide, involving the controlled attachment and reconfiguration of nanoparticles and clusters on organic templates. However, the understanding of templated amorphous silica mineralization remains limited, hindering the rational design of complex silica-based materials. Here, we report the finding of ultrastable and monodispersed cationic silica cluster (CSC) and their assembly using DNA nanostructures as programmable attachment templates. Cryo-EM imaging reveal that a typical CSC with a diameter of gyration of ~3.9 nm and an average molecular weight of ~8, 262 Da is characteristic of a branched hierarchical structure. We demonstrate high-fidelity silicification by tuning the composition and structure of CSC, providing a unified model of silicification by cluster attachment. Our findings pave the way toward the molecular tuning of pre- and postnucleation stages of sol–gel reactions and provide insights for the design of silica-based materials with controlled organization and functionality.

Article Details

Volume / Issue Vol. 123, Issue 6
Published February 10, 2026
ISSN 0027-8424
Publisher National Academy of Sciences

Authors (18)

X

Xinxin Jing

State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhang Jiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University

H

Haozhi Wang

State Key Laboratory of Synergistic Chem-Bio Synthesis, 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

J

Jianxiang Huang

Y

Yingying Liu

Institute of Intelligent Machines, Hefei Institutes of Physical Science

Z

Zimu Li

J

Jielin Chen

State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhang Jiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University

Y

Yiqun Xu

State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhang Jiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University

L

Lingyun Li

State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhang Jiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University

Y

Yunxiao Lin

State Key Laboratory of Synergistic Chem-Bio Synthesis, 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

D

Damiano Buratto

Institute of Quantitative Biology, College of Life Sciences, and Department of Physics, Zhejiang University

Q

Qinglin Xia

Division of Physical Biology, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences

M

Muchen Pan

Division of Physical Biology, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences

Y

Yue Wang

M

Mingqiang Li

State Key Laboratory of Synergistic Chem-Bio Synthesis, State Key Laboratory of Micro-Nano Engineering Science, 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

R

Ruhong Zhou

S

Stephen Mann

C

Chunhai Fan

State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhang Jiang Institute for Advanced Study and National Center for Translational Medicine

X

Xiaoguo Liu

State Key Laboratory of Synergistic Chem-Bio Synthesis, 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