1
|
Zhang Y, Wu L, Su X, Liang H. Construction of a highly efficient DNA nanotube sensor with peroxide-like activity. J Mater Chem B 2023; 12:240-249. [PMID: 38086676 DOI: 10.1039/d3tb01984e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The G-quadruplex/heme complexes are special DNA-based artificial metalloenzymes with peroxidase-like activity and are widely used in biosensing and biocatalysis. However, their peroxidase-like activity is not satisfactory. Due to the high programmability and good stability of DNA, DNA as a scaffold material is promising for enhancing the activity of artificial metalloenzymes. In this work, an effective DNA nanotube-based peroxidase was constructed using a self-assembly strategy. To improve the activity of G-quadruplex/heme complexes, a new method for the construction of G-quadruplex/heme complex arrays was proposed in a simple and inexpensive way. By designing the toes of DNA nanotubes as G-quadruplexes, G-quadruplex arrays could be formed on pure DNA nanotubes, and then the G-quadruplex arrays bind to heme to form a nanotube-supported DNAzyme termed as DNTzyme. Agarose gel electrophoresis, circular dichroism, and fluorescence microscopy were used to characterize DNTzyme. What is more, because the loading of DNAzyme on DNA nanotubes can increase their biological stability, a hydrogen peroxide detection sensor was constructed using the enhanced enzymatic activity and excellent stability of DNTzyme. The sensor could accurately and efficiently detect peroxide and show enhanced fluorescence with a detection limit of 49 nM for H2O2 and 1.4 μM for TBHP, and a color development time of about 5 min. This sensor is expected to have applications in bio-detection, biocatalysis, and drug delivery.
Collapse
Affiliation(s)
- Ying Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Lingqi Wu
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Hao Liang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| |
Collapse
|
2
|
Qi L, Tian Y, Li N, Mao M, Fang X, Han D. Engineering Circular Aptamer Assemblies with Tunable Selectivity to Cell Membrane Antigens In Vitro and In Vivo. ACS APPLIED MATERIALS & INTERFACES 2023; 15:12822-12830. [PMID: 36856721 DOI: 10.1021/acsami.2c22820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The strategy of enhancing molecular recognition by improving the binding affinity of drug molecules against targets has generated a lot of successful therapeutic applications. However, one critical consequence of such affinity improvement, generally called "on-target, off-tumor" toxicity, emerged as a major obstacle limiting their clinical usage. Herein, we provide a modular assembly strategy that affords affinity-tunable DNA nanostructures allowing for immobilizing multiple aptamers that bind to the example antigen of EpCAM with different affinities. We develop a theoretical model proving that the apparent affinity of aptamer assemblies to target cells varies with antigen density as well as aptamer valency. More importantly, we demonstrate experimentally that the theoretical model can be used to predict the least valency required for discrimination between EpCAMhigh and EpCAMlow cells in vitro and in vivo. We believe that our strategy will have broad applications in an engineering nucleic acid-based delivery platform for targeted and cell therapy.
Collapse
Affiliation(s)
- Liqing Qi
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, School of Medicine, Shanghai Jiao Tong University, Renji Hospital, Institute of Molecular Medicine, Shanghai 200127, China
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Yuan Tian
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, School of Medicine, Shanghai Jiao Tong University, Renji Hospital, Institute of Molecular Medicine, Shanghai 200127, China
| | - Na Li
- National Genomics Data Center, China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Menghan Mao
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, School of Medicine, Shanghai Jiao Tong University, Renji Hospital, Institute of Molecular Medicine, Shanghai 200127, China
| | - Xiaohong Fang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Da Han
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, School of Medicine, Shanghai Jiao Tong University, Renji Hospital, Institute of Molecular Medicine, Shanghai 200127, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| |
Collapse
|
3
|
Kanlidere Z. Template-Directed Incorporation of Functional Molecules into DNA. Chembiochem 2023; 24:e202200554. [PMID: 36520932 DOI: 10.1002/cbic.202200554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/30/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
We report a versatile method for the incorporation of functional molecules into oligonucleotides carrying reactive groups by using a template-directed postsynthetic approach in the solution phase. For this purpose, we prepared oligonucleotides carrying an amino group on the backbone by using an acylic threoninol scaffold. The resulting oligonucleotides could be used to introduce almost any molecule carrying aldehyde, which can be, among other things, a metal-binding ligand or a fluorophore. In our study, we incorporated aldehyde-bearing phenanthroline, a metal-binding ligand, into oligonucleotides by template-directed reversible conjugation. We observed that the use of an abasic sugar site instead of a natural nucleobase in the template strand increased the yield of conjugation and induced selective incorporation of the phenanthroline. This method could lead progress in the development of probes for the recognition of abasic regions in duplex DNA. Moreover, template-directed formation of metal ligand-oligonucleotide conjugates might have potential applications in hybrid biocatalysis for enantioselective transformations.
Collapse
Affiliation(s)
- Zeynep Kanlidere
- Department of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Acibadem Mehmet Ali Aydinlar University, Kayisdagi Cad. No: 32 Atasehir, 34752, Istanbul, Turkey
| |
Collapse
|
4
|
Duchemin N, Aubert S, de Souza JV, Bethge L, Vonhoff S, Bronowska AK, Smietana M, Arseniyadis S. New Benchmark in DNA-Based Asymmetric Catalysis: Prevalence of Modified DNA/RNA Hybrid Systems. JACS AU 2022; 2:1910-1917. [PMID: 36032523 PMCID: PMC9400053 DOI: 10.1021/jacsau.2c00271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/27/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
By harnessing the chirality of the DNA double helix, chemists have been able to obtain new, reliable, selective, and environmentally friendly biohybrid catalytic systems with tailor-made functions. Nonetheless, despite all the advances made throughout the years in the field of DNA-based asymmetric catalysis, many challenges still remain to be faced, in particular when it comes to designing a "universal" catalyst with broad reactivity and unprecedented selectivity. Rational design and rounds of selection have allowed us to approach this goal. We report here the development of a DNA/RNA hybrid catalytic system featuring a covalently attached bipyridine ligand, which exhibits unmatched levels of selectivity throughout the current DNA toolbox and opens new avenues in asymmetric catalysis.
Collapse
Affiliation(s)
- Nicolas Duchemin
- Queen
Mary University of London, Department of Chemistry, Mile End Road, London E1 4NS, United
Kingdom
- NOXXON
Pharma AG, Max-Dohrn-Strasse 8-10, Berlin 10589, Germany
| | - Sidonie Aubert
- Queen
Mary University of London, Department of Chemistry, Mile End Road, London E1 4NS, United
Kingdom
| | - João V. de Souza
- Chemistry−School
of Natural and Environmental Sciences, Newcastle
University, Newcastle NE1 7RU, United Kingdom
| | - Lucas Bethge
- NOXXON
Pharma AG, Max-Dohrn-Strasse 8-10, Berlin 10589, Germany
| | - Stefan Vonhoff
- NOXXON
Pharma AG, Max-Dohrn-Strasse 8-10, Berlin 10589, Germany
| | - Agnieszka K. Bronowska
- Chemistry−School
of Natural and Environmental Sciences, Newcastle
University, Newcastle NE1 7RU, United Kingdom
| | - Michael Smietana
- Institut
des Biomolécules Max Mousseron, Université
de Montpellier, CNRS, ENSCM, 1919 Route de Mende, Montpellier 34095, France
| | - Stellios Arseniyadis
- Queen
Mary University of London, Department of Chemistry, Mile End Road, London E1 4NS, United
Kingdom
| |
Collapse
|