Home Nano Research Article
Article Link
Cite
EndNote(RIS) BibTeX
Collect
Submit Manuscript
Show Outline
Outline
Graphical Abstract
Abstract
Keywords
Electronic Supplementary Material
References
Show full outline
Hide outline
Research Article

Insight on metal ions inducing chiral self-assembly of DNA in silica mineralization

Arepati Azhati1, Lu Han2, Zhibei Qu3(), Zhouhong Ren4, Xi Liu4(), Liwei Chen4, Shunai Che1,2()
School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai 200240, China
School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China
Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
School of Chemical Science and Engineering, In-situ Center for Physical Sciences, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200240, China
Show Author Information

Graphical Abstract

View original image Download original image
There are 31 types of multivalent cationic metal ions were found to induce formation of chiral impeller-like DNA-silica complexes in the periodic table due to the chiral stacking of DNA. Based on this directing concept, 31 types of ultra-small metal nanoparticles (UMNPs) were easily confined in chiral mesostructured silica supports leading to widespread applications.

Abstract

The self-assembly of DNA provides an attractive approach to understanding structural formation mechanism in living organisms and to assisting applications in materials chemistry. Herein, we investigated the effect of metal ions on chiral self-assembly of DNA through the synthesis of chiral mesostructured silica via self-assembly of metal ions, DNA, and silica source. 31 types of multivalent cationic metal ions were found to induce formation of chiral impeller-like DNA-silica complexes due to the chiral stacking of DNA. The strength of the interaction between the metal ion and phosphate group of DNA was speculated for the chiral stacking of DNA due to close distance of adjacent DNA to assure mutual recognition. Theoretical calculations indicated that chiral packing of DNA depends on the stability of the bridging phosphate-metal ion-phosphate bonds of DNA based on electron delocalization in d-orbital conjugation of metal ions.

Keywords

chiralityDNADNA-metal ions interactionsilicaultra-small metal-nanoparticle

Electronic Supplementary Material

Download File(s)
12274_2022_4460_MOESM1_ESM.pdf (7 MB)

References

[1]

Lakes, R. Materials with structural hierarchy. Nature 1993, 361, 511–515.

Crossref Google Scholar
[2]

Reich, Z.; Schramm, O.; Brumfeld, V.; Minsky, A. Chiral discrimination in DNA–peptide interactions involving chiral DNA mesophases:  A geometric analysis. J. Am. Chem. Soc. 1996, 118, 6345–6349.

Crossref Google Scholar
[3]

Reich, Z.; Wachtel, E. J.; Minsky, A. Liquid-crystalline mesophases of plasmid DNA in bacteria. Science 1994, 264, 1460–1463.

Crossref Google Scholar
[4]

Strey, H. H.; Podgornik, R.; Rau, D. C.; Parsegian, V. A. DNA–DNA interactions. Curr. Opin. Struct. Biol. 1998, 8, 309–313.

Crossref Google Scholar
[5]

Bustamante, C.; Samori, B.; Builes, E. Daunomycin inverts the long-range chirality of DNA condensed states. Biochemistry 1991, 30, 5661–5666.

Crossref Google Scholar
[6]

Minsky, A. The chiral code: From DNA primary structures to quaternary assemblies. Chirality 1998, 10, 405–414.

Crossref Google Scholar
[7]

Berti, L.; Burley, G. A. Nucleic acid and nucleotide-mediated synthesis of inorganic nanoparticles. Nat. Nanotechnol. 2008, 3, 81–87.

Crossref Google Scholar
[8]

Tanaka, K.; Yamada, Y.; Shionoya, M. Formation of silver(i)-mediated DNA duplex and triplex through an alternative base pair of pyridine nucleobases. J. Am. Chem. Soc. 2002, 124, 8802–8803.

Crossref Google Scholar
[9]
Theophanides, T.; Anastassopoulou, J.; Demunno, G. Metal–DNA interactions. In Metal–ligand interactions. Russo, N. ; Salahub, D. R.; Witko, M., Eds.; Springer: Dordrecht, 2003; pp 285–300.
Crossref
[10]

Sigel, H.; Griesser, R. Nucleoside 5′-triphosphates: Self-association, acid-base, and metal ion-binding properties in solution. Chem. Soc. Rev. 2005, 34, 875–900.

Crossref Google Scholar
[11]

Liu, B.; Han, L.; Che, S. A. Formation of enantiomeric impeller-like helical architectures by DNA self-assembly and silica mineralization. Angew. Chem., Int. Ed. 2012, 51, 923–927.

Crossref Google Scholar
[12]

Cao, Y. Y.; Kao, K. C.; Mou, C. Y.; Han, L.; Che, S. A. Oriented chiral DNA-silica film guided by a natural mica substrate. Angew. Chem. 2016, 128, 2077–2081.

Crossref Google Scholar
[13]

Cao, Y. Y.; Che, S. A. Optically active chiral DNA-silica hybrid free-standing films. Chem. Mater. 2015, 27, 7844–7851.

Crossref Google Scholar
[14]

Liu, B.; Han, L.; Duan, Y. Y.; Cao, Y. Y.; Feng, J.; Yao, Y.; Che, S. A. Growth of optically active chiral inorganic films through DNA self-assembly and silica mineralisation. Sci. Rep. 2014, 4, 4866.

Crossref Google Scholar
[15]

Liu, B.; Han, L.; Che, S. A. Silica mineralisation of DNA chiral packing: Helicity control and formation mechanism of impeller-like DNA-silica helical architectures. J. Mater. Chem. B. 2013, 1, 2843–2850.

Crossref Google Scholar
[16]

Cao, Y. Y.; Xie, J. J.; Liu, B.; Han, L.; Che, S. A. Synthesis and characterization of multi-helical DNA-silica fibers. Chem. Commun. 2013, 49, 1097–1099.

Crossref Google Scholar
[17]

Liu, B.; Han, L.; Che, S. A. Formation of enantiomeric impeller-like helical architectures by DNA self-assembly and silica mineralization. Angew. Chem. 2012, 124, 947–951.

Crossref Google Scholar
[18]

Várnai, P.; Timsit, Y. Differential stability of DNA crossovers in solution mediated by divalent cations. Nucleic Acids Res. 2010, 38, 4163–4172.

Crossref Google Scholar
[19]

Timsit, Y.; Vilbois, E.; Moras, D. Base-pairing shift in the major groove of (CA)n tracts by B-DNA crystal structures. Nature 1991, 354, 167–170.

Crossref Google Scholar
[20]

Cherstvy, A. G. DNA cholesteric phases: The role of DNA molecular chirality and DNA–DNA electrostatic interactions. J. Phys. Chem. B 2008, 112, 12585–12595.

Crossref Google Scholar
[21]

Athanasiadou, D.; Carneiro, K. M. M. DNA nanostructures as templates for biomineralization. Nat. Rev. Chem. 2021, 5, 93–108.

Crossref Google Scholar
[22]

Zhao, Y.; Dai, X. P.; Wang, F.; Zhang, X. L.; Fan, C. H.; Liu, X. G. Nanofabrication based on DNA nanotechnology. Nano Today 2019, 26, 123–148.

Crossref Google Scholar
[23]

Winogradoff, D.; Li, P. Y.; Joshi, H.; Quednau, L.; Maffeo, C.; Aksimentiev, A. Chiral systems made from DNA. Adv. Sci. 2021, 8, 2003113.

Crossref Google Scholar
[24]

Fan, J. C.; Kotov, N. A. Chiral nanoceramics. Adv. Mater. 2020, 32, 1906738.

Crossref Google Scholar
[25]

Maestre, M. F.; Reich, C. Contribution of light scattering to the circular dichroism of deoxyribonucleic acid films, deoxyribonucleic acid-polylysine complexes, and deoxyribonucleic acid particles in ethanolic buffers. Biochemistry 1980, 19, 5214–5223.

Crossref Google Scholar
[26]

Livolant, F.; Maestre, M. F. Circular dichroism microscopy of compact forms of DNA and chromatin in vivo and in vitro: Cholesteric liquid-crystalline phases of DNA and single dinoflagellate nuclei. Biochemistry 1988, 27, 3056–3068.

Crossref Google Scholar
[27]

Jmdan, C. F.; Lerman, L. S.; Jun, J. H. V. Structure and circular dichroism of DNA in concentrated polymer solutions. Nat. New Biol. 1972, 236, 67–70.

Crossref Google Scholar
[28]

Pittelkow, M.; Brock-Nannestad, T.; Moth-Poulsen, K.; Christensen, J. B. Chiral dendrimer encapsulated Pd and Rh nanoparticles. Chem. Commun. 2008, 2358–2360.

Crossref Google Scholar
[29]
Kraut-Vass, A. Nist x-ray photoelectron spectroscopy database, version 4.1. NIST X-ray Photoelectron Spectroscopy Database 2000, Version 4. 1.
[30]

Bai, J.; Xu, G. R.; Xing, S. H.; Zeng, J. H.; Jiang, J. X.; Chen, Y. Hydrothermal synthesis and catalytic application of ultrathin rhodium nanosheet nanoassemblies. ACS Appl. Mater. Interfaces 2016, 8, 33635–33641.

Crossref Google Scholar
[31]

Jin, L. Q.; Zhang, X.; Zhao, W. F.; Chen, S. Q.; Shi, Z. Q.; Wang, J. X.; Xie, Y.; Liang, F.; Zhao, C. S. General method for synthesizing transition-metal phosphide/N-doped carbon nanomaterials for hydrogen evolution. Langmuir 2019, 35, 9161–9168.

Crossref Google Scholar
[32]

Wang, N.; Lin, R. Y.; Xue, M. Z.; Duan, Y. Y.; Che, S. A. Handedness inversion of chiral mesoporous silica: A diffuse-reflectance circular dichroism study. Chin. Chem. Lett. 2019, 30, 139–142.

Crossref Google Scholar
[33]

Zanchetta, G.; Giavazzi, F.; Nakata, M.; Buscaglia, M.; Cerbino, R.; Clark, N. A.; Bellini, T. Right-handed double-helix ultrashort DNA yields chiral nematic phases with both right- and left-handed director twist. Proc. Natl. Acad. Sci. USA 2010, 107, 17497–17502.

Crossref Google Scholar
[34]

Sarkar, S.; Maity, A.; Phukon, A. S.; Ghosh, S.; Chakrabarti, R. Salt induced structural collapse, swelling, and signature of aggregation of two ssDNA strands: Insights from molecular dynamics simulation. J. Phys. Chem. B 2019, 123, 47–56.

Crossref Google Scholar
[35]

Qiu, X. Y.; Andresen, K.; Kwok, L. W.; Lamb, J. S.; Park, H. Y.; Pollack, L. Inter-DNA attraction mediated by divalent counterions. Phys. Rev. Lett. 2007, 99, 038104.

Crossref Google Scholar
[36]

Saminathan, M.; Antony, T.; Shirahata, A.; Sigal, L. H.; Thomas, T.; Thomas, T. J. Ionic and structural specificity effects of natural and synthetic polyamines on the aggregation and resolubilization of single-, double-, and triple-stranded DNA. Biochemistry 1999, 38, 3821–3830.

Crossref Google Scholar
[37]

Duguid, J. G.; Bloomfield, V. A. Aggregation of melted DNA by divalent metal ion-mediated cross-linking. Biophys. J. 1995, 69, 2642–2648.

Crossref Google Scholar
[38]

Qu, Z. B.; Feng, W. J.; Wang, Y. C.; Romanenko, F.; Kotov, N. A. Diverse nanoassemblies of graphene quantum dots and their mineralogical counterparts. Angew. Chem., Int. Ed. 2020, 59, 8542–8551.

Crossref Google Scholar
[39]

Qu, Z. B.; Zhou, X. G.; Zhang, M.; Shen, J. L.; Li, Q.; Xu, F.; Kotov, N.; Fan, C. H. Metal-bridged graphene-protein supraparticles for analog and digital nitric oxide sensing. Adv. Mater. 2021, 33, 2007900.

Crossref Google Scholar
Nano Research
Volume 16 Issue 3,
March 2023
Pages 3998-4003
DOI: 10.1007/s12274-022-4460-x
Cite this article:
Azhati A, Han L, Qu Z, et al. Insight on metal ions inducing chiral self-assembly of DNA in silica mineralization. Nano Research, 2023, 16(3): 3998-4003. https://doi.org/10.1007/s12274-022-4460-x
Topics:
DNA
Metrics & Citations  
Article History
Copyright
Return