1
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Zhou W, Wan W, Miao W, Bao Y, Liu Y, Jia G, Li C. K +-Specification with Flavone P0 Probe in a G-Quadruplex DNA. Anal Chem 2024; 96:10835-10840. [PMID: 38889097 DOI: 10.1021/acs.analchem.4c02368] [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: 06/20/2024]
Abstract
G-quadruplex (G4) DNA is considered as a prospective therapeutic target due to its potential biological significance. To understand G4 biological roles and function, a G4-specific fluorescent probe is necessary. However, it is difficult for versatile G4 to precisely recognize without perturbing their folding dynamics. Herein, we reported that flavone P0 can be a fluorescent probe for G4 DNA-specific recognition and have developed a highly selective detection of K+ ion by dimeric G4/P0 system. When comparing various nucleic acid structures, including G4, i-motif, ss/ds-DNA, and triplex, an apparent fluorescence enhancement is observed in the presence of G4 DNA for 85-fold, but only 8-fold for non-G4 DNA. Furthermore, based on fluorescent probe of flavone P0 for G4 DNA screening, the noncovalent dimeric G4/P0 system is exploited as a K+ sensor, that selectively responds to K+ with a 513-fold fluorescence enhancement and a detection range for K+ ion concentration from 0 to 500 mM. This K+ sensor also has a remarkably anti-interference ability for other metal cations, especially for a high concentration of Na+. These results have demonstrated that flavone P0 is an efficient tool for monitoring G-quadruplex DNA and endows flavone P0 with bioanalytical and medicinal applications.
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Affiliation(s)
- Wenqin Zhou
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Wang Wan
- Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Wenhui Miao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Yu Bao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Yu Liu
- Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Can Li
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
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2
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Huang LH, Hsieh YY, Yang FA, Liao WC. DNA-modified Prussian blue nanozymes for enhanced electrochemical biosensing. NANOSCALE 2024; 16:9770-9780. [PMID: 38597919 DOI: 10.1039/d4nr00387j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Prussian blue nanoparticles exhibit the potential to be employed in bioanalytical applications due to their robust stability, peroxidase-like catalytic functionality, straightforward synthesis, and biocompatibility. An efficient approach is presented for the synthesis of nucleic acid-modified Prussian blue nanoparticles (DNA-PBNPs), utilizing nanoparticle porosity to adsorb nucleic acids (polyT). This strategic adsorption leads to the exposure of nucleic acid sequences on the particle surface while retaining catalytic activity. DNA-PBNPs further couple with functional nucleic acid sequences and aptamers through complementary base pairing to act as transducers in biosensors and amplify signal acquisition. Subsequently, we integrated a copper ion-dependent DNAzyme (Cu2+-DNAzyme) and a vascular endothelial growth factor aptamer (VEGF aptamer) onto screen-printed electrodes to serve as recognition elements for analytes. Significantly, our approach leverages DNA-PBNPs as a superior alternative to traditional enzyme-linked antibodies in electrochemical biosensors, thereby enhancing both the efficiency and adaptability of these devices. Our study conclusively demonstrates the application of DNA-PBNPs in two different biosensing paradigms: the sensitive detection of copper ions and vascular endothelial growth factor (VEGF). These results indicate the promising potential of DNA-modified Prussian blue nanoparticles in advancing bioanalytical sensing technologies.
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Affiliation(s)
- Lin-Hui Huang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
| | - Yu-Yu Hsieh
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
| | - Fu-An Yang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
| | - Wei-Ching Liao
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
- Medical Device Innovation and Translation Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
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3
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Paul R, Paul R, Dutta D, Dash J. pH-dependent complex formation with TAR RNA and DNA: application towards logic gates. Analyst 2024; 149:1976-1980. [PMID: 38465447 DOI: 10.1039/d4an00074a] [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: 03/12/2024]
Abstract
Nucleic acid-based logic gates have shown great potential in biotechnology, medicine as well as diagnostics. Herein, we have constructed pH-responsive logic devices by utilizing HIV-1 TAR hairpins in combination with a thiazole peptide that exhibits turn-on fluorescence upon interacting with TAR RNA or DNA. Based on this, INHIBIT-AND and YES-INHIBIT-AND logic gates were constructed in parallel. The pH alteration leads to conformational changes of the hairpin structure, enabling the construction of a multi-reset reusable logic system which could be developed for in vitro sensing of the HIV-1 viral RNA.
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Affiliation(s)
- Rakesh Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Raj Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Debasish Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
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4
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Lai R, Zeng X, Xu Q, Xu Y, Li X, Ru Y, Wang Y, Wang D, Zhou X, Shao Y. Ratiometric G-quadruplex/hemin DNAzymes with low-dosage associative substrates. Anal Chim Acta 2024; 1295:342320. [PMID: 38355221 DOI: 10.1016/j.aca.2024.342320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND G-quadruplex (G4)/hemin DNAzymes with conversion of substrates into colorimetric readouts are well recognized as convenient biocatalysis tools in sensor development. However, the previously developed colorimetric G4/hemin DNAzymes are diffusive substrate-based DNAzymes (DSBDs). The current colorimetric DSBDs have several drawbacks including high dosage (∼mM) of diffusive substrates (DSs), colorimetric product toxicity, and single colorimetric readout without tolerance to fluctuation of experimental factors and background. In addition, the usage of high-dosage DSs can smear the G4 foldings and their discard is more harmful to environment. Therefore, exploring alternative DNAzymes with potential to overcome these drawbacks of DSBDs is urgently needed. RESULTS We herein developed associative substrate-based DNAzymes (ASBDs). Cyanine dyes were selected as associative substrates (ASs) due to their binding competency with G4/hemin DNAzymes. With respect to DSBDs, ASBDs needed only low dosage (∼10 μM) of ASs to be able to cause a rapid and visible substrate conversion. In addition, since cyanine dyes are NIR dyes with high extinction coefficients and their conversion products have absorption bands at shorter wavelength. Therefore, a colorimetric ratio response can be developed to follow activities of G4/hemin DNAzymes with competency to tolerate fluctuation of experimental factors and background. In particular, herein developed ASBDs can endure somewhat concentration fluctuation of H2O2. ASBDs are able to cowork with other enzymes (for example, glucose oxidase) to realize cascade sensing. SIGNIFICANCE The developed ASBDs can operate at low dosage of substrates with a colorimetric ratio response and can overcome the drawbacks met in DSBDs. We expect that, by designing ASs with fruitful color panel in the future, our work will inspire more interesting in developing environment-benign and low-carbon G4/hemin DNAzymes and desired colorful high-performance sensors.
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Affiliation(s)
- Rong Lai
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xingli Zeng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Qiuda Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Ying Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xueni Li
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yulu Ru
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yilin Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China.
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5
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Shi C, Yang D, Ma X, Pan L, Shao Y, Arya G, Ke Y, Zhang C, Wang F, Zuo X, Li M, Wang P. A Programmable DNAzyme for the Sensitive Detection of Nucleic Acids. Angew Chem Int Ed Engl 2024; 63:e202320179. [PMID: 38288561 DOI: 10.1002/anie.202320179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Indexed: 02/17/2024]
Abstract
Nucleic acids in biofluids are emerging biomarkers for the molecular diagnostics of diseases, but their clinical use has been hindered by the lack of sensitive detection assays. Herein, we report the development of a sensitive nucleic acid detection assay named SPOT (sensitive loop-initiated DNAzyme biosensor for nucleic acid detection) by rationally designing a catalytic DNAzyme of endonuclease capability into a unified one-stranded allosteric biosensor. SPOT is activated once a nucleic acid target of a specific sequence binds to its allosteric module to enable continuous cleavage of molecular reporters. SPOT provides a highly robust platform for sensitive, convenient and cost-effective detection of low-abundance nucleic acids. For clinical validation, we demonstrated that SPOT could detect serum miRNAs for the diagnostics of breast cancer, gastric cancer and prostate cancer. Furthermore, SPOT exhibits potent detection performance over SARS-CoV-2 RNA from clinical swabs with high sensitivity and specificity. Finally, SPOT is compatible with point-of-care testing modalities such as lateral flow assays. Hence, we envision that SPOT may serve as a robust assay for the sensitive detection of a variety of nucleic acid targets enabling molecular diagnostics in clinics.
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Affiliation(s)
- Chenzhi Shi
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaowei Ma
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li Pan
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yuanchuan Shao
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, 27708, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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6
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Zhang Z, Wei W, Chen S, Yang J, Song D, Chen Y, Zhao Z, Chen J, Wang F, Wang J, Li Z, Liang Y, Yu H. Chemoenzymatic Installation of Site-Specific Chemical Groups on DNA Enhances the Catalytic Activity. J Am Chem Soc 2024; 146:7052-7062. [PMID: 38427585 DOI: 10.1021/jacs.4c00484] [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: 03/03/2024]
Abstract
Functional DNAs are valuable molecular tools in chemical biology and analytical chemistry but suffer from low activities due to their limited chemical functionalities. Here, we present a chemoenzymatic method for site-specific installation of diverse functional groups on DNA, and showcase the application of this method to enhance the catalytic activity of a DNA catalyst. Through chemoenzymatic introduction of distinct chemical groups, such as hydroxyl, carboxyl, and benzyl, at specific positions, we achieve significant enhancements in the catalytic activity of the RNA-cleaving deoxyribozyme 10-23. A single carboxyl modification results in a 100-fold increase, while dual modifications (carboxyl and benzyl) yield an approximately 700-fold increase in activity when an RNA cleavage reaction is catalyzed on a DNA-RNA chimeric substrate. The resulting dually modified DNA catalyst, CaBn, exhibits a kobs of 3.76 min-1 in the presence of 1 mM Mg2+ and can be employed for fluorescent imaging of intracellular magnesium ions. Molecular dynamics simulations reveal the superior capability of CaBn to recruit magnesium ions to metal-ion-binding site 2 and adopt a catalytically competent conformation. Our work provides a broadly accessible strategy for DNA functionalization with diverse chemical modifications, and CaBn offers a highly active DNA catalyst with immense potential in chemistry and biotechnology.
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Affiliation(s)
- Ze Zhang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
| | - Siqi Chen
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Jintao Yang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Dongfan Song
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yinghan Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zerun Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jiawen Chen
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Fulong Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Jiahuan Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Zhe Li
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hanyang Yu
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
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7
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Fan H, Lu Y. Improving the Sensitivity of a Mn(II)-Specific DNAzyme for Cellular Imaging Sensor through Sequence Mutations. Anal Chem 2024; 96:3853-3858. [PMID: 38375826 PMCID: PMC11060987 DOI: 10.1021/acs.analchem.3c05280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Detection of Mn2+ in living cells is important in understanding the roles of Mn2+ in cellular processes and investigating its potential implications in various diseases and disorders. Toward this goal, we have previously selected a Mn2+-specific 11-5 DNAzyme through an in vitro selection method and converted it into a fluorescence sensor for intracellular Mn2+ sensing. Despite the progress, the nucleotides responsible for the activity are unclear, and the performance of the DNAzyme needs to be improved in order for more effective applications in biological systems. To address these issues, we herein report site-specific mutations within the catalytic domain of the selected 11-5 DNAzyme. As a result, we successfully identified a variant DNAzyme, designated as Mn5V, which exhibited a twofold increase in activity compared to the original 11-5 DNAzyme. Importantly, Mn5V DNAzyme maintained its high selectivity for Mn2+ over other competing metal ions. Upon the addition of Mn2+, Mn5V DNAzyme exhibited a higher fluorescence signal within the tumor cells compared to that of the 11-5 DNAzyme. This study therefore provides a better understanding of how the DNAzyme functions and a more sensitive probe for investigating Mn2+ in biological systems.
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Affiliation(s)
- Huanhuan Fan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
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8
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Ding M, Xiao X, Yang Y, Yao Z, Dong Z, Gao Q, Tian B. AND-Logic Cascade Rolling Circle Amplification for Optomagnetic Detection of Dual Target SARS-CoV-2 Sequences. Anal Chem 2024; 96:455-462. [PMID: 38123506 DOI: 10.1021/acs.analchem.3c04533] [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
DNA logic operations are accurate and specific molecular strategies that are appreciated in target multiplexing and intelligent diagnostics. However, most of the reported DNA logic operation-based assays lack amplifiers prior to logic operation, resulting in detection limits at the subpicomolar to nanomolar level. Herein, a homogeneous and isothermal AND-logic cascade amplification strategy is demonstrated for optomagnetic biosensing of two different DNA inputs corresponding to a variant of concern sequence (containing spike L452R) and a highly conserved sequence from SARS-CoV-2. With an "amplifiers-before-operator" configuration, two input sequences are recognized by different padlock probes for amplification reactions, which generate amplicons used, respectively, as primers and templates for secondary amplification, achieving the AND-logic operation. Cascade amplification products can hybridize with detection probes grafted onto magnetic nanoparticles (MNPs), leading to hydrodynamic size increases and/or aggregation of MNPs. Real-time optomagnetic MNP analysis offers a detection limit of 8.6 fM with a dynamic detection range spanning more than 3 orders of magnitude. The accuracy, stability, and specificity of the system are validated by testing samples containing serum, salmon sperm, a single-nucleotide variant, and biases of the inputs. Clinical samples are tested with both quantitative reverse transcription-PCR and our approach, showing highly consistent measurement results.
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Affiliation(s)
- Mingming Ding
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Xiaozhou Xiao
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Yulin Yang
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Ziyang Yao
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Zhuxin Dong
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
- Furong Laboratory, Changsha 410008, China
| | - Qian Gao
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Bo Tian
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
- Furong Laboratory, Changsha 410008, China
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9
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Hussein Z, Nour MAY, Kozlova AV, Kolpashchikov DM, Komissarov AB, El-Deeb AA. DNAzyme Nanomachine with Fluorogenic Substrate Delivery Function: Advancing Sensitivity in Nucleic Acid Detection. Anal Chem 2023; 95:18667-18672. [PMID: 38079240 DOI: 10.1021/acs.analchem.3c04420] [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: 12/27/2023]
Abstract
We have developed a hook-equipped DNA nanomachine (HDNM) for the rapid detection of specific nucleic acid sequences without a preamplification step. HDNM efficiently unwinds RNA structures and improves the detection sensitivity. Compared to the hookless system, HDNM offers an 80-fold and 13-fold enhancement in DNA and RNA detection, respectively, reducing incubation time from 3 to 1 h.
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Affiliation(s)
- Zain Hussein
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Moustapha A Y Nour
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Anastasia V Kozlova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, Florida 32816, United States
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32816, United States
- National Center for Forensic Science, University of Central Florida, Orlando, Florida 32816, United States
| | - Andrey B Komissarov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russian Federation
| | - Ahmed A El-Deeb
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
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10
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Shen H, Cui G, Liang H, Yang H, Chen M, Xu ZL, Liu W, Liu Y. DNA Nanomachine-Driven Heterogeneous Quadratic Amplification for Sensitive and Programmable miRNA Profiling. Anal Chem 2023; 95:15769-15777. [PMID: 37734028 DOI: 10.1021/acs.analchem.3c03306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Inspired by the molecular crowding effect in biological systems, a novel heterogeneous quadratic amplification molecular circuit (HEQAC) was developed for sensitive bimodal miRNA profiling (HEQAC-BMP) by combining an MNAzyme-based DNA nanomachine with an entropy-driven catalytic hairpin assembly (E-CHA) autocatalytic circuit. Utilizing ferromagnetic nanomaterials as the substrate for DNA nanomachines, a biomimetic heterogeneous interface was established; thus, a localized molecular crowding system was created that can elevate the local reaction concentration and accelerate the molecular recognition process for a significant threshold signal. Simultaneously, the threshold signal undergoes further amplification by E-CHA and is transformed into a chemical signal, enabling a colorimetric-fluorescence bimodal signal readout. The HEQAC-BMP enables miRNA detection from 10 aM to 10 nM with detection limits of 3.7 aM (colorimetry) and 4.8 aM (fluorometry), respectively. Moreover, the design principle and strategy of HEQAC-BMP can be customized to address other critical viruses or diseases with life-threatening and socioeconomic impacts, enhancing healthcare outcomes for individuals.
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Affiliation(s)
- Haoran Shen
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Guosheng Cui
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Hongzhi Liang
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Hui Yang
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Mengting Chen
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhen-Lin Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Weipeng Liu
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Yingju Liu
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
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11
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Fischer A, Ehrlich A, Plotkin Y, Ouyang Y, Asulin K, Konstantinos I, Fan C, Nahmias Y, Willner I. Stimuli-Responsive Hydrogel Microcapsules Harnessing the COVID-19 Immune Response for Cancer Therapeutics. Angew Chem Int Ed Engl 2023; 62:e202311590. [PMID: 37675854 DOI: 10.1002/anie.202311590] [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: 08/09/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/08/2023]
Abstract
The combination of gene therapy and immunotherapy concepts, along recent advances in DNA nanotechnology, have the potential to provide important tools for cancer therapies. We present the development of stimuli-responsive microcapsules, loaded with a viral immunogenetic agent, harnessing the immune response against the Coronavirus Disease 2019, COVID-19, to selectively attack liver cancer cells (hepatoma) or recognize breast cancer or hepatoma, by expression of green fluorescence protein, GFP. The pH-responsive microcapsules, modified with DNA-tetrahedra nanostructures, increased hepatoma permeation by 50 %. Incorporation of a GFP-encoding lentivirus vector inside the tumor-targeting pH-stimulated miRNA-triggered and Alpha-fetoprotein-dictated microcapsules enables the demonstration of neoplasm selectivity, with approximately 5,000-, 8,000- and 50,000-fold more expression in the cancerous cells, respectively. The incorporation of the SARS-CoV-2 spike protein in the gene vector promotes specific recognition of the immune-evading hepatoma by the COVID-19-analogous immune response, which leads to cytotoxic and inflammatory activity, mediated by serum components taken from vaccinated or recovered COVID-19 patients, resulting in effective elimination of the hepatoma (>85 % yield).
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Affiliation(s)
- Amit Fischer
- Institute of Chemistry, The Minerva Center for Bio-hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Avner Ehrlich
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yevgeni Plotkin
- The Department of Anesthesiology, Critical Care and Pain Medicine, Hadassah University Hospital, Jerusalem, 9112001, Israel
- Faculty of Medicine, Hebrew University of Jerusalem Jerusalem, 9112001, (Israel)
| | - Yu Ouyang
- Institute of Chemistry, The Minerva Center for Bio-hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Klil Asulin
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ioannidis Konstantinos
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yaakov Nahmias
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Bio-hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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12
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Kim Y, Jang S, Chang C, Kim KT. Facile Strategy to Output Fluorescein from Nucleic Acid Interactions. Bioconjug Chem 2023; 34:1606-1612. [PMID: 37639511 DOI: 10.1021/acs.bioconjchem.3c00276] [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: 08/31/2023]
Abstract
Biomolecular operations, which involve the conversion of molecular signals or interactions into specific functional outputs, are fundamental to the field of biology and serve as the important foundation for the design of diagnostic and therapeutic systems. To maximize their functionalities and broaden their applicability, it is crucial to develop novel outputs and facile chemical transformation methods. With this aim, in this study, we present a straightforward method for converting nucleic acid signals into fluorescein outputs that exhibit a wide range of functionalities. This operation is designed through a DNA-templated reaction based on riboflavin-photocatalyzed oxidation of dihydrofluorescein, which is readily prepared by simple NaBH4 reduction of the fluorescein with no complicated chemical caging steps. The templated photooxidation exhibits high efficiency (kapp = 2.7 × 10-3/s), generating a clear fluorescein output signal distinguishable from a low background, originating from the high stability of the synthesized dihydrofluorescein. This facile and efficient operation allows the nucleic acid-initiated activation of various fluorescein functions, such as fluorescence and artificial oxidase activity, which are applied in the design of novel bioanalytical systems, including fluorescent and colorimetric DNA sensors. The operation presented herein would expand the scope of biomolecular circuit systems for diagnostic and therapeutic applications.
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Affiliation(s)
- Yeojin Kim
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Sarah Jang
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Chuljoo Chang
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ki Tae Kim
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea
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13
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Yu M, He T, Wang Q, Cui C. Unraveling the Possibilities: Recent Progress in DNA Biosensing. BIOSENSORS 2023; 13:889. [PMID: 37754122 PMCID: PMC10526863 DOI: 10.3390/bios13090889] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/29/2023] [Accepted: 09/09/2023] [Indexed: 09/28/2023]
Abstract
Due to the advantages of its numerous modification sites, predictable structure, high thermal stability, and excellent biocompatibility, DNA is the ideal choice as a key component of biosensors. DNA biosensors offer significant advantages over existing bioanalytical techniques, addressing limitations in sensitivity, selectivity, and limit of detection. Consequently, they have attracted significant attention from researchers worldwide. Here, we exemplify four foundational categories of functional nucleic acids: aptamers, DNAzymes, i-motifs, and G-quadruplexes, from the perspective of the structure-driven functionality in constructing DNA biosensors. Furthermore, we provide a concise overview of the design and detection mechanisms employed in these DNA biosensors. Noteworthy advantages of DNA as a sensor component, including its programmable structure, reaction predictility, exceptional specificity, excellent sensitivity, and thermal stability, are highlighted. These characteristics contribute to the efficacy and reliability of DNA biosensors. Despite their great potential, challenges remain for the successful application of DNA biosensors, spanning storage and detection conditions, as well as associated costs. To overcome these limitations, we propose potential strategies that can be implemented to solve these issues. By offering these insights, we aim to inspire subsequent researchers in related fields.
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Affiliation(s)
| | | | | | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China; (M.Y.)
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14
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Su J, Sun C, Du J, Xing X, Wang F, Dong H. RNA-Cleaving DNAzyme-Based Amplification Strategies for Biosensing and Therapy. Adv Healthc Mater 2023; 12:e2300367. [PMID: 37084038 DOI: 10.1002/adhm.202300367] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Indexed: 04/22/2023]
Abstract
Since their first discovery in 1994, DNAzymes have been extensively applied in biosensing and therapy that act as recognition elements and signal generators with the outstanding properties of good stability, simple synthesis, and high sensitivity. One subset, RNA-cleaving DNAzymes, is widely employed for diverse applications, including as reporters capable of transmitting detectable signals. In this review, the recent advances of RNA-cleaving DNAzyme-based amplification strategies in scaled-up biosensing are focused, the application in diagnosis and disease treatment are also discussed. Two major types of RNA-cleaving DNAzyme-based amplification strategies are highlighted, namely direct response amplification strategies and combinational response amplification strategies. The direct response amplification strategies refer to those based on novel designed single-stranded DNAzyme, and the combinational response amplification strategies mainly include two-part assembled DNAzyme, cascade reactions, CHA/HCR/RCA, DNA walker, CRISPR-Cas12a and aptamer. Finally, the current status of DNAzymes, the challenges, and the prospects of DNAzyme-based biosensors are presented.
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Affiliation(s)
- Jiaxin Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Chenyang Sun
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Jinya Du
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Xiaotong Xing
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Fang Wang
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
- Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ), Shenzhen, Guangdong, 518060, P. R. China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
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15
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Zhang C, Paluzzi VE, Sha R, Jonoska N, Mao C. Implementing Logic Gates by DNA Crystal Engineering. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2302345. [PMID: 37220213 DOI: 10.1002/adma.202302345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/03/2023] [Indexed: 05/25/2023]
Abstract
DNA self-assembly computation is attractive for its potential to perform massively parallel information processing at the molecular level while at the same time maintaining its natural biocompatibility. It has been extensively studied at the individual molecule level, but not as much as ensembles in 3D. Here, the feasibility of implementing logic gates, the basic computation operations, in large ensembles: macroscopic, engineered 3D DNA crystals is demonstrated. The building blocks are the recently developed DNA double crossover-like (DXL) motifs. They can associate with each other via sticky-end cohesion. Common logic gates are realized by encoding the inputs within the sticky ends of the motifs. The outputs are demonstrated through the formation of macroscopic crystals that can be easily observed. This study points to a new direction of construction of complex 3D crystal architectures and DNA-based biosensors with easy readouts.
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Affiliation(s)
- Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Victoria E Paluzzi
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Natasha Jonoska
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, 33620, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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16
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Yang S, Wang Y, Wang Q, Li F, Ling D. DNA-Driven Dynamic Assembly/Disassembly of Inorganic Nanocrystals for Biomedical Imaging. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:340-355. [PMID: 37501793 PMCID: PMC10369495 DOI: 10.1021/cbmi.3c00028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/20/2023] [Accepted: 04/07/2023] [Indexed: 07/29/2023]
Abstract
DNA-mediated programming is emerging as an effective technology that enables controlled dynamic assembly/disassembly of inorganic nanocrystals (NC) with precise numbers and spatial locations for biomedical imaging applications. In this review, we will begin with a brief overview of the rules of NC dynamic assembly driven by DNA ligands, and the research progress on the relationship between NC assembly modes and their biomedical imaging performance. Then, we will give examples on how the driven program is designed by different interactions through the configuration switching of DNA-NC conjugates for biomedical applications. Finally, we will conclude with the current challenges and future perspectives of this emerging field. Hopefully, this review will deepen our knowledge on the DNA-guided precise assembly of NCs, which may further inspire the future development of smart chemical imaging devices and high-performance biomedical imaging probes.
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Affiliation(s)
- Shengfei Yang
- Institute
of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yuqi Wang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
| | - Qiyue Wang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
| | - Fangyuan Li
- Institute
of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
- Hangzhou
Institute of Innovative Medicine, Zhejiang
University, Hangzhou 310058, P. R. China
| | - Daishun Ling
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
- Hangzhou
Institute of Innovative Medicine, Zhejiang
University, Hangzhou 310058, P. R. China
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17
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Chen B, Yu X, Gao T, Wu Y, Zhang X, Li S. Selection of allosteric dnazymes that can sense phenylalanine by expression-SELEX. Nucleic Acids Res 2023; 51:e66. [PMID: 37207331 PMCID: PMC10287898 DOI: 10.1093/nar/gkad424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 04/13/2023] [Accepted: 05/10/2023] [Indexed: 05/21/2023] Open
Abstract
Aptamers are ligand-binding RNA or DNA molecules and have been widely examined as biosensors, diagnostic tools, and therapeutic agents. The application of aptamers as biosensors commonly requires an expression platform to produce a signal to report the aptamer-ligand binding event. Traditionally, aptamer selection and expression platform integration are two independent steps and the aptamer selection requires the immobilization of either the aptamer or the ligand. These drawbacks can be easily overcome through the selection of allosteric DNAzymes (aptazymes). Herein, we used the technique of Expression-SELEX developed in our laboratory to select for aptazymes that can be specifically activated by low concentrations of l-phenylalanine. We chose a previous DNA-cleaving DNAzyme known as II-R1 as the expression platform for its low cleavage rate and used stringent selection conditions to drive the selection of high-performance aptazyme candidates. Three aptazymes were chosen for detailed characterization and these DNAzymes were found to exhibit a dissociation constant for l-phenylalanine as low as 4.8 μM, a catalytic rate constant improvement as high as 20 000-fold in the presence of l-phenylalanine, and the ability to discriminate against closely related l-phenylalanine analogs including d-phenylalanine. This work has established the Expression-SELEX as an effective SELEX method to enrich high-quality ligand-responsive aptazymes.
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Affiliation(s)
- Binfen Chen
- Medical School, Huaqiao University, Xiamen 361021, P.R. China
| | - Xinmei Yu
- Medical School, Huaqiao University, Xiamen 361021, P.R. China
| | - Ting Gao
- Medical School, Huaqiao University, Xiamen 361021, P.R. China
| | - Yaoyao Wu
- Medical School, Huaqiao University, Xiamen 361021, P.R. China
| | - Xiaojun Zhang
- Chemical Engineering Institute, Huaqiao University, Xiamen 361021, P.R. China
| | - Sanshu Li
- Medical School, Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, Huaqiao University, Xiamen 361021, P.R. China
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18
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Ishaqat A, Zhang X, Liu Q, Zheng L, Herrmann A. Programming DNA Circuits for Controlled Immunostimulation through CpG Oligodeoxynucleotide Delivery. J Am Chem Soc 2023. [PMID: 37267596 DOI: 10.1021/jacs.2c09359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Herein, we present a DNA circuit programmed for the delivery of CpG oligodeoxynucleotides (CpG ODNs) with the pharmacological immunostimulation function. The circuit employs a complementary DNA (cDNA) strand to deactivate the biological function of CpG ODNs via hybridization, while T7 exonuclease mediates the activation by hydrolyzing the cDNA and releasing the CpG ODN as an active moiety. We investigated the influence of several factors on the kinetic profile and temporal behavior of the circuit. These include the design of the cDNA strand, the concentration of the DNA duplex, and the concentration of T7 exonuclease. The DNA circuit's in vitro activation resulted in toll-like receptor 9 stimulation in the HEK-engineered cell line, as well as tumor necrosis factor-alpha release by J774A.1 macrophages. By programming the DNA circuit to control the release of the CpG ODN, we achieved an altered pharmacological profile with acute and potent immunostimulation, in comparison to a system without controlled CpG ODN release, which exhibited a slow and delayed response. Our findings demonstrate the potential of DNA circuits in controlling the pharmacological activity of DNA strands for controlled drug delivery.
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Affiliation(s)
- Aman Ishaqat
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Xiaofeng Zhang
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Qing Liu
- Wenzhou Institute, University of Chinese Academy of Sciences, 25001 Wenzhou, China
| | - Lifei Zheng
- Wenzhou Institute, University of Chinese Academy of Sciences, 25001 Wenzhou, China
| | - Andreas Herrmann
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
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19
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Khaksari S, Abnous K, Hadizadeh F, Ramezani M, Taghdisi SM, Mousavi Shaegh SA. Signal amplification strategies in biosensing of extracellular vesicles (EVs). Talanta 2023; 256:124244. [PMID: 36640707 DOI: 10.1016/j.talanta.2022.124244] [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: 09/17/2022] [Revised: 12/25/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022]
Abstract
Extracellular vesicles (EVs) are membrane-enclosed vesicles secreted from mammalian cells. EVs act as multicomponent delivery vehicles to carry a wide variety of biological molecular information and participate in intercellular communications. Since elevated levels of EVs are associated with some pathological states such as inflammatory diseases and cancers, probing circulating EVs holds a great potential for early diagnostics. To this end, several detection methods have been developed in which biosensors have attracted great attentions in identification of EVs due to their simple instrumentation, versatile design and portability for point-of-care applications. The concentrations of EVs in bodily fluids are extremely low (i.e. 1-100 per μl) at early stages of a disease, which necessitates the use of signal amplification strategies for EVs detection. In this way, this review presents and discusses various amplification strategies for EVs biosensors based on detection modalities including surface plasmon resonance (SPR), calorimetry, fluorescence, electrochemical and electrochemiluminescence (ECL). In addition, microfluidic systems employed for signal amplification are reviewed and discussed in terms of their design and integration with the detection methods.
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Affiliation(s)
- Sedighe Khaksari
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Laboratory of Microfluidics and Medical Microsystems, Bu Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Khalil Abnous
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Farzin Hadizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Ali Mousavi Shaegh
- Orthopedic Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Clinical Research Unit, Mashhad University of Medical Sciences, Mashhad, Iran; Laboratory of Microfluidics and Medical Microsystems, Bu Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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20
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Xiao Y, Yi H, Zhu J, Chen S, Wang G, Liao Y, Lei Y, Chen L, Zhang X, Ye F. Evaluation of DNA adduct damage using G-quadruplex-based DNAzyme. Bioact Mater 2023; 23:45-52. [DOI: 10.1016/j.bioactmat.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/15/2022] [Accepted: 10/02/2022] [Indexed: 11/11/2022] Open
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21
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Shen H, Li Z, Dou B, Feng Q, Wang P. An amplified logic gate driven by in situ synthesis of silver nanoclusters for identification of biomarkers. Chem Commun (Camb) 2023; 59:5705-5708. [PMID: 37083922 DOI: 10.1039/d3cc00643c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
An amplified DNA logic sensor was constructed for the identification of multiple biomarkers, in which the inputs of targets triggered the disassembly of a V-shaped probe (VSP) structure by a strand displacement reaction, leading to the synthesis of silver nanoclusters (AgNCs) for electrocatalytic reduction of H2O2. The sensing platform achieved sensitive detection of methylated DNA and microRNA 122 with detection limits down to 3.4 and 4.1 fM, respectively, and can be used for the assay of clinical serum samples from healthy volunteers and liver injury patients with satisfactory results. The DNA logic sensor exhibited the advantages of convenience, low cost, and versatility without the involvement of electroactive label modification, which is helpful for disease diagnosis as well as the fundamental investigation of interfacial electrochemistry and molecular biology.
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Affiliation(s)
- Hui Shen
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
| | - Zhimin Li
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
| | - Baoting Dou
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
| | - Qiumei Feng
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
| | - Po Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
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22
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Ma Q, Yang Y, Yang W, Yun W, Zhang M. AuNPs-DNAzyme motor triggered two colors DNA tweezer for fluorescent amplified detection of bisphenol A. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 290:122261. [PMID: 36571865 DOI: 10.1016/j.saa.2022.122261] [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] [Received: 09/22/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 06/18/2023]
Abstract
An AuNPs-DNAzyme motor triggered ultrasensitive, two colors DNA tweezer was developed for fluorescent detection of bisphenol A (BPA). BPA can bind with its aptamer on the gold nanoparticles (AuNPs) and reactivate the Pb2+ enzyme strands. Thus, Pb2+ enzyme strands can cleave the substrate strand on AuNPs and release a DNA fragment from AuNPs. The released DNA fragment can bind with the loop of the Y shaped DNA tweezer to form Mg2+-specific DNAzyme, the following cleavage causing the leaving of another two DNA fragments. Then, these two DNA fragments can open the two ends of the Y shaped DNA tweezer, causing the recovery of fluorescent signals. This strategy shows a good linear relationship for BPA detection from 0.44 to 2.2 × 103 pM. The sensitivity has been significantly improved by the two levels of amplification strategy DNAzyme motor and cyclic cleavage of the loop. Importantly, it also can significantly reduce the false positive result by two colors signals. Moreover, it also exhibits satisfactory performance in practical sample detection.
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Affiliation(s)
- Qin Ma
- Division of Gastrointestinal Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yun Yang
- Colorectal Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Wenming Yang
- Division of Gastrointestinal Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Wen Yun
- Chongqing Key Laboratory of Catalysis and New Environmental Materials, College of Environment and Resources, Chongqing Technology and Business University, Chongqing, 400067, China
| | - Mingming Zhang
- Colorectal Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China.
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23
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Wang Z, Lou X. Recent Progress in Functional-Nucleic-Acid-Based Fluorescent Fiber-Optic Evanescent Wave Biosensors. BIOSENSORS 2023; 13:bios13040425. [PMID: 37185500 PMCID: PMC10135899 DOI: 10.3390/bios13040425] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/20/2023] [Accepted: 03/25/2023] [Indexed: 05/17/2023]
Abstract
Biosensors capable of onsite and continuous detection of environmental and food pollutants and biomarkers are highly desired, but only a few sensing platforms meet the "2-SAR" requirements (sensitivity, specificity, affordability, automation, rapidity, and reusability). A fiber optic evanescent wave (FOEW) sensor is an attractive type of portable device that has the advantages of high sensitivity, low cost, good reusability, and long-term stability. By utilizing functional nucleic acids (FNAs) such as aptamers, DNAzymes, and rational designed nucleic acid probes as specific recognition ligands, the FOEW sensor has been demonstrated to be a general sensing platform for the onsite and continuous detection of various targets ranging from small molecules and heavy metal ions to proteins, nucleic acids, and pathogens. In this review, we cover the progress of the fluorescent FNA-based FOEW biosensor since its first report in 1995. We focus on the chemical modification of the optical fiber and the sensing mechanisms for the five above-mentioned types of targets. The challenges and prospects on the isolation of high-quality aptamers, reagent-free detection, long-term stability under application conditions, and high throughput are also included in this review to highlight the future trends for the development of FOEW biosensors capable of onsite and continuous detection.
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Affiliation(s)
- Zheng Wang
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing 100048, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing 100048, China
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Pandey R, Lu Y, McConnell EM, Osman E, Scott A, Gu J, Hoare T, Soleymani L, Li Y. Electrochemical DNAzyme-based biosensors for disease diagnosis. Biosens Bioelectron 2023; 224:114983. [PMID: 36640547 DOI: 10.1016/j.bios.2022.114983] [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: 09/10/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 01/01/2023]
Abstract
DNAzyme-based electrochemical biosensors provide exceptional analytical sensitivity and high target recognition specificity for disease diagnosis. This review provides a critical perspective on the fundamental and applied impact of incorporating DNAzymes in the field of electrochemical biosensing. Specifically, we highlight recent advances in creating DNAzyme-based electrochemical biosensors for diagnosing infectious diseases, cancer and regulatory diseases. We also develop an understanding of challenges around translating the research in the field of DNAzyme-based electrochemical biosensors from labs to clinics, followed by a discussion on different strategies that can be applied to enhance the performance of the currently existing technologies to create truly point-of-care electrochemical DNAzyme biosensors.
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Affiliation(s)
- Richa Pandey
- Department of Engineering Physics, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Department of Biomedical Engineering, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
| | - Yang Lu
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Enas Osman
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Alexander Scott
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Todd Hoare
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Department of Chemical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Leyla Soleymani
- Department of Engineering Physics, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Michael G. DeGroot Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
| | - Yingfu Li
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada; Michael G. DeGroot Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada.
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25
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Kieffer C, Genot AJ, Rondelez Y, Gines G. Molecular Computation for Molecular Classification. Adv Biol (Weinh) 2023; 7:e2200203. [PMID: 36709492 DOI: 10.1002/adbi.202200203] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/28/2022] [Indexed: 01/30/2023]
Abstract
DNA as an informational polymer has, for the past 30 years, progressively become an essential molecule to rationally build chemical reaction networks endowed with powerful signal-processing capabilities. Whether influenced by the silicon world or inspired by natural computation, molecular programming has gained attention for diagnosis applications. Of particular interest for this review, molecular classifiers have shown promising results for disease pattern recognition and sample classification. Because both input integration and computation are performed in a single tube, at the molecular level, this low-cost approach may come as a complementary tool to molecular profiling strategies, where all biomarkers are quantified independently using high-tech instrumentation. After introducing the elementary components of molecular classifiers, some of their experimental implementations are discussed either using digital Boolean logic or analog neural network architectures.
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Affiliation(s)
- Coline Kieffer
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
| | - Anthony J Genot
- LIMMS, CNRS-Institute of Industrial Science, IRL 2820, University of Tokyo, Tokyo, 153-8505, Japan
| | - Yannick Rondelez
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
| | - Guillaume Gines
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
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26
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Recent advance in nucleic acid amplification-integrated methods for DNA methyltransferase assay. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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27
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Yang FA, Wu YT, Liu YW, Liao WC. Hybridization chain reaction-assisted enzyme cascade genosensor for the detection of Listeria monocytogenes. Talanta 2023; 254:124193. [PMID: 36549135 DOI: 10.1016/j.talanta.2022.124193] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022]
Abstract
Foodborne diseases caused by pathogens may threaten public health and the social economy. We demonstrated a method for identifying pathogenic Listeria monocytogenes using DNA logic operations. To achieve accurate species distinguishing, three specific sequences of Listeria monocytogenes genomic DNA were screened out and used as the feature sequences. Three complementary probes with tag modification were designed as sensing elements and exert affinity for magnetic beads, glucose oxidase (GOx), and horseradish peroxidase (HRP). To obtain a digital output (YES/NO answer) for rapid determination, a Boolean logic function was employed. Three sensing probes enabled the recognition of the target sequence (input) and the formation of a target DNA/probe hybrid. Through magnetic separation and affinity binding events, the target DNA/probes hybrid led to the construction of GOx/HRP enzyme cascade, which produced a visualized color signal (output) in the presence of substrates, glucose, and 3, 3', 5, 5'-tetramethylbenzidine (TMB). A hybridization chain reaction (HCR) was coupled with this sensing scaffold to increase the binding of the enzyme cascade and amplify the output signal. The logical functional biosensor showed high selectivity of Listeria monocytogenes over other Listeria species. This sensing platform provides a simple, sensitive, and highly specific method for detecting Listeria monocytogenes.
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Affiliation(s)
- Fu-An Yang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Yi-Ting Wu
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan
| | - Yen-Wenn Liu
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Wei-Ching Liao
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; Medical Device Innovation and Translation Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
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28
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Tang J, Liang A, Yao C, Yang D. Assembly of Rolling Circle Amplification-Produced Ultralong Single-Stranded DNA to Construct Biofunctional DNA Materials. Chemistry 2023; 29:e202202673. [PMID: 36263767 DOI: 10.1002/chem.202202673] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022]
Abstract
The Review by Yang, Yao and colleagues (DOI: 10.1002/chem.202202673) describes recent developments in biofunctional DNA hydrogels and DNA nanocomplexes based on rolling circle amplification (RCA) and introduces assembly strategies and functionalization methods of the ultralong single-strand DNA produced by RCA to construct biofunctional materials.
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Affiliation(s)
- Jianpu Tang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Aiqi Liang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
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29
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Zhou C, Song Y, Jin X, Li B, Pang C. Construction of a scalable DNA computing nano-system for large-scale and complex logical operations. NANOSCALE HORIZONS 2023; 8:176-184. [PMID: 36524605 DOI: 10.1039/d2nh00525e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The predictability of Watson-Crick base pairing provides unique structural programmability to DNA, facilitating the development and application of biomolecules in biocomputing. However, in DNA-based biocomputing, the scale of operation that can be achieved by an existing reaction system is very limited. How to expand the operation range of a logic circuit and realize the integration and extensibility of circuits is always the key problem to be solved in this field. In this work, by designing a multifunctional DNA-nanostructure-based reaction platform, which can realize an output of up to 2n scalable fluorescence signals, combined with the construction of an input "library" and a modular distribution strategy of output signals, for the first time, we successfully performed the calculation of both square roots and cube roots of consecutive integers within a decimal number of "10" and in each result of the operation, two digits after the decimal point are preserved (). We believe that the design concept presented in this work can help effectively solve the urgent problems of biological computing in terms of computational scaling, integration and scalability, and can open up new horizons for the design of new functional devices and complex computing circuits.
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Affiliation(s)
- Chunyang Zhou
- Biomedical Engineering, School of Life Science and Technology, Changchun University of Science and Technology, Changchun, 130031, China.
| | - Yiwei Song
- Biomedical Engineering, School of Life Science and Technology, Changchun University of Science and Technology, Changchun, 130031, China.
| | - Xiuyan Jin
- Biomedical Engineering, School of Life Science and Technology, Changchun University of Science and Technology, Changchun, 130031, China.
| | - Bei Li
- Changchun Institute of Optics, Precision Machinery and Physics, Chinese Academy of Sciences, Changchun, 130031, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunying Pang
- Biomedical Engineering, School of Life Science and Technology, Changchun University of Science and Technology, Changchun, 130031, China.
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30
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Du X, He PP, Wang C, Wang X, Mu Y, Guo W. Fast Transport and Transformation of Biomacromolecular Substances via Thermo-Stimulated Active "Inhalation-Exhalation" Cycles of Hierarchically Structured Smart pNIPAM-DNA Hydrogels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2206302. [PMID: 36268982 DOI: 10.1002/adma.202206302] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Although smart hydrogels hold great promise in biosensing and biomedical applications, their response to external stimuli is governed by the passive diffusion-dependent substance transport between hydrogels and environments and within the 3D hydrogel matrices, resulting in slow response to biomacromolecules and limiting their extensive applications. Herein, inspired by the respiration systems of organisms, an active strategy to achieve highly efficient biomolecular substance transport through the thermo-stimulated "inhalation-exhalation" cycles of hydrogel matrices is demonstrated. The cryo-structured poly(N-isopropylacrylamide) (pNIPAM)-DNA hydrogels, composed of functional DNA-tethered pNIPAM networks and free-water-containing macroporous channels, exhibit thermally triggered fast and reversible shrinking/swelling cycles with high-volume changes, which drive the formation of dynamic water stream to accelerate the intake of external substances and expelling of endogenous substances, thus promoting the functional properties of hydrogel systems. Demonstrated by catalytic DNAzyme and CRISPR-Cas12a-incorporating hydrogels, significantly enhanced catalytic efficiency with up to 280% and 390% is achieved, upon the introduction of active "inhalation-exhalation" cycles, respectively. Moreover, remotely near-infrared (NIR)-triggering of "inhalation-exhalation" cycles is achieved after the introduction of NIR-responsive MXene nanosheets into the hydrogel matrix. These hydrogel systems with enhanced substance transport and transformation properties hold promise in the development of more effective biosensing and therapeutic systems.
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Affiliation(s)
- Xiaoxue Du
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Ping-Ping He
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Chunyan Wang
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Xiaowen Wang
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Yali Mu
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Weiwei Guo
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
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31
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Discovery and translation of functional nucleic acids for clinically diagnosing infectious diseases: Opportunities and challenges. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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32
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Wang Q, Wang Z, He Y, Xiong B, Li Y, Wang F. Chemical and structural modification of RNA-cleaving DNAzymes for efficient biosensing and biomedical applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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33
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Lu JY, Jiang Q, Lei JJ, He YX, Huang WT. Molecular ‘email’: Electrochemical aptasensing of fish pathogens, molecular information encoding, encryption and hiding applications. Anal Chim Acta 2022; 1232:340483. [DOI: 10.1016/j.aca.2022.340483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/01/2022]
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34
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Wang Z, Yang J, Qin G, Zhao C, Ren J, Qu X. An Intelligent Nanomachine Guided by DNAzyme Logic System for Precise Chemodynamic Therapy. Angew Chem Int Ed Engl 2022; 61:e202204291. [DOI: 10.1002/anie.202204291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Zhao Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Jie Yang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Geng Qin
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
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35
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Label-free and dual-mode biosensor for HPV DNA based on DNA/silver nanoclusters and G-quadruplex/hemin DNAzyme. Talanta 2022; 247:123554. [DOI: 10.1016/j.talanta.2022.123554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 12/15/2022]
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36
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Luminescent Aptamer-Based Bioassays for Sensitive Detection of Food Allergens. BIOSENSORS 2022; 12:bios12080644. [PMID: 36005040 PMCID: PMC9405952 DOI: 10.3390/bios12080644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 02/06/2023]
Abstract
The presence of hidden allergens in food products, often due to unintended contamination along the food supply chain (production, transformation, processing, and transport), has raised the urgent need for rapid and reliable analytical methods for detecting trace levels of such species in food products. Indeed, food allergens represent a high-risk factor for allergic subjects due to potentially life-threatening adverse reactions. Portable biosensors based on immunoassays have already been developed as rapid, sensitive, selective, and low-cost analytical platforms that can replace analyses with traditional bench-top instrumentation. Recently, aptamers have attracted great interest as alternative biorecognition molecules for bioassays, since they can bind a variety of targets with high specificity and selectivity, and they enable the development of assays exploiting a variety of transduction and detection technologies. In particular, aptasensors based on luminescence detection have been proposed, taking advantage of the development of ultrasensitive tracers and enhancers. This review aims to summarize and discuss recent efforts in the field of food allergen analysis using aptamer-based bioassays with luminescence detection.
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37
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Cao Y, Li W, Pei R. Exploring the catalytic mechanism of multivalent G-quadruplex/hemin DNAzymes by modulating the position and spatial orientation of connected G-quadruplexes. Anal Chim Acta 2022; 1221:340105. [DOI: 10.1016/j.aca.2022.340105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/06/2022] [Accepted: 06/18/2022] [Indexed: 11/15/2022]
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38
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Wang Z, Yang J, Qin G, Zhao C, Ren J, Qu X. An Intelligent Nanomachine Guided by DNAzyme Logic System for Precise Chemodynamic Therapy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zhao Wang
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization CHINA
| | - Jie Yang
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization CHINA
| | - Geng Qin
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization CHINA
| | - Chuanqi Zhao
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization CHINA
| | - Jinsong Ren
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization CHINA
| | - Xiaogang Qu
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry 5625 Renmin Street 130022 Changchun CHINA
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39
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Su Z, Wen Q, Li S, Guo L, Li M, Xiong Y, Li W, Ren J. A G-quadruplex/hemin structure-undamaged method to inhibit peroxidase-mimic DNAzyme activity for biosensing development. Anal Chim Acta 2022; 1221:340143. [DOI: 10.1016/j.aca.2022.340143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/28/2022] [Accepted: 07/02/2022] [Indexed: 11/29/2022]
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40
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Mao D, Li Q, Li Q, Wang P, Mao C. A conformational study of the 10-23 DNAzyme via programmed DNA self-assembly. Chem Commun (Camb) 2022; 58:6188-6191. [PMID: 35521655 DOI: 10.1039/d2cc01144a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This communication measures the inter-helical angle of the 10-23 DNAzyme-substrate complex by atomic force microscopy (AFM). Herein, we have devised a strategy to assemble the DNAzyme-substrate complex into a periodic DNA 2D array, which allows reliable study of the conformation of the 10-23 DNAzyme by AFM imaging and fast Fourier transform (FFT). Specifically, the angle between the two flanking helical domains of the catalytic core has been determined via the repeating distance of the 2D array. We expect that the same strategy can generally be applicable for studying other nucleic acid structures.
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Affiliation(s)
- Dake Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
| | - Qian Li
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA. .,College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qian Li
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
| | - Pengfei Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
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41
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Wei J, Li Y, Si Q, Xiao Q, Chen Q, Jiao T, Chen Q, Chen X. Hemin/G-quadruplex based electrochemical sensor for highly sensitive detection of ATP in fish. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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42
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van der Linden AJ, Pieters PA, Bartelds MW, Nathalia BL, Yin P, Huck WTS, Kim J, de Greef TFA. DNA Input Classification by a Riboregulator-Based Cell-Free Perceptron. ACS Synth Biol 2022; 11:1510-1520. [PMID: 35381174 PMCID: PMC9016768 DOI: 10.1021/acssynbio.1c00596] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability to recognize molecular patterns is essential for the continued survival of biological organisms, allowing them to sense and respond to their immediate environment. The design of synthetic gene-based classifiers has been explored previously; however, prior strategies have focused primarily on DNA strand-displacement reactions. Here, we present a synthetic in vitro transcription and translation (TXTL)-based perceptron consisting of a weighted sum operation (WSO) coupled to a downstream thresholding function. We demonstrate the application of toehold switch riboregulators to construct a TXTL-based WSO circuit that converts DNA inputs into a GFP output, the concentration of which correlates to the input pattern and the corresponding weights. We exploit the modular nature of the WSO circuit by changing the output protein to the Escherichia coli σ28-factor, facilitating the coupling of the WSO output to a downstream reporter network. The subsequent introduction of a σ28 inhibitor enabled thresholding of the WSO output such that the expression of the downstream reporter protein occurs only when the produced σ28 exceeds this threshold. In this manner, we demonstrate a genetically implemented perceptron capable of binary classification, i.e., the expression of a single output protein only when the desired minimum number of inputs is exceeded.
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Affiliation(s)
- Ardjan J. van der Linden
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Pascal A. Pieters
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Mart W. Bartelds
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Bryan L. Nathalia
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wilhelm T. S. Huck
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Tom F. A. de Greef
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, 3584 CB Utrecht, The Netherlands
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Yerrapragada R M, Mampallil D. Interferon-γ detection in point of care diagnostics: Short review. Talanta 2022; 245:123428. [PMID: 35427946 DOI: 10.1016/j.talanta.2022.123428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/15/2022] [Accepted: 03/30/2022] [Indexed: 12/21/2022]
Abstract
Interferon (IFN)-γ is a cytokine secreted by immune cells. The elevated levels of IFN-γ are an early indicator of multiple diseases such as tuberculosis and autoimmune diseases. This short review focuses on different sensing methods based on optical, electrochemical, and mechanical principles. We explain how specific biorecognition molecules such as antibodies and aptamers are employed in the sensing methods. We also compare different surface functionalization methods and their details. Although the review gives an overview of only IFN-γ sensing, the same strategies can be applied to sensing other analytes with appropriate modifications.
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Affiliation(s)
- Manjoosha Yerrapragada R
- Indian Institute of Science Education and Research Tirupati, Mangalam P O, Tirupati, 517507, India.
| | - Dileep Mampallil
- Indian Institute of Science Education and Research Tirupati, Mangalam P O, Tirupati, 517507, India.
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44
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Zhao R, Yu C, Lu B, Li B. Coupling nucleic acid circuitry with the CRISPR-Cas12a system for universal and signal-on detection. RSC Adv 2022; 12:10374-10378. [PMID: 35425009 PMCID: PMC8977996 DOI: 10.1039/d2ra01332k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
We report a universal and signal-on HCR based detection platform via innovatively coupling the CRISPR-Cas12a system with HCR. By using this CRISPR-HCR pathway, we can detect different targets by only changing the crRNA. The CRISPR-HCR platform coupling with an upstream amplifier can achieve a practical sensitivity as low as ∼aM of ASFV gene in serum.
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Affiliation(s)
- Rujian Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China .,School of Applied Chemistry and Engineering, University of Science and Technology of China Hefei Anhui 230026 China
| | - Chunxu Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China .,School of Applied Chemistry and Engineering, University of Science and Technology of China Hefei Anhui 230026 China
| | - Baiyang Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China
| | - Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China .,School of Applied Chemistry and Engineering, University of Science and Technology of China Hefei Anhui 230026 China
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45
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Adeoye RI, Okaiyeto K, Igunnu A, Oguntibeju OO. Systematic mapping of DNAzymes research from 1995 to 2019. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:384-406. [PMID: 35343361 DOI: 10.1080/15257770.2022.2052318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
DNAzymes (catalytic DNA) have gained significant diagnostic and therapeutic applications with increasing research output over the years. Functional oligonucleotides are used as molecular recognition elements within biosensors for detection of analytes and viral infections such as SARS-CoV-2. DNAzymes are also applied for silencing and regulating cancer specific genes. However, there has not been any report on systematic analysis to track research status, reveal hotspots, and map knowledge in this field. Therefore, in the present study, research articles on DNAzymes from 1995 to 2019 were extracted from Web of Science (SCI-Expanded) after which, 1037 articles were imported into Rstudio (version 3.6.2) and analysed accordingly. The highest number of articles was published in 2019 (n = 138), while the least was in 1995 (n = 1). The articles were published across 216 journals by 2344 authors with 2337 multi-author and 7 single authors. The most prolific authors were Li Y (n = 47), Liu J (n = 46), Wang L (n = 33), Willner I (n = 33) and Zhang L (n = 33). The top three most productive countries were China (n = 2018), USA (n = 447) and Canada (n = 251). The most productive institutions were Hunan University, China (n = 141), University of Illinois, USA (n = 139) and Fuzhou University, China (n = 101). Despite the increasing interest in this field, international collaborations between institutions were very low which requires immediate attention to mitigate challenges such as limited funding, access to facilities, and existing knowledge gap.
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Affiliation(s)
- Raphael Idowu Adeoye
- Enzymology Unit, Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- Biochemistry Unit, Department of Chemistry and Biochemistry, College of Pure and Applied Sciences, Caleb University, Imota, Lagos, Nigeria
| | - Kunle Okaiyeto
- Phytomedicine and Phytochemistry Group, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
| | - Adedoyin Igunnu
- Enzymology Unit, Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Oluwafemi Omoniyi Oguntibeju
- Phytomedicine and Phytochemistry Group, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
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46
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Yum JH, Sugiyama H, Park S. Harnessing DNA as a Designable Scaffold for Asymmetric Catalysis: Recent Advances and Future Perspectives. CHEM REC 2022; 22:e202100333. [PMID: 35312235 DOI: 10.1002/tcr.202100333] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/27/2022]
Abstract
Since the first report of DNAzyme by in vitro selection in 1994, catalytic DNA has investigated extensively, and their application has expanded continually in virtue of rapid advances in molecular biology and biotechnology. Nowadays, DNA is in the second prime time by way of DNA-based hybrid catalysts and DNA metalloenzymes in which helical chirality of DNA serves to asymmetric catalysis. DNA-based hybrid catalysts are attractive system to respond the demand of the times to pursuit green and sustainable society beyond traditional catalytic systems that value reaction efficiency. Herein, we highlight the recent advances and perspective of DNA-based hybrid catalysts with various aspects of DNA as a versatile scaffold for asymmetric synthesis. We hope that scientists in a variety of fields will be encouraged to join and promote remarkable evolution of this interesting research.
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Affiliation(s)
- Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Soyoung Park
- Immunology Frontier Research Center (iFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Japan.,Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Japan
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47
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Quan MX, Yao QF, Liu QY, Bu ZQ, Ding XZ, Xia LQ, Lu JY, Huang WT. Microwave-Assisted Synthesis of Silver Nanoparticles for Multimode Colorimetric Sensing of Multiplex Metal Ions and Molecular Informatization Applications. ACS APPLIED MATERIALS & INTERFACES 2022; 14:9480-9491. [PMID: 35138082 DOI: 10.1021/acsami.1c23559] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plasmonic materials have been widely used in chemo/biosensing and biomedicine. However, little attention has been paid to the application of plasmonic materials in terms of the transition from molecular sensing to molecular informatization. Herein, we demonstrated that silver nanoparticles (AgNPs) prepared through facile and rapid microwave heating have multimode colorimetric sensing capabilities to different metal ions (Cr3+, Hg2+, and Ni2+), which can be further transformed into interesting and powerful molecular information technology (massively parallel molecular logic computing and molecular information protection). The prepared AgNPs can quantitatively and sensitively detect Cr3+ and Hg2+ in actual water samples. The AgNPs' multimode-guided multianalyte sensing processing was further investigated to construct a series of basic logic gates and advanced cascaded logic circuits by considering the analytes as the inputs and the colorimetric signals (like color, absorbance, wavelength shift) as the outputs. Moreover, the selective responses and molecular logic computing ability of AgNPs were also utilized to develop molecular cryptosteganography for encrypting and hiding some specific information, which proves that the molecular world and the information world are interconnected and use each other. This research not only opens the door for the transition from molecular sensing to molecular informatization but also provides an excellent opportunity for the construction of the "metaverse" of the molecular world.
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Affiliation(s)
- Min Xia Quan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, P. R. China
| | - Qing Feng Yao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, P. R. China
| | - Qing Yu Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, P. R. China
| | - Zhen Qi Bu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, P. R. China
| | - Xue Zhi Ding
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, P. R. China
| | - Li Qiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, P. R. China
| | - Jiao Yang Lu
- Academician Workstation, Changsha Medical University, Changsha 410219, P. R. China
| | - Wei Tao Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, P. R. China
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48
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Li F, Song N, Dong Y, Li S, Li L, Liu Y, Li Z, Yang D. A Proton-Activatable DNA-Based Nanosystem Enables Co-Delivery of CRISPR/Cas9 and DNAzyme for Combined Gene Therapy. Angew Chem Int Ed Engl 2022; 61:e202116569. [PMID: 34982495 DOI: 10.1002/anie.202116569] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Indexed: 12/11/2022]
Abstract
CRISPR/Cas9 is emerging as a platform for gene therapeutics, and the treatment efficiency is expected to be enhanced by combination with other therapeutic agents. Herein, we report a proton-activatable DNA-based nanosystem that enables co-delivery of Cas9/sgRNA and DNAzyme for the combined gene therapy of cancer. Ultra-long ssDNA chains, which contained the recognition sequences of sgRNA in Cas9/sgRNA, DNAzyme sequence and HhaI enzyme cleavage site, were synthesized as the scaffold of the nanosystem. The DNAzyme cofactor Mn2+ was used to compress DNA chains to form nanoparticles and acid-degradable polymer-coated HhaI enzymes were assembled on the surface of nanoparticles. In response to protons in lysosome, the polymer coating was decomposed and HhaI enzyme was consequently exposed to recognize and cut off the cleavage sites, thus triggering the release of Cas9/sgRNA and DNAzyme to regulate gene expressions to achieve a high therapeutic efficacy of breast cancer.
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Affiliation(s)
- Feng Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
| | - Nachuan Song
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
| | - Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
| | - Shuai Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
| | - Linghui Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
| | - Yujie Liu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
| | - Zhemian Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P.R. China
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49
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Abstract
Stimuli-responsive DNA-based hydrogels are attracting growing interest because of their smart responsiveness, excellent biocompatibility, regulated biodegradability, and programmable design properties. Integration of reconfigurable DNA architectures and switchable supramolecular moieties (as cross-linkers) in hydrogels by responding to external stimuli provides an ideal approach for the reversible tuning structural and mechanical properties of the hydrogels, which can be exploited in the development of intelligent DNA-based materials. This review highlights recent advances in the design of responsive pure DNA hydrogels, DNA-polymer hybrid hydrogels, and autonomous DNA-based hydrogels with transient behaviors. A variety of chemically and physically triggered DNA-based stimuli-responsive hydrogels and their versatile applications in biosensing, biocatalysis, cell culture and separation, drug delivery, shape memory, self-healing, and robotic actuators are summarized. Finally, we address the key challenges that the field will face in the coming years, and future prospects are identified.
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Affiliation(s)
- Chen Wang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Junji Zhang
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology, No. 130 Meilong Road, Shanghai 200237, China
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50
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Sato Y, Takinoue M. Capsule-like DNA Hydrogels with Patterns Formed by Lateral Phase Separation of DNA Nanostructures. JACS AU 2022; 2:159-168. [PMID: 35098232 PMCID: PMC8790810 DOI: 10.1021/jacsau.1c00450] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Indexed: 05/03/2023]
Abstract
Phase separation is a key phenomenon in artificial cell construction. Recent studies have shown that the liquid-liquid phase separation of designed-DNA nanostructures induces the formation of liquid-like condensates that eventually become hydrogels by lowering the solution temperature. As a compartmental capsule is an essential artificial cell structure, many studies have focused on the lateral phase separation of artificial lipid vesicles. However, controlling phase separation using a molecular design approach remains challenging. Here, we present the lateral liquid-liquid phase separation of DNA nanostructures that leads to the formation of phase-separated capsule-like hydrogels. We designed three types of DNA nanostructures (two orthogonal and a linker nanostructure) that were adsorbed onto an interface of water-in-oil (W/O) droplets via electrostatic interactions. The phase separation of DNA nanostructures led to the formation of hydrogels with bicontinuous, patch, and mix patterns, due to the immiscibility of liquid-like DNA during the self-assembly process. The frequency of appearance of these patterns was altered by designing DNA sequences and altering the mixing ratio of the nanostructures. We constructed a phase diagram for the capsule-like DNA hydrogels by investigating pattern formation under various conditions. The phase-separated DNA hydrogels did not only form on the W/O droplet interface but also on the inner leaflet of lipid vesicles. Notably, the capsule-like hydrogels were extracted into an aqueous solution, maintaining the patterns formed by the lateral phase separation. In addition, the extracted hydrogels were successfully combined with enzymatic reactions, which induced their degradation. Our results provide a method for the design and control of phase-separated hydrogel capsules using sequence-designed DNAs. We envision that by incorporating various DNA nanodevices into DNA hydrogel capsules, the capsules will gain molecular sensing, chemical-information processing, and mechanochemical actuating functions, allowing the construction of functional molecular systems.
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Affiliation(s)
- Yusuke Sato
- Frontier
Research Institute for Interdisciplinary Sciences, Tohoku University, Miyagi 980-8579, Japan
- Department
of Computer Science, Tokyo Institute of
Technology, Kanagawa 226-8502, Japan
| | - Masahiro Takinoue
- Department
of Computer Science, Tokyo Institute of
Technology, Kanagawa 226-8502, Japan
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