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Jia X, He J, Li M, Ye J, Zhang Y, Yang C, Yuan R, Xu W. Stimulus-Responsive Four-Stranded DNA Nanoring Assembly to Host Multiple Nanosilver Clusters for Cooperatively Enhanced Fluorescence Biosensing. Anal Chem 2024; 96:10677-10685. [PMID: 38889311 DOI: 10.1021/acs.analchem.4c01538] [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
Exploring the ability of four-stranded DNA nanorings (fsDNRs) to host multiple nanosilver clusters (NAgCs) for cooperatively amplifiable fluorescence biosensing to a specific initiator (tI*) is fascinating. By designing three DNA single strands and three analogous stem-loop hairpins, we developed a functional fsDNR through sequential cross-opening and overlapped hybridization. Note that a substrate strand (SS) was programmed with six modules: two severed splits (sT and sT') of NAgCs template, two sequestered segments by a middle unpaired spacer, and a partition for tI*-recognizable displacement, while sT and sT' were also tethered in two ends of three hairpins. At first, a triple dsDNA complex with stimulus-responsiveness was formed to guide the specific binding to tI*, while the exposed toehold of the SS activated the forward cascade hybridization of three hairpins, until the ring closure in the tailored self-assembly pathway for forming the fsDNR. The resulting four duplexes forced each pair of sT/sT' to be merged as the parent template in four nicks, guiding the preferential synthesis of four clusters in the shared fsDNR, thereby cooperatively amplifying the green fluorescence signal for sensitive assay of tI*. Meanwhile, the topological conformation of fsDNR can be stabilized by the as-formed cluster adducts to rivet the pair of two splits in the nicks. Benefitting from the self-enhanced effect of multiple emitters, this label-free fluorescent sensing strategy features simplicity, rapidity, and high on-off contrast, without involving complicated nucleic acid amplifiers.
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Affiliation(s)
- Xinyue Jia
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education; Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies; School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jiayang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education; Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies; School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Mengdie Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education; Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies; School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jingjing Ye
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education; Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies; School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yuqing Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education; Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies; School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Chunli Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education; Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies; School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education; Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies; School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education; Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies; School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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Liu M, Tan Y, Zhou C, Fu Z, Huang R, Li J, Li L. Fluorogenic Aptamer-Based Hybridization Chain Reaction for Signal-Amplified Imaging of Apurinic/Apyrimidinic Endonuclease 1 in Living Cells. BIOSENSORS 2024; 14:274. [PMID: 38920578 PMCID: PMC11202136 DOI: 10.3390/bios14060274] [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: 04/08/2024] [Revised: 04/28/2024] [Accepted: 05/01/2024] [Indexed: 06/27/2024]
Abstract
A fluorogenic aptamer (FA)-based hybridization chain reaction (HCR) could provide a sensitive and label-free signal amplification method for imaging molecules in living cells. However, existing FA-HCR methods usually face some problems, such as a complicated design and significant background leakage, which greatly limit their application. Herein, we developed an FA-centered HCR (FAC-HCR) method based on a remote toehold-mediated strand displacement reaction. Compared to traditional HCRs mediated by four hairpin probes (HPs) and two HPs, the FAC-HCR displayed significantly decreased background leakage and improved sensitivity. Furthermore, the FAC-HCR was used to test a non-nucleic acid target, apurinic/apyrimidinic endonuclease 1 (APE1), an important BER-involved endonuclease. The fluorescence analysis results confirmed that FAC-HCR can reach a detection limit of 0.1174 U/mL. By using the two HPs for FAC-HCR with polyetherimide-based nanoparticles, the activity of APE1 in living cells can be imaged. In summary, this study could provide a new idea to design an FA-based HCR and improve the performance of HCRs in live cell imaging.
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Affiliation(s)
- Meixi Liu
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572024, China; (M.L.); (Y.T.); (C.Z.); (Z.F.)
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572024, China
| | - Yunjie Tan
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572024, China; (M.L.); (Y.T.); (C.Z.); (Z.F.)
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572024, China
| | - Chen Zhou
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572024, China; (M.L.); (Y.T.); (C.Z.); (Z.F.)
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572024, China
| | - Zhaoming Fu
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572024, China; (M.L.); (Y.T.); (C.Z.); (Z.F.)
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572024, China
| | - Ru Huang
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572024, China; (M.L.); (Y.T.); (C.Z.); (Z.F.)
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572024, China
| | - Jin Li
- Department of Painology, Hainan Cancer Hospital, Haikou 570311, China
| | - Le Li
- NHC Key Laboratory of Tropical Disease Control, Hainan Medical University, Haikou 571199, China;
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Wang W, Li X, Zeng K, Lu Y, Jia B, Lv J, Wu C, Wang X, Zhang X, Zhang Z. Improved Catalytic Activity of Spherical Nucleic Acid Enzymes by Hybridization Chain Reaction and Its Application for Sensitive Analysis of Aflatoxin B1. SENSORS (BASEL, SWITZERLAND) 2024; 24:2325. [PMID: 38610537 PMCID: PMC11014268 DOI: 10.3390/s24072325] [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: 02/26/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024]
Abstract
Conventional spherical nucleic acid enzymes (SNAzymes), made with gold nanoparticle (AuNPs) cores and DNA shells, are widely applied in bioanalysis owing to their excellent physicochemical properties. Albeit important, the crowded catalytic units (such as G-quadruplex, G4) on the limited AuNPs surface inevitably influence their catalytic activities. Herin, a hybridization chain reaction (HCR) is employed as a means to expand the quantity and spaces of G4 enzymes for their catalytic ability enhancement. Through systematic investigations, we found that when an incomplete G4 sequence was linked at the sticky ends of the hairpins with split modes (3:1 and 2:2), this would significantly decrease the HCR hybridization capability due to increased steric hindrance. In contrast, the HCR hybridization capability was remarkably enhanced after the complete G4 sequence was directly modified at the non-sticky end of the hairpins, ascribed to the steric hindrance avoided. Accordingly, the improved SNAzymes using HCR were applied for the determination of AFB1 in food samples as a proof-of-concept, which exhibited outstanding performance (detection limit, 0.08 ng/mL). Importantly, our strategy provided a new insight for the catalytic activity improvement in SNAzymes using G4 as a signaling molecule.
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Affiliation(s)
- Wenjun Wang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
| | - Xuesong Li
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
| | - Kun Zeng
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
| | - Yanyan Lu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
| | - Boyuan Jia
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
| | - Jianxia Lv
- National Narcotics Laboratory Beijing Regional Center, Beijing 100164, China; (J.L.); (C.W.)
| | - Chenghao Wu
- National Narcotics Laboratory Beijing Regional Center, Beijing 100164, China; (J.L.); (C.W.)
| | - Xinyu Wang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
| | - Xinshuo Zhang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
| | - Zhen Zhang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
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Kosara S, Singh R, Bhatia D. Structural DNA nanotechnology at the nexus of next-generation bio-applications: challenges and perspectives. NANOSCALE ADVANCES 2024; 6:386-401. [PMID: 38235105 PMCID: PMC10790967 DOI: 10.1039/d3na00692a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024]
Abstract
DNA nanotechnology has significantly progressed in the last four decades, creating nucleic acid structures widely used in various biological applications. The structural flexibility, programmability, and multiform customization of DNA-based nanostructures make them ideal for creating structures of all sizes and shapes and multivalent drug delivery systems. Since then, DNA nanotechnology has advanced significantly, and numerous DNA nanostructures have been used in biology and other scientific disciplines. Despite the progress made in DNA nanotechnology, challenges still need to be addressed before DNA nanostructures can be widely used in biological interfaces. We can open the door for upcoming uses of DNA nanoparticles by tackling these issues and looking into new avenues. The historical development of various DNA nanomaterials has been thoroughly examined in this review, along with the underlying theoretical underpinnings, a summary of their applications in various fields, and an examination of the current roadblocks and potential future directions.
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Affiliation(s)
- Sanjay Kosara
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar Palaj Gujarat 382355 India
| | - Ramesh Singh
- Department of Mechanical Engineering, Colorado State University Fort Collins CO USA
| | - Dhiraj Bhatia
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar Palaj Gujarat 382355 India
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Lin B, Xiao F, Jiang J, Zhao Z, Zhou X. Engineered aptamers for molecular imaging. Chem Sci 2023; 14:14039-14061. [PMID: 38098720 PMCID: PMC10718180 DOI: 10.1039/d3sc03989g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
Molecular imaging, including quantification and molecular interaction studies, plays a crucial role in visualizing and analysing molecular events occurring within cells or organisms, thus facilitating the understanding of biological processes. Moreover, molecular imaging offers promising applications for early disease diagnosis and therapeutic evaluation. Aptamers are oligonucleotides that can recognize targets with a high affinity and specificity by folding themselves into various three-dimensional structures, thus serving as ideal molecular recognition elements in molecular imaging. This review summarizes the commonly employed aptamers in molecular imaging and outlines the prevalent design approaches for their applications. Furthermore, it highlights the successful application of aptamers to a wide range of targets and imaging modalities. Finally, the review concludes with a forward-looking perspective on future advancements in aptamer-based molecular imaging.
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Affiliation(s)
- Bingqian Lin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Feng Xiao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Jinting Jiang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Zhengjia Zhao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
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Lee M, Shin S, Kim S, Park N. Recent Advances in Biological Applications of Aptamer-Based Fluorescent Biosensors. Molecules 2023; 28:7327. [PMID: 37959747 PMCID: PMC10647268 DOI: 10.3390/molecules28217327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Aptamers have been spotlighted as promising bio-recognition elements because they can be tailored to specific target molecules, bind to targets with a high affinity and specificity, and are easy to chemically synthesize and introduce functional groups to. In particular, fluorescent aptasensors are widely used in biological applications to diagnose diseases as well as prevent diseases by detecting cancer cells, viruses, and various biomarkers including nucleic acids and proteins as well as biotoxins and bacteria from food because they have the advantages of a high sensitivity, selectivity, rapidity, a simple detection process, and a low price. We introduce screening methods for isolating aptamers with q high specificity and summarize the sequences and affinities of the aptamers in a table. This review focuses on aptamer-based fluorescence detection sensors for biological applications, from fluorescent probes to mechanisms of action and signal amplification strategies.
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Affiliation(s)
- Minhyuk Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea; (M.L.); (S.K.)
| | - Seonhye Shin
- Department of Chemistry, The Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Republic of Korea;
| | - Sungjee Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea; (M.L.); (S.K.)
| | - Nokyoung Park
- Department of Chemistry, The Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Republic of Korea;
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Wu K, Ma C, Wang Y. Functional Nucleic Acid Probes Based on Two-Photon for Biosensing. BIOSENSORS 2023; 13:836. [PMID: 37754070 PMCID: PMC10527542 DOI: 10.3390/bios13090836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023]
Abstract
Functional nucleic acid (FNA) probes have been widely used in environmental monitoring, food analysis, clinical diagnosis, and biological imaging because of their easy synthesis, functional modification, flexible design, and stable properties. However, most FNA probes are designed based on one-photon (OP) in the ultraviolet or visible regions, and the effectiveness of these OP-based FNA probes may be hindered by certain factors, such as their potential for photodamage and limited light tissue penetration. Two-photon (TP) is characterized by the nonlinear absorption of two relatively low-energy photons of near-infrared (NIR) light with the resulting emission of high-energy ultraviolet or visible light. TP-based FNA probes have excellent properties, including lower tissue self-absorption and autofluorescence, reduced photodamage and photobleaching, and higher spatial resolution, making them more advantageous than the conventional OP-based FNA probes in biomedical sensing. In this review, we summarize the recent advances of TP-excited and -activated FNA probes and detail their applications in biomolecular detection. In addition, we also share our views on the highlights and limitations of TP-based FNA probes. The ultimate goal is to provide design approaches for the development of high-performance TP-based FNA probes, thereby promoting their biological applications.
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Affiliation(s)
- Kefeng Wu
- GBA Branch of Aerospace Information Research Institute, Chinese Academy of Sciences, Guangzhou 510700, China
- Guangdong Provincial Key Laboratory of Terahertz Quantum Electromagnetics, Guangzhou 510700, China
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Yisen Wang
- GBA Branch of Aerospace Information Research Institute, Chinese Academy of Sciences, Guangzhou 510700, China
- Guangdong Provincial Key Laboratory of Terahertz Quantum Electromagnetics, Guangzhou 510700, China
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Li J, Yan R, Shi S, Lin Y. Recent progress and application of the tetrahedral framework nucleic acid materials on drug delivery. Expert Opin Drug Deliv 2023; 20:1511-1530. [PMID: 37898874 DOI: 10.1080/17425247.2023.2276285] [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: 09/16/2023] [Accepted: 10/24/2023] [Indexed: 10/30/2023]
Abstract
INTRODUCTION The application of DNA framework nucleic acid materials in the biomedical field has witnessed continual expansion. Among them, tetrahedral framework nucleic acids (tFNAs) have gained significant traction as the foremost biological vectors due to their superior attributes of editability, low immunogenicity, biocompatibility, and biodegradability. tFNAs have demonstrated promising results in numerous in vitro and in vivo applications. AREAS COVERED This review summarizes the latest research on tFNAs in drug delivery, including a discussion of the advantages of tFNAs in regulating biological behaviors, and highlights the updated development and advantageous applications of tFNAs-based nanostructures from static design to dynamically responsive design. EXPERT OPINION tFNAs possess distinct biological regulatory attributes and can be taken up by cells without the requirement of transfection, differentiating them from other biological vectors. tFNAs can be easily physically/chemically modified and seamlessly incorporated with other functional systems. The static design of the tFNAs-based drug delivery system makes it versatile, reproducible, and predictable. Further use of the dynamic response mechanism of DNA to external stimuli makes tFNAs-based drug delivery more effective and specific, improving the uptake and utilization of the payload by the intended target. Dynamic targeting is poised to become the future primary approach for drug delivery.
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Affiliation(s)
- Jiajie Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, Department of Plastic Surgery and Cosmetic Dermatology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Ran Yan
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan, China
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