A 2017 ACS Nano study showed that a guanine-rich nucleic acid and a histidine-rich peptide spontaneously co-assemble with the heme cofactor hemin into a nanoparticle whose active site mimics that of hemoprotein peroxidases, achieving peroxidase-like peroxide turnover numbers with a synergy neither molecular component provides alone. Whether this heteromolecular self-assembly strategy is general — whether such nucleic-acid/peptide co-assemblies can be designed to catalyze bond-forming or bond-cleaving reactions beyond peroxidase-type oxidation, and which scaffold and cofactor combinations realize such chemistry — remains open: the 2017 paper's abstract reports implications for the precise design of supramolecular enzyme mimetics, particularly those with hierarchical active sites, and the originating authors' iScience 2023 review states that the catalytic activities of these self-assembled artificial enzymes 'are restricted to emulate only a few types of natural enzymes', calling for new sequences, new cofactors, and multicomponent co-assembly 'to expand the catalytic repertoire'. All nucleic-acid/peptide co-assembled catalysts reported to date remain redox-mimetic (peroxidase- or oxidase-like), while peptide-only amyloid assemblies have recently demonstrated stereoselective carbene transfer and carboligation, proving feasibility in principle but without a nucleic-acid component. The problem remains open.

Background

Artificial enzymes (enzyme mimetics) are designed molecular systems that reproduce the catalytic behavior of natural enzymes while being far smaller and more robust. Natural enzymes position a handful of chemically reactive groups and cofactors with sub-angstrom precision inside a folded macromolecule; reproducing that precision synthetically is the central difficulty of the field. One bottom-up route is supramolecular self-assembly: small molecules spontaneously organize into nanostructures whose internal surfaces array functional groups in repeating, enzyme-like patterns. Two families dominate this approach. Catalytic amyloids are short peptides that stack into cross-beta sheet fibrils exposing ordered residues, and they have been shown to catalyze ester and organophosphate hydrolysis, retro-aldol cleavage, and, very recently, stereoselective carbene transfer and carbon-carbon bond formation. Separately, guanine-rich DNA strands fold into G-quadruplexes (four-stranded structures stacked on central potassium ions) that bind hemin (iron protoporphyrin IX, the active cofactor of heme proteins) to form peroxidase-mimicking DNAzymes; a peroxidase oxidizes a substrate using hydrogen peroxide (H2O2H_2O_2) through the ferryl Compound I intermediate, the two-electron-oxidized iron(IV)-oxo porphyrin species of heme chemistry. In 2017, Liu, Wang, Shi, Wang and Ding combined the two families: a histidine-rich peptide (supplying the imidazole side chains that hemoproteins use as the axial ligand of heme iron) and a guanine-rich nucleic acid (folding into a G-quadruplex that binds hemin) co-assembled into a hemin-containing nanoparticle. The two components were each individually weak, but together they generated a synergistic active site whose peroxide turnover number reached the order of that of natural peroxidases and whose catalytic efficiency was comparable to myoglobin. The study's abstract notes implications of these results for the precise design of supramolecular enzyme mimetics, particularly those with hierarchical active sites. Three practical limitations of this hybrid chemistry are documented in the literature: the chemistry of these hybrids is limited to peroxidation; the assemblies suffer peroxide-induced inactivation at high H2O2H_2O_2 concentrations (as natural peroxidases do); and the proposed density-functional-theory mechanism, including Compound I formation at the hybrid active site, has not been directly experimentally validated. What has changed since is that peptide-only self-assembled catalysts have now crossed into non-redox, bond-forming and bond-cleaving chemistry — stereoselective cyclopropanation and hydrolase-like cascade activity by hemin-binding short-peptide amyloids (2025), and thiazolium-coenzyme-mediated enantioselective benzoin-type carbon-carbon bond formation in amyloid microphases (2026) — while every reported nucleic-acid/peptide co-assembly, including the originating group's oxidase-mimetic copper and photoswitchable variants, still catalyzes only redox transformations. Whether the hybrid architecture — which uniquely combines the folding, charge pattern, and nucleobase chemistry of nucleic acids with the side-chain functionality of peptides — can host genuinely bond-forming or hydrolytic active sites is therefore a well-posed, currently unanswered question about the generality of the 2017 design principle.

Problem Statement

Establish the generality of the heteromolecular nucleic-acid/peptide self-assembly strategy introduced by the 2017 DNA/peptide/hemin synergistic nanoparticle, whose catalysis is currently confined to peroxidase- and oxidase-type redox reactions, by experimentally extending it beyond substrate oxidation. The open question is whether a rationally designed, self-assembled co-assembly containing both a nucleic-acid component (e.g., a guanine-rich strand folding into a G-quadruplex or another defined nucleic-acid structure) and a peptide component, with or without a metal or organic cofactor, can catalyze a bond-forming reaction (such as non-oxidative carbon-carbon, carbon-nitrogen, or carbon-oxygen bond formation) or a bond-cleaving reaction (such as ester, amide, phosphate, or glycosidic bond hydrolysis) — that is, a reaction class beyond substrate oxidation, the substrate itself not being oxidized (oxidative coupling and other substrate oxidations do not qualify) — with multiple turnovers and demonstrable synergy, meaning the co-assembled system is more active than the simple mixture of its individual components (exceeding each individual component alone being necessary but not sufficient). The objective is to determine which scaffold and cofactor combination realizes the new chemistry and what the responsible co-assembled active site is. Oxidative robustness (resistance to peroxide-induced inactivation of heme-containing variants while preserving turnover) and, for heme-based designs, experimental mechanistic evidence (intermediate detection, proton-transfer or isotope-effect measurements, or quantitative activation barriers) validating the proposed catalytic pathway rather than relying on computation alone are desirable properties of the design, though not necessary to establish the claim. The question is resolved by an experimentally realized co-assembly that catalyzes one bond-forming or bond-cleaving reaction class beyond substrate oxidation with the responsible active site identified; a survey or a purely computational design without experimental realization would leave it open.

References

  1. Qing Liu, Hui Wang, Xinghua Shi, Zhen-Gang Wang, Baoquan Ding. Self-Assembled DNA/Peptide-Based Nanoparticle Exhibiting Synergistic Enzymatic Activity. ACS Nano 2017, 11(7), 7251–7258. DOI: 10.1021/acsnano.7b03195. https://doi.org/10.1021/acsnano.7b03195
  2. Zhen-Gang Wang, Hui Wang, Qing Liu, Fangyuan Duan, Xinghua Shi, Baoquan Ding. Designed Self-Assembly of Peptides with G-Quadruplex/Hemin DNAzyme into Nanofibrils Possessing Enzyme-Mimicking Active Sites and Catalytic Functions. ACS Catalysis 2018, 8(8), 7016–7024. DOI: 10.1021/acscatal.8b00896. https://doi.org/10.1021/acscatal.8b00896
  3. Qing Liu, Akinori Kuzuya, Zhen-Gang Wang. Supramolecular enzyme-mimicking catalysts self-assembled from peptides. iScience 2023, 26(1), 105831. DOI: 10.1016/j.isci.2022.105831. https://doi.org/10.1016/j.isci.2022.105831
  4. Yuanxi Liu, Zhen-Gang Wang. Heme-Dependent Supramolecular Nanocatalysts: A Review. ACS Nano 2023, 17(14), 13000–13016. DOI: 10.1021/acsnano.2c11894. https://doi.org/10.1021/acsnano.2c11894
  5. Shichao Xu, Haifeng Wu, Siyuan Liu, Peidong Du, Hui Wang, Haijun Yang, Wenjie Xu, Shuangming Chen, Li Song, Jikun Li, Xinghua Shi, Zhen-Gang Wang. A supramolecular metalloenzyme possessing robust oxidase-mimetic catalytic function. Nature Communications 2023, 14, 4040. DOI: 10.1038/s41467-023-39779-6. https://doi.org/10.1038/s41467-023-39779-6
  6. Shichao Xu, Yuanxi Liu, Baoli Zhang, Shan Li, Xiangyu Ye, Zhen-Gang Wang. Self-Assembly of Multimolecular Components for Engineering Enzyme-Mimetic Materials. Accounts of Materials Research 2024, 5(9), 1072–1086. DOI: 10.1021/accountsmr.4c00143. https://doi.org/10.1021/accountsmr.4c00143
  7. Shichao Xu, Haifeng Wu, Yuanxi Liu, Zhen-Gang Wang. Self-Assembled G-fold DNA/Amino Acid Amphiphiles-Based Oxidase-Mimetic Materials Exhibiting Drug-Degrading and Photoswitchable Capabilities. Chemistry of Materials 2024, 36(9), 4357–4367. DOI: 10.1021/acs.chemmater.3c03281. https://doi.org/10.1021/acs.chemmater.3c03281
  8. Shichao Xu, Haifeng Wu, Yuanxi Liu, Baoli Zhang, Zhen-Gang Wang. Self-Assembly of Minimalist Amyloid Peptides to Produce Metal-Free Nanofibrils Possessing Robust and Photoswitchable Metallooxidase-Mimetic Catalytic Functions. Small 2025, 21(32), 2501778. DOI: 10.1002/smll.202501778. https://doi.org/10.1002/smll.202501778
  9. Ruikai Du, Yunbo Lv, Haifeng Wu, Baoli Zhang, Yuanxi Liu, Shichao Xu, Shan Li, Zhen-Gang Wang. N-methylation of histidine to tune tautomeric preferences in histidine-heme coordination and enzyme-mimetic catalysis. Smart Molecules 2024, 2(3), e20240012. DOI: 10.1002/smo.20240012. https://doi.org/10.1002/smo.20240012
  10. Yuanyuan Xie, Menghan Xue, Yunbo Lv, Qian Ling, Zhen-Gang Wang. A Nonheme Iron Peroxidase Mimic Enabled by Histidine Methylation and Supramolecular Self-Assembly. ChemBioChem 2026, 27(11), e70432. DOI: 10.1002/cbic.70432. https://doi.org/10.1002/cbic.70432
  11. Xiaobo Zhang, Dehui Qiu, Jielin Chen, Yue Zhang, Jiawei Wang, Desheng Chen, Yuan Liu, Mingpan Cheng, David Monchaud, Jean-Louis Mergny, Huangxian Ju, Jun Zhou. Chimeric Biocatalyst Combining Peptidic and Nucleic Acid Components Overcomes the Performance and Limitations of the Native Horseradish Peroxidase. Journal of the American Chemical Society 2023, 145(8), 4517–4526. DOI: 10.1021/jacs.2c11318. https://doi.org/10.1021/jacs.2c11318
  12. Hongchao Ma, Xifeng Ma, Tiantian Dong, Xinyu Bian, Xiaokang Zhang, Yanhui Wei. Aptamer-functionalized biomimetic supramolecular nanozyme constructed by dipeptide, glutaraldehyde and hemin and its excellent sensing performances for tetrodotoxin. Biosensors and Bioelectronics 2025, 283, 117524. DOI: 10.1016/j.bios.2025.117524. https://doi.org/10.1016/j.bios.2025.117524
  13. Chiranjit Mahato, Bapan Saha, Dibyendu Das. Stereoselective Carbene Transfer and Cascade Activity by Short-Peptide-Based Cross-β Amyloids. ACS Applied Materials & Interfaces 2025, 17(45), 61775–61783. DOI: 10.1021/acsami.5c16753. https://doi.org/10.1021/acsami.5c16753
  14. Janardan Chakraborty, Payel Parvin, Syed Pavel Afrose, Ratan W. Jadhav, Dibyendu Das. Coenzyme-Mediated Enantioselective Carboligation via Cross-β Amyloid Microphases. Journal of the American Chemical Society 2026, 148(13), 14370–14378. DOI: 10.1021/jacs.6c01473. https://doi.org/10.1021/jacs.6c01473
  15. Fangzhou Zhao, Martin Frandsen, Sabrina Capodaglio, Hanadi F. Sleiman. DNA-Mediated Peptide Assembly into Protein Mimics. Journal of the American Chemical Society 2024, 146(3), 1946–1956. DOI: 10.1021/jacs.3c08984. https://doi.org/10.1021/jacs.3c08984
  16. Hao Sun, Haifeng Wu, Qiao Teng, Yuanxi Liu, Hui Wang, Zhen-Gang Wang. Enzyme-Mimicking Materials from Designed Self-Assembly of Lysine-Rich Peptides and G-Quadruplex DNA/Hemin DNAzyme: Charge Effect of the Key Residues on the Catalytic Functions. Biomacromolecules 2022, 23(8), 3469–3476. DOI: 10.1021/acs.biomac.2c00620. https://doi.org/10.1021/acs.biomac.2c00620
  17. Siyuan Liu, Peidong Du, Hao Sun, Hai-Yin Yu, Zhen-Gang Wang. Bioinspired Supramolecular Catalysts from Designed Self-Assembly of DNA or Peptides. ACS Catalysis 2020, 10(24), 14937–14958. DOI: 10.1021/acscatal.0c03753. https://doi.org/10.1021/acscatal.0c03753