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Zhang J, Bai D, Xie G, Xie Y, Lin Y, Hou Y, Yu Y, Zhang Y, Zhao R, Wang Z, Wang L, Chen H. A novel entropy-driven dual-output mode integrated with DNAzyme for enhanced microRNA detection. Talanta 2024; 275:126123. [PMID: 38663065 DOI: 10.1016/j.talanta.2024.126123] [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: 12/22/2023] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 05/30/2024]
Abstract
Accurate microRNA (miRNA) detection is pivotal in the diagnosis and monitoring of cancer. Entropy-driven catalysis (EDC) has attracted widespread attention as an enzyme-free, isothermal technique for miRNA detection owing to its inherent simplicity and reliability. However, conventional EDC is a single-output mode, limiting the efficiency of signal amplification. In this study, a novel EDC dual-output mode was employed in conjunction with DNAzyme, resulting in the development of an EDC dual-end DNAzyme (EDC-DED) approach for highly sensitive miRNA detection. In this system, miRNA-21 initiated the EDC reaction, producing a large amount of catalytically active dual-end Mg2+-dependent DNAzyme. The DNAzyme further cleaved the reporter cyclically, generating a notably amplified fluorescence signal. The proposed method achieved a low detection limit of 2 pM. Compared with the traditional EDC single-end DNAzyme (EDC-SED) strategy, the present method exhibited superior amplification efficiency, enhancing detection sensitivity by approximately 46.5-fold. Furthermore, this platform demonstrated ideal specificity, satisfactory reproducibility and acceptable detection capabilities in clinical serum samples. Therefore, the straightforward and convenient strategy is a potential tool for miRNA analysis, which may provide a new perspective for biological analysis and clinical application.
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Affiliation(s)
- Jianhong Zhang
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Dan Bai
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Guoming Xie
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yaxing Xie
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yu Lin
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Yulei Hou
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Ying Yu
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Yaoyi Zhang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Rong Zhao
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhongzhong Wang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Luojia Wang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Hui Chen
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
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2
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Wu KY, Wang XC, Anderson M, Tran SD. Advancements in Nanosystems for Ocular Drug Delivery: A Focus on Pediatric Retinoblastoma. Molecules 2024; 29:2263. [PMID: 38792122 PMCID: PMC11123804 DOI: 10.3390/molecules29102263] [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: 03/31/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The eye's complex anatomical structures present formidable barriers to effective drug delivery across a range of ocular diseases, from anterior to posterior segment pathologies. Emerging as a promising solution to these challenges, nanotechnology-based platforms-including but not limited to liposomes, dendrimers, and micelles-have shown the potential to revolutionize ophthalmic therapeutics. These nanocarriers enhance drug bioavailability, increase residence time in targeted ocular tissues, and offer precise, localized delivery, minimizing systemic side effects. Focusing on pediatric ophthalmology, particularly on retinoblastoma, this review delves into the recent advancements in functionalized nanosystems for drug delivery. Covering the literature from 2017 to 2023, it comprehensively examines these nanocarriers' potential impact on transforming the treatment landscape for retinoblastoma. The review highlights the critical role of these platforms in overcoming the unique pediatric eye barriers, thus enhancing treatment efficacy. It underscores the necessity for ongoing research to realize the full clinical potential of these innovative drug delivery systems in pediatric ophthalmology.
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Affiliation(s)
- Kevin Y. Wu
- Department of Surgery, Division of Ophthalmology, University of Sherbrooke, Sherbrooke, QC J1G 2E8, Canada; (K.Y.W.)
| | - Xingao C. Wang
- Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3T 1J4, Canada
| | - Maude Anderson
- Department of Surgery, Division of Ophthalmology, University of Sherbrooke, Sherbrooke, QC J1G 2E8, Canada; (K.Y.W.)
| | - Simon D. Tran
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC H3A 1G1, Canada
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3
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Dubovichenko MV, Batsa M, Bobkov GA, Vlasov GS, El-Deeb AA, Kolpashchikov DM. Multivalent DNAzyme agents for cleaving folded RNA. Nucleic Acids Res 2024:gkae295. [PMID: 38661191 DOI: 10.1093/nar/gkae295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024] Open
Abstract
Multivalent recognition and binding of biological molecules is a natural phenomenon that increases the binding stability (avidity) without decreasing the recognition specificity. In this study, we took advantage of this phenomenon to increase the efficiency and maintain high specificity of RNA cleavage by DNAzymes (Dz). We designed a series of DNA constructs containing two Dz agents, named here bivalent Dz devices (BDD). One BDD increased the cleavage efficiency of a folded RNA fragment up to 17-fold in comparison with the Dz of a conventional design. Such an increase was achieved due to both the improved RNA binding and the increased probability of RNA cleavage by the two catalytic cores. By moderating the degree of Dz agent association in BDD, we achieved excellent selectivity in differentiating single-base mismatched RNA, while maintaining relatively high cleavage rates. Furthermore, a trivalent Dz demonstrated an even greater efficiency than the BDD in cleaving folded RNA. The data suggests that the cooperative action of several RNA-cleaving units can significantly improve the efficiency and maintain high specificity of RNA cleavage, which is important for the development of Dz-based gene knockdown agents.
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Affiliation(s)
- Mikhail V Dubovichenko
- Laboratory of Frontier Nucleic Acid Technologies in Gene Therapy of Cancer, SCAMT Institute, ITMO University, Saint-Petersburg, 191002, Russia
| | - Michael Batsa
- Laboratory of Frontier Nucleic Acid Technologies in Gene Therapy of Cancer, SCAMT Institute, ITMO University, Saint-Petersburg, 191002, Russia
| | - Gleb A Bobkov
- Laboratory of Frontier Nucleic Acid Technologies in Gene Therapy of Cancer, SCAMT Institute, ITMO University, Saint-Petersburg, 191002, Russia
| | - Gleb S Vlasov
- Laboratory of Frontier Nucleic Acid Technologies in Gene Therapy of Cancer, SCAMT Institute, ITMO University, Saint-Petersburg, 191002, Russia
| | - Ahmed A El-Deeb
- Laboratory of Frontier Nucleic Acid Technologies in Gene Therapy of Cancer, SCAMT Institute, ITMO University, Saint-Petersburg, 191002, Russia
| | - Dmitry M Kolpashchikov
- Laboratory of Frontier Nucleic Acid Technologies in Gene Therapy of Cancer, SCAMT Institute, ITMO University, Saint-Petersburg, 191002, Russia
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
- National Center for Forensic Science, University of Central Florida, Orlando, FL, 32816, USA
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4
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Ali M, Nair P, Capretta A, Brennan JD. In-vitro Clinical Diagnostics using RNA-Cleaving DNAzymes. Chembiochem 2024:e202400085. [PMID: 38574237 DOI: 10.1002/cbic.202400085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/06/2024]
Abstract
Over the last three decades, significant advancements have been made in the development of biosensors and bioassays that use RNA-cleaving DNAzymes (RCDs) as molecular recognition elements. While early examples of RCDs were primarily responsive to metal ions, the past decade has seen numerous RCDs reported for more clinically relevant targets such as bacteria, cancer cells, small metabolites, and protein biomarkers. Over the past 5 years several RCD-based biosensors have also been evaluated using either spiked biological matrixes or patient samples, including blood, serum, saliva, nasal mucus, sputum, urine, and faeces, which is a critical step toward regulatory approval and commercialization of such sensors. In this review, an overview of the methods used to generate RCDs and the properties of key RCDs that have been utilized for in vitro testing is first provided. Examples of RCD-based assays and sensors that have been used to test either spiked biological samples or patient samples are then presented, highlighting assay performance in different biological matrixes. A summary of current prospects and challenges for development of in vitro diagnostic tests incorporating RCDs and an overview of future directions of the field is also provided.
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Affiliation(s)
- Monsur Ali
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Parameswaran Nair
- Division of Respirology, McMaster University, and, Firestone Institute of Respiratory Health at St. Joseph's Health Care, Hamilton, ON, L8N 4A6, Canada
| | - Alfredo Capretta
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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Li Y, Zhou P, Wang Z, Ren Y, Zhu X, Wang J, Yan H, Hua L, Gao F. Sea Anemone-like Nanomachine Based on DNA Strand Displacement Composed of Three Boolean Logic Gates: Diversified Input for Intracellular Multitarget Detection. Anal Chem 2024; 96:4120-4128. [PMID: 38412037 DOI: 10.1021/acs.analchem.3c05059] [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: 02/29/2024]
Abstract
Efficient and accurate acquisition of cellular biomolecular information is crucial for exploring cell fate, achieving early diagnosis, and the effective treatment of various diseases. However, current DNA biosensors are mostly limited to single-target detection, with few complex logic circuits for comprehensive analysis of three or more targets. Herein, we designed a sea anemone-like DNA nanomachine based on DNA strand displacement composed of three logic gates (YES-AND-YES) and delivered into the cells using gold nano bipyramid carriers. The AND gate activation depends on the trigger chain released by upstream DNA strand displacement reactions, while the output signal relies on the downstream DNAzyme structure. Under the influence of diverse inputs (including enzymes, miRNA, and metal ions), the interconnected logic gates simultaneously perform logical analysis on multiple targets, generating a unique output signal in the YES/NO format. This sensor can successfully distinguish healthy cells from tumor cells and can be further used for the diagnosis of different tumor cells, providing a promising platform for accurate cell-type identification.
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Affiliation(s)
- Yuting Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
| | - Peng Zhou
- Department of Orthopedics, The Affiliated Huai'an Hospital of Xuzhou Medical University, The Second People's Hospital of Huai'an, Huai'an 223002, China
| | - Zhenxin Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
| | - Yiping Ren
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
| | - Xu Zhu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
| | - Jin Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
| | - Hanrong Yan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
| | - Lei Hua
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China
| | - Fenglei Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
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Hu X, Zhang D, Huang L, Zeng Z, Su Y, Chen S, Lin X, Hong S. Construction of a Functional Nucleic Acid-Based Artificial Vesicle-Encapsulated Composite Nanoparticle and Its Application in Retinoblastoma-Targeted Theranostics. ACS Biomater Sci Eng 2024; 10:1830-1842. [PMID: 38408449 DOI: 10.1021/acsbiomaterials.3c01972] [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] [Indexed: 02/28/2024]
Abstract
Retinoblastoma (RB) is an aggressive tumor of the infant retina. However, the ineffective targeting of its theranostic agents results in poor imaging and therapeutic efficacy, which makes it difficult to identify and treat RB at an early stage. In order to improve the imaging and therapeutic efficacy, we constructed an RB-targeted artificial vesicle composite nanoparticle. In this study, the MnO2 nanosponge (hMNs) was used as the core to absorb two fluorophore-modified DNAzymes to form the Dual/hMNs nanoparticle; after loaded with the artificial vesicle derived from human red blood cells, the RB-targeted DNA aptamers were modified on the surface, thus forming the Apt-EG@Dual/hMNs complex nanoparticle. The DNA aptamer endows this nanoparticle to target the nucleolin-overexpressed RB cell membrane specifically and enters cells via endocytosis. The nanoparticle could release fluorophore-modified DNAzymes and supplies Mn2+ as a DNAzyme cofactor and a magnetic resonance imaging (MRI) agent. Subsequently, the DNAzymes can target two different mRNAs, thereby realizing fluorescence/MR bimodal imaging and dual-gene therapy. This study is expected to provide a reliable and valuable basis for ocular tumor theranostics.
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Affiliation(s)
- Xueqi Hu
- School of Medical Imaging, Fujian Medical University, Fuzhou, Fujian 350122, PR China
| | - Dongdong Zhang
- School of Medical Imaging, Fujian Medical University, Fuzhou, Fujian 350122, PR China
| | - Linjie Huang
- School of Medical Imaging, Fujian Medical University, Fuzhou, Fujian 350122, PR China
| | - Zheng Zeng
- School of Medical Imaging, Fujian Medical University, Fuzhou, Fujian 350122, PR China
| | - Yina Su
- School of Medical Imaging, Fujian Medical University, Fuzhou, Fujian 350122, PR China
| | - Shanshan Chen
- Department of Clinical Laboratory, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, Fujian 350122, PR China
| | - Xiahui Lin
- School of Medical Imaging, Fujian Medical University, Fuzhou, Fujian 350122, PR China
| | - Shanni Hong
- School of Medical Imaging, Fujian Medical University, Fuzhou, Fujian 350122, PR China
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7
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Shen T, Huang X, Zhang Y, Tong Y, Shi Y, Guo J, Zou X, Xu Y, Dai Z. Dephosphorylation Switch DNAzyme-RCA Circuit: A Robust Strategy for the Homogeneous and Reliable Detection of FTO Demethylase. Anal Chem 2024; 96:1686-1692. [PMID: 38118402 DOI: 10.1021/acs.analchem.3c04762] [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: 12/22/2023]
Abstract
Fat mass and obesity-associated protein (FTO) plays a crucial role in regulating the dynamic modification of N6-methyladenosine (m6A) in eukaryotic mRNA. Sensitive detection of the FTO level and efficient evaluation of the FTO demethylase activity are of great importance to early cancer diagnosis and anticancer drug discovery, which are currently challenged by limited sensitivity/precision and low throughput. Herein, a robust strategy based on the dephosphorylation switch DNAzyme-rolling circle amplification (RCA) circuit, termed DSD-RCA, is developed for highly sensitive detection of FTO and inhibitor screening. Initially, the catalytic activity of DNAzyme is silenced by engineering with an m6A modification in its catalytic core. Only in the presence of target FTO can the methyl group on DNAzyme be eliminated, resulting in the activation of the catalytic activity of DNAzyme and thus cleaving the hairpin substrate to release numerous primers. Different from the conventional methods that use the downstream cleavage primer with the original 3'-hydroxyl end directly as the RCA primer with the problem of high background signal, which should be compensated by additional separation and wash steps in heterogeneous format, our DSD-RCA assay uses the upstream cleavage primer with a 2',3'-cyclic phosphate terminus at the 3'-end serving as an intrinsically blocked 3' end. Only after a dephosphorylation reaction mediated by T4 polynucleotide kinase can the upstream cleavage primers with a resultant 3'-hydroxyl end be extended by RCA. With the high signal-to-noise ratio and homogeneous property, the proposed platform can sensitively detect FTO with a limit of detection of 31.4 pM, and the relative standard deviations (RSDs %) ranging from 0.8 to 2.0% were much lower than the heterogeneous methods. The DSD-RCA method was applied for analyzing FTO in cytoplasmic lysates from different cell lines and tissues of breast cancer patients and further used for screening FTO inhibitors without the need for separation or cleaning, providing an opportunity for achieving high throughput and demonstrating the potential applications of this strategy in disease diagnostics, drug discovery, and biological applications.
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Affiliation(s)
- Taorong Shen
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xing Huang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen 518107, China
| | - Yanfei Zhang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen 518107, China
| | - Yanli Tong
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen 518107, China
| | - Yakun Shi
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen 518107, China
| | - Jianhe Guo
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen 518107, China
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuzhi Xu
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen 518107, China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen 518107, China
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8
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Wu R, Chen Y, Zhang Y, Liu R, Zhang Q, Zhang C. Catalytic Gold Nanoparticle Assembly Programmed by DNAzyme Circuits. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2307107. [PMID: 38191832 DOI: 10.1002/smll.202307107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/19/2023] [Indexed: 01/10/2024]
Abstract
Assembled gold nanoparticle (AuNP) superstructures can generate unique physicochemical characteristics and be used in various applications, thus becoming an attractive research field. Recently, several DNA-assisted gold nanoparticle assembly methods have been rigorously developed that typically require a non-catalytic equimolar molecular assembly to guarantee the designed assembly. Although efficient and accurate, exploring such non-catalytic nanoparticle assemblies in the complex cellular milieu under low trigger concentrations remains challenging. Therefore, developing a catalytic method that facilitates gold nanoparticle assemblies with relatively low DNA trigger concentrations is desirable. In this report, a catalytic method to program gold nanoparticle assemblies by DNAzyme circuits is presented, where only a small number of DNA triggers are able to induce the production of a large number of the desired nanoparticle assemblies. The feasibility of using logic DNAzyme circuits to control catalytic nanoparticle assemblies is experimentally verified. Additionally, catalytic AuNP assembly systems are established with cascading and feedback functions. The work provides an alternative research direction to enrich the tool library of nanoparticle assembly and their application in biosensing and nanomedicine.
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Affiliation(s)
- Ranfeng Wu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yiming Chen
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing, 100871, China
| | - Yongpeng Zhang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 100096, China
| | - Rongming Liu
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Cheng Zhang
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing, 100871, China
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9
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Lei L, Burton ZF. The 3 31 Nucleotide Minihelix tRNA Evolution Theorem and the Origin of Life. Life (Basel) 2023; 13:2224. [PMID: 38004364 PMCID: PMC10672568 DOI: 10.3390/life13112224] [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: 10/16/2023] [Revised: 11/08/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
There are no theorems (proven theories) in the biological sciences. We propose that the 3 31 nt minihelix tRNA evolution theorem be universally accepted as one. The 3 31 nt minihelix theorem completely describes the evolution of type I and type II tRNAs from ordered precursors (RNA repeats and inverted repeats). Despite the diversification of tRNAome sequences, statistical tests overwhelmingly support the theorem. Furthermore, the theorem relates the dominant pathway for the origin of life on Earth, specifically, how tRNAomes and the genetic code may have coevolved. Alternate models for tRNA evolution (i.e., 2 minihelix, convergent and accretion models) are falsified. In the context of the pre-life world, tRNA was a molecule that, via mutation, could modify anticodon sequences and teach itself to code. Based on the tRNA sequence, we relate the clearest history to date of the chemical evolution of life. From analysis of tRNA evolution, ribozyme-mediated RNA ligation was a primary driving force in the evolution of complexity during the pre-life-to-life transition. TRNA formed the core for the evolution of living systems on Earth.
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Affiliation(s)
- Lei Lei
- School of Biological Sciences, University of New England, Biddeford, ME 04005, USA;
| | - Zachary Frome Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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Zhu X, Xu J, Ling G, Zhang P. Tunable metal-organic frameworks assist in catalyzing DNAzymes with amplification platforms for biomedical applications. Chem Soc Rev 2023; 52:7549-7578. [PMID: 37817667 DOI: 10.1039/d3cs00386h] [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: 10/12/2023]
Abstract
Various binding modes of tunable metal organic frameworks (MOFs) and functional DNAzymes (Dzs) synergistically catalyze the emergence of abundant functional nanoplatforms. Given their serial variability in formation, structural designability, and functional controllability, Dzs@MOFs tend to be excellent building blocks for the precise "intelligent" manufacture of functional materials. To present a clear outline of this new field, this review systematically summarizes the progress of Dz integration into MOFs (MOFs@Dzs) through different methods, including various surface infiltration, pore encapsulation, covalent binding, and biomimetic mineralization methods. Atomic-level and time-resolved catalytic mechanisms for biosensing and imaging are made possible by the complex interplay of the distinct molecular structure of Dzs@MOF, conformational flexibility, and dynamic regulation of metal ions. Exploiting the precision of DNAzymes, MOFs@Dzs constructed a combined nanotherapy platform to guide intracellular drug synthesis, photodynamic therapy, catalytic therapy, and immunotherapy to enhance gene therapy in different ways, solving the problems of intracellular delivery inefficiency and insufficient supply of cofactors. MOFs@Dzs nanostructures have become excellent candidates for biosensing, bioimaging, amplification delivery, and targeted cancer gene therapy while emphasizing major advancements and seminal endeavors in the fields of biosensing (nucleic acid, protein, enzyme activity, small molecules, and cancer cells), biological imaging, and targeted cancer gene delivery and gene therapy. Overall, based on the results demonstrated to date, we discuss the challenges that the emerging MOFs@Dzs might encounter in practical future applications and briefly look forward to their bright prospects in other fields.
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Affiliation(s)
- Xiaoguang Zhu
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Jiaqi Xu
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Guixia Ling
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Peng Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
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