1
|
Masurier A, Sieskind R, Gines G, Rondelez Y. DNA circuit-based immunoassay for ultrasensitive protein pattern classification. Analyst 2024. [PMID: 39206940 DOI: 10.1039/d4an00728j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Cytokines are important immune modulators, and pivotal biomarkers for the diagnostic of various diseases. In standard analytical procedure, each protein is detected individually, using for instance gold standard ELISA protocols or nucleic acid amplification-based immunoassays. In recent years, DNA nanotechnology has been employed for creating sophisticated biomolecular systems that perform neuromorphic computing on molecular inputs, opening the door to concentration pattern recognition for biomedical applications. This work introduces immuno-PUMA (i-PUMA), an isothermal amplification-based immunoassay for ultrasensitive protein detection. The assay couples the convenience of supported format of an ELISA protocol with the computing capabilities of a DNA/enzyme circuit. We demonstrate a limit of detection of 2.1 fM, 8.7 fM and 450 aM for IL12, IL4 and IFNγ cytokines, respectively, outperforming the traditional ELISA format. i-PUMA's versatility extends to molecular computation, allowing the creation of 2-input perceptron-like classifiers for IL12 and IL4, with tunable weight sign and amplitude. Overall, i-PUMA represents a sensitive, low-cost, and versatile immunoassay with potential applications in multimarker-based sample classification, complementing existing molecular profiling techniques.
Collapse
Affiliation(s)
- Antoine Masurier
- Gulliver Laboratory, ESPCI Paris Université PSL, 10 rue Vauquelin, 75005 Paris, France.
| | - Rémi Sieskind
- Gulliver Laboratory, ESPCI Paris Université PSL, 10 rue Vauquelin, 75005 Paris, France.
| | - Guillaume Gines
- Gulliver Laboratory, ESPCI Paris Université PSL, 10 rue Vauquelin, 75005 Paris, France.
| | - Yannick Rondelez
- Gulliver Laboratory, ESPCI Paris Université PSL, 10 rue Vauquelin, 75005 Paris, France.
| |
Collapse
|
2
|
Gao Y, Ang YS, Yung LYL. One-Pot Detection of Proteins Using a Two-Way Extension-Based Assay with Cas12a. ACS Sens 2024; 9:3928-3937. [PMID: 39078660 DOI: 10.1021/acssensors.4c00370] [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: 07/31/2024]
Abstract
Protein biomarkers are an important class of biomarkers in disease diagnosis and are traditionally detected by enzyme-linked immunosorbent assay and mass spectrometry, which involve multiple steps and a complex workflow. In recent years, many CRISPR-Cas12a-based methods for protein detection have been developed; however, most of them have not overcome the workflow complications observed in traditional assays, limiting their applicability in point-of-care testing. In this work, we designed a single-step, one-pot, and proximity-based isothermal immunoassay integrating CRISPR Cas12a for homogeneous protein target detection with a simplified workflow and high sensitivity. Probes consisting of different binders (small molecule, aptamer, and antibody) conjugated with oligonucleotides undergo two-way extension upon binding to the protein targets, leading to downstream DNA amplification by a pair of nicking enzymes and polymerases to generate target sequences for Cas12a signal generation. We used the streptavidin-biotin model to demonstrate the design of our assay and proved that all three elements of protein detection (target protein binding, DNA amplification, and Cas12a signal generation) could coexist in one pot and proceed isothermally in a single buffer system at a low reaction volume of 10 μL. The plug-and-play applicability of our assay has been successfully demonstrated using four different protein targets, streptavidin, PDGF-BB, antidigoxigenin antibody, and IFNγ, with the limit of detection ranging from fM to pM.
Collapse
Affiliation(s)
- Yahui Gao
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Yan Shan Ang
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Lin-Yue Lanry Yung
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| |
Collapse
|
3
|
Newman SS, Wilson BD, Mamerow D, Wollant BC, Nyein H, Rosenberg-Hasson Y, Maecker HT, Eisenstein M, Soh HT. Extending the dynamic range of biomarker quantification through molecular equalization. Nat Commun 2023; 14:4192. [PMID: 37443317 PMCID: PMC10344875 DOI: 10.1038/s41467-023-39772-z] [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: 02/17/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Precision medicine requires highly scalable methods of multiplexed biomarker quantification that can accurately describe patient physiology. Unfortunately, contemporary molecular detection methods are generally limited to a dynamic range of sensitivity spanning just 3-4 orders of magnitude, whereas the actual physiological dynamic range of the human plasma proteome spans more than 10 orders of magnitude. Current methods rely on sample splitting and differential dilution to compensate for this mismatch, but such measures greatly limit the reproducibility and scalability that can be achieved-in particular, the effects of non-linear dilution can greatly confound the analysis of multiplexed assays. We describe here a two-pronged strategy for equalizing the signal generated by each analyte in a multiplexed panel, thereby enabling simultaneous quantification of targets spanning a wide range of concentrations. We apply our 'EVROS' strategy to a proximity ligation assay and demonstrate simultaneous quantification of four analytes present at concentrations spanning from low femtomolar to mid-nanomolar levels. In this initial demonstration, we achieve a dynamic range spanning seven orders of magnitude in a single 5 µl sample of undiluted human serum, highlighting the opportunity to achieve sensitive, accurate detection of diverse analytes in a highly multiplexed fashion.
Collapse
Affiliation(s)
- Sharon S Newman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Brandon D Wilson
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Radiology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Daniel Mamerow
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Radiology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Benjamin C Wollant
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Hnin Nyein
- Department of Radiology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Yael Rosenberg-Hasson
- Institute for Immunity, Transplantation, and Infection, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation, and Infection, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Michael Eisenstein
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Radiology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - H Tom Soh
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
- Department of Radiology, School of Medicine, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| |
Collapse
|
4
|
Park YS, Choi S, Jang HJ, Yoo TH. Assay methods based on proximity-enhanced reactions for detecting non-nucleic acid molecules. Front Bioeng Biotechnol 2023; 11:1188313. [PMID: 37456730 PMCID: PMC10343955 DOI: 10.3389/fbioe.2023.1188313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
Accurate and reliable detection of biological molecules such as nucleic acids, proteins, and small molecules is essential for the diagnosis and treatment of diseases. While simple homogeneous assays have been developed and are widely used for detecting nucleic acids, non-nucleic acid molecules such as proteins and small molecules are usually analyzed using methods that require time-consuming procedures and highly trained personnel. Recently, methods using proximity-enhanced reactions (PERs) have been developed for detecting non-nucleic acids. These reactions can be conducted in a homogeneous liquid phase via a single-step procedure. Herein, we review three assays based on PERs for the detection of non-nucleic acid molecules: proximity ligation assay, proximity extension assay, and proximity proteolysis assay.
Collapse
Affiliation(s)
- Ye Seop Park
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Sunjoo Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Hee Ju Jang
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, Republic of Korea
| |
Collapse
|
5
|
Alkhamis O, Canoura J, Willis C, Wang L, Perry J, Xiao Y. Comparison of Aptamer Signaling Mechanisms Reveals Disparities in Sensor Response and Strategies to Eliminate False Signals. J Am Chem Soc 2023. [PMID: 37217444 DOI: 10.1021/jacs.3c03640] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Aptamers are nucleic acid-based affinity reagents that have been incorporated into a variety of molecular sensor formats. However, many aptamer sensors exhibit insufficient sensitivity and specificity for real-world applications, and although considerable effort has been dedicated to improving sensitivity, sensor specificity has remained largely neglected and understudied. In this work, we have developed a series of sensors using aptamers for the small-molecule drugs flunixin, fentanyl, and furanyl fentanyl and compare their performance─in particular, focusing on their specificity. Contrary to expectations, we observe that sensors using the same aptamer operating under the same physicochemical conditions produce divergent responses to interferents depending on their signal transduction mechanism. For instance, aptamer beacon sensors are susceptible to false-positives from interferents that weakly associate with DNA, while strand-displacement sensors suffer from false-negatives due to interferent-associated signal suppression when both the target and interferent are present. Biophysical analyses suggest that these effects arise from aptamer-interferent interactions that are either nonspecific or induce aptamer conformational changes that are distinct from those induced by true target-binding events. We also demonstrate strategies for improving the sensitivity and specificity of aptamer sensors with the development of a "hybrid beacon," wherein the incorporation of a complementary DNA competitor into an aptamer beacon selectively hinders interferent─but not target─binding and signaling, while simultaneously overcoming signal suppression by interferents. Our results highlight the need for systematic and thorough testing of aptamer sensor response and new aptamer selection methods that optimize specificity more effectively than traditional counter-SELEX.
Collapse
Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Juan Canoura
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Connor Willis
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Linlin Wang
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Jacob Perry
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Yi Xiao
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| |
Collapse
|
6
|
Li C, Wang Y, Li PF, Fu Q. Construction of rolling circle amplification products-based pure nucleic acid nanostructures for biomedical applications. Acta Biomater 2023; 160:1-13. [PMID: 36764595 DOI: 10.1016/j.actbio.2023.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023]
Abstract
Nucleic acid nanomaterials with good biocompatibility, biodegradability, and programmability have important applications in biomedical field. Nucleic acid nanomaterials are usually combined with some inorganic nanomaterials to improve their biological stability. However, undefined toxic side effects of composite nanocarriers hamper their application in vivo. As a nanotool capable of avoiding potential biotoxicity, nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in the field of biomedicine in recent years. Rolling circle amplification (RCA) is an isothermal enzymatic nucleic acid amplification technology for large-scale production of periodic DNA/RNA with pre-designed desirable structures and functions. RCA products with different functional parts can be customized by changing the sequence of the circular template, thereby generating complex multifunctional DNA nanostructures, such as DNA nanowire, nanoflower, origami, nanotube, nanoribbon, etc. More importantly, RCA products as nonnicked building blocks can enhance the biostability of DNA nanostructures, especially in vivo. These RCA products-based nucleic acid nanostructures can be used as scaffolds or nanocarriers to interact or load with metal nanoparticles, proteins, lipids, cationic polymers, therapeutic nucleic acids or drugs, etc. This paper reviews the assembly strategies of RCA based DNA nanostructures with different shape and their applications in biosensing, bioimaging and biomedicine. Finally, the development prospects of the nucleic acid nanomaterials in clinical diagnosis and treatment of diseases are described. STATEMENT OF SIGNIFICANCE: As a nanotool capable of avoiding potential biotoxicity, nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in the field of biomedicine in recent years. Rolling circle amplification (RCA) is an isothermal enzymatic nucleic acid amplification technology for large-scale production of periodic DNA/RNA with pre-designed desirable structures and functions. This paper reviews the construction of various shapes of pure nucleic acid nanomaterials based on RCA products and their applications in biosensing, bioimaging and biomedicine. This will promote the development of biocompatible DNA nanovehicles and their further application in living systems, including bioimaging, molecular detection, disease diagnosis and drug delivery, finally producing a significant impact in the field of nanotechnology and nanomedicine.
Collapse
Affiliation(s)
- Congcong Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Pei-Feng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Qinrui Fu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| |
Collapse
|
7
|
Pan J, Xu W, Li W, Chen S, Dai Y, Yu S, Zhou Q, Xia F. Electrochemical Aptamer-Based Sensors with Tunable Detection Range. Anal Chem 2023; 95:420-432. [PMID: 36625123 DOI: 10.1021/acs.analchem.2c04498] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Jing Pan
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Wenxia Xu
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Wanlu Li
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Shuwen Chen
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Yu Dai
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Shanwu Yu
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Qitao Zhou
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| |
Collapse
|
8
|
Liu F, Li N, Shang Y, Wang Y, Liu Q, Ma Z, Jiang Q, Ding B. A DNA‐Based Plasmonic Nanodevice for Cascade Signal Amplification. Angew Chem Int Ed Engl 2022; 61:e202114706. [DOI: 10.1002/anie.202114706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Fengsong Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Na Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
| | - Yiming Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
| | - Zhentao Ma
- He'nan Institute of Advanced Technology School of Materials Science and Engineering Zhengzhou University Zhengzhou 450001 China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
- He'nan Institute of Advanced Technology School of Materials Science and Engineering Zhengzhou University Zhengzhou 450001 China
| |
Collapse
|
9
|
Liu F, Li N, Shang Y, Wang Y, Liu Q, Ma Z, Jiang Q, Ding B. A DNA‐based plasmonic nanodevice for cascade signal amplification. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Fengsong Liu
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Na Li
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Yingxu Shang
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Yiming Wang
- National Center for Nanoscience and Technology CAS Key Labortory of Nanosystem and Hierarchical Fabrication CHINA
| | - Qing Liu
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Zhentao Ma
- Zhengzhou University School of Materials Science and Engineering CHINA
| | - Qiao Jiang
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Baoquan Ding
- National Center for Nanoscience and Technology, China CAS Key Laboratory of Nanosystem and Hierarchical Fabrication No. 11, BeiYiTiao, ZhongGuanCun 100190 Beijing CHINA
| |
Collapse
|
10
|
Shen T, Zhang Y, Mei L, Zhang XB, Zhu G. Single-stranded circular DNA theranostics. Theranostics 2022; 12:35-47. [PMID: 34987632 PMCID: PMC8690921 DOI: 10.7150/thno.66466] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/10/2021] [Indexed: 02/04/2023] Open
Abstract
The past decade has witnessed the blossom of nucleic acid therapeutics and diagnostics (theranostics). Unlike conventional small molecule medicines or protein biologics, nucleic acid theranostics have characteristic features such as the intrinsic ability as “information drugs” to code and execute genetic and theranostic information, ready programmability for nucleic acid engineering, intrinsic stimulatory or regulatory immunomodulation, versatile functionalities, and easy conformational recovery upon thermal or chemical denaturation. Single-stranded circular DNA (circDNA) are a class of single-stranded DNAs (ssDNA) featured with their covalently-closed topology. In addition to the basic advantages of nucleic acids-based materials, such as low cost, biocompatibility, and simplicity of chemical modification, the lack of terminals in circDNA prevents exonuclease degradation, resulting in enhanced biostability relative to the corresponding linear ssDNA. circDNA has been explored for versatile theranostic applications. For instance, circDNA has been extensively studied as templates for bioanalytical signal amplification and the synthesis of nano-/micro-/macro- biomaterials via rolling circle amplification (RCA) and rolling circle transcription (RCT) technologies. circDNA has also been commonly used as the scaffolds for the self-assembly of versatile DNA origami. Finally, circDNA has been implemented as theranostic aptamers, miRNA inhibitors, as well as clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) gene editing donors. In this review article, we will discuss the chemistry, characteristic properties, and the theranostic applications of circDNA (excluding double-stranded circular DNA such as plasmids); we will also envision the challenges and opportunities in this research field.
Collapse
|
11
|
De Falco M, De Felice M, Rota F, Zappi D, Antonacci A, Scognamiglio V. Next-generation diagnostics: augmented sensitivity in amplification-powered biosensing. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
12
|
Bialy RM, Mainguy A, Li Y, Brennan JD. Functional nucleic acid biosensors utilizing rolling circle amplification. Chem Soc Rev 2022; 51:9009-9067. [DOI: 10.1039/d2cs00613h] [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
Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.
Collapse
Affiliation(s)
- Roger M. Bialy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Alexa Mainguy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Yingfu Li
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
- Department of Biochemistry and Biomedical Sciences, 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 4O3, Canada
| |
Collapse
|
13
|
Wang Y, Liu X, Wu L, Ding L, Effah CY, Wu Y, Xiong Y, He L. Construction and bioapplications of aptamer-based dual recognition strategy. Biosens Bioelectron 2022; 195:113661. [PMID: 34592501 DOI: 10.1016/j.bios.2021.113661] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 02/08/2023]
Abstract
Aptamer-based dual recognition strategy, using dual aptamers or the cooperation of aptamers with other recognition elements, can better utilize the advantages of each recognition molecule and increase the design flexibility to effectively overcome the limitations of a single molecule recognition strategy, thereby improving the sensitivity and selectivity and facilitating the regulation of biological process. Hence, this review systematically tracks the construction and application of dual aptamers recognition strategy in the versatile detection of protein biomarkers, pathogenic microorganisms, cancer cells, and the treatment of some diseases and, more importantly, in functional regulation and imaging of cell-surface protein receptors. Then, the cooperation of aptamers with other recognition elements are briefly introduced. Potential challenges facing this field have been highlighted, aiming to expand bioanalytical applications of aptamer-based dual or multiple recognition strategies and meet the growing demand for precision medicine.
Collapse
Affiliation(s)
- Ya Wang
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Xinlian Liu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Longjie Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Lihua Ding
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Clement Yaw Effah
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yamin Xiong
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Leiliang He
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China.
| |
Collapse
|
14
|
Cyclic strand displacement polymerase reaction to turn-on molecular beacons for rapid detection of Staphylococcus aureus. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
15
|
Li J, Feng YW, Huang LJ, Jiang R, Shen XF. Strand-displacement DNA polymerase induced isothermal circular amplification fluorescence sensor for identification of pork component. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
16
|
Ren H, Song L, Zhang W, Xu L. Synthesis, Stability, and Anti-Tumour Activity of a New Category of "Stapled" Antisense Oligonucleotides with Stimuli-Responsive Feature. J Pharm Sci 2021; 110:3166-3170. [PMID: 34102202 DOI: 10.1016/j.xphs.2021.05.024] [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: 01/08/2021] [Revised: 05/31/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The development of nucleic acid drugs with unique structures and mechanisms has stimulated great research interest. Herein, we report a general strategy to construct "stapled" structures of single-stranded antisense oligonucleotides (ASONs) with a stimuli-responsive feature. "Stapled" cyclic structures can be synthesized with reactive bifunctional handles that react with thiol groups of phosphorothioate (PS)-modified ASONs, and can be alternatively adjusted depending on the desired PS sites in the ASON strand. The disulphide group in the stapled handle can be cleaved in the reducing microenvironment of tumour cells. Thus, "stapled" ASONs may be transformed back to a linear conformation to facilitate binding to target mRNAs. Stapling conferred protection against degradation, and enhanced anti-tumour activity compared to linear counterparts. This study provides a new, effective, and convenient strategy for designing ASONs with "stapled" structures, and also adds a further contribution to facilitate the stability and biological efficacy of novel nucleic acid-based therapeutics.
Collapse
Affiliation(s)
- Hongqian Ren
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Liya Song
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Wei Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Liang Xu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China.
| |
Collapse
|
17
|
Ni S, Zhuo Z, Pan Y, Yu Y, Li F, Liu J, Wang L, Wu X, Li D, Wan Y, Zhang L, Yang Z, Zhang BT, Lu A, Zhang G. Recent Progress in Aptamer Discoveries and Modifications for Therapeutic Applications. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9500-9519. [PMID: 32603135 DOI: 10.1021/acsami.0c05750] [Citation(s) in RCA: 258] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Aptamers are oligonucleotide sequences with a length of about 25-80 bases which have abilities to bind to specific target molecules that rival those of monoclonal antibodies. They are attracting great attention in diverse clinical translations on account of their various advantages, including prolonged storage life, little batch-to-batch differences, very low immunogenicity, and feasibility of chemical modifications for enhancing stability, prolonging the half-life in serum, and targeted delivery. In this Review, we demonstrate the emerging aptamer discovery technologies in developing advanced techniques for producing aptamers with high performance consistently and efficiently as well as requiring less cost and resources but offering a great chance of success. Further, the diverse modifications of aptamers for therapeutic applications including therapeutic agents, aptamer-drug conjugates, and targeted delivery materials are comprehensively summarized.
Collapse
Affiliation(s)
- Shuaijian Ni
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Zhenjian Zhuo
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Yufei Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuanyuan Yu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Fangfei Li
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Jin Liu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Luyao Wang
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Xiaoqiu Wu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Dijie Li
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Youyang Wan
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Bao-Ting Zhang
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Aiping Lu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Ge Zhang
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| |
Collapse
|
18
|
Li Q, Zhang S, Li W, Ge Z, Fan C, Gu H. Programming CircLigase Catalysis for DNA Rings and Topologies. Anal Chem 2020; 93:1801-1810. [PMID: 33382236 DOI: 10.1021/acs.analchem.0c04668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Circular single-stranded (ss) DNA is an essential element in rolling circle amplification and many DNA nanotechnology constructions. It is commonly synthesized from linear ssDNA by a ligase, which nevertheless suffers from low and inconsistent efficiency due to the simultaneous formation of concatemeric byproducts. Here, we design an intramolecular terminal hybridization strategy to program the ring formation catalytic process of CircLigase, a thermostable RNA ligase 1 that can ligate ssDNA in an intramolecular fashion. With the enthalpy gained from the programmed hybridization to override disfavored entropic factors associated with end coupling, we broke the limit of natural CircLigase on circularization of ssDNA, realizing over 75% yields of byproduct-free monomeric rings on a series of hundred-to-half-kilo-based linear DNAs. We found that this hybridization strategy can be twisted from intra- to intermolecular to also program CircLigase to efficiently and predominantly join one ssDNA strand to another. We focused on DNA rings premade by CircLigase and demonstrated their utility in elevating the preparation, quantity, and quality of DNA topologies. We expect that the new insights on engineering CircLigase will further promote the development of nucleic acid biotechnology and nanotechnology.
Collapse
Affiliation(s)
- Qingting Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200032, China.,Department of Systems Biology for Medicine, Shanghai Pudong Hospital, Fudan University, Shanghai 200433, China
| | - Shu Zhang
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200032, China
| | - Wei Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200032, China.,Department of Systems Biology for Medicine, Shanghai Pudong Hospital, Fudan University, Shanghai 200433, China
| | - Zhilei Ge
- 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
| | - 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
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200032, China.,Department of Systems Biology for Medicine, Shanghai Pudong Hospital, Fudan University, Shanghai 200433, China
| |
Collapse
|
19
|
Mao Y, Gu J, Chang D, Wang L, Yao L, Ma Q, Luo Z, Qu H, Li Y, Zheng L. Evolution of a highly functional circular DNA aptamer in serum. Nucleic Acids Res 2020; 48:10680-10690. [PMID: 33021630 PMCID: PMC7641760 DOI: 10.1093/nar/gkaa800] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/26/2020] [Accepted: 09/15/2020] [Indexed: 01/05/2023] Open
Abstract
Circular DNA aptamers are powerful candidates for therapeutic applications given their dramatically enhanced biostability. Herein we report the first effort to evolve circular DNA aptamers that bind a human protein directly in serum, a complex biofluid. Targeting human thrombin, this strategy has led to the discovery of a circular aptamer, named CTBA4T-B1, that exhibits very high binding affinity (with a dissociation constant of 19 pM), excellent anticoagulation activity (with the half maximal inhibitory concentration of 90 pM) and high stability (with a half-life of 8 h) in human serum, highlighting the advantage of performing aptamer selection directly in the environment where the application is intended. CTBA4T-B1 is predicted to adopt a unique structural fold with a central two-tiered guanine quadruplex capped by two long stem–loops. This structural arrangement differs from all known thrombin binding linear DNA aptamers, demonstrating the added advantage of evolving aptamers from circular DNA libraries. The method described here permits the derivation of circular DNA aptamers directly in biological fluids and could potentially be adapted to generate other types of aptamers for therapeutic applications.
Collapse
Affiliation(s)
- Yu Mao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8S4K1, Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8S4K1, Canada
| | - Lei Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Lili Yao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Qihui Ma
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Zhaofeng Luo
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Hao Qu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8S4K1, Canada
| | - Lei Zheng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| |
Collapse
|
20
|
Cheng YH, Liu SJ, Jiang JH. Enzyme-free electrochemical biosensor based on amplification of proximity-dependent surface hybridization chain reaction for ultrasensitive mRNA detection. Talanta 2020; 222:121536. [PMID: 33167244 DOI: 10.1016/j.talanta.2020.121536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/04/2020] [Accepted: 08/08/2020] [Indexed: 01/03/2023]
Abstract
The ability to recognize mRNA with high efficiency in cells would greatly facilitate the elucidation of mRNA-mediated cellular cascades and their disease associations. However, most traditional electrochemical strategies targeting nucleotides are always confronted with cumbersome interface operation and washing procedures, as well as the high cost of labeling and the strict reaction conditions of tool enzymes, limiting their potential applications. To address these issues, herein we reported, for the first time, a simple label-free, isothermal, non-enzymatic, and ultrasensitive homogeneous electrochemical biosensor based on autonomous proximity-dependent surface hybridization chain reaction (HCR), for sensitive signal amplification and highly specific detection of target survivin mRNA with a detection limit of 3 fM. The target triggers hybridization chain reaction and mRNA-fueled surface hybridization of ferrocene-tagged metastable DNA hairpin probes on proximity-dependent surface hybridization, resulting in the formation of multiple long-range duplex DNA chains which are immobilized onto the gold electrodes with a substantially stable ferrocene-mediated redox current. Thus, a significant electrochemical signal increase is observed dependent on the concentration of the target RNA, with a very low detection limit. Mo-reover, this molecular biosensor also exhibits excellent specificity to distinguish even single base mismatched, with strong reliability. The developed biosensor provides a novel promising tool for ultra-sensitive and selective detection, and it has great potential to be applied in mRNA-related biochemical research and clinical cancer diagnostics in more detail.
Collapse
Affiliation(s)
- Yu-Hong Cheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Si-Jia Liu
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Key Laboratory of Regenerative Medicine, Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, School of Basic Medical Sciences, Center for Translational Medicine, Guangxi Medical University, Nanning, 530021, PR China.
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
| |
Collapse
|
21
|
Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
Collapse
Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| |
Collapse
|
22
|
Bialy RM, Ali MM, Li Y, Brennan JD. Protein-Mediated Suppression of Rolling Circle Amplification for Biosensing with an Aptamer-Containing DNA Primer. Chemistry 2020; 26:5085-5092. [PMID: 32096262 DOI: 10.1002/chem.202000245] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/21/2020] [Indexed: 12/22/2022]
Abstract
We report a method to detect proteins via suppression of rolling circle amplification (RCA) by using an appropriate aptamer as the linear primer (denoted as an aptaprimer) to initiate RCA. In the absence of a protein target, the aptaprimer is free to initiate RCA, which can produce long DNA products that are detected via binding of a fluorescent intercalating dye. Introduction of a target causes the primer region within the aptamer to become unavailable for binding to the circular template, inhibiting RCA. Using SYBR Gold or QuantiFluor dyes as fluorescent probes to bind to the RCA reaction product, it is possible to produce a generic protein-modulated RCA assay system that does not require fluorophore- or biotin-modified DNA species, substantially reducing complexity and cost of reagents. Based on this modulation of RCA, we demonstrate the ability to produce both solution and paper-based assays for rapid and quantitative detection of proteins including platelet derived growth factor and thrombin.
Collapse
Affiliation(s)
- Roger M Bialy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Monsur M Ali
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Yingfu Li
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada.,Department of Biochemistry and Biomedical Sciences, 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 4O3, Canada
| |
Collapse
|
23
|
Chaturvedi P, Vuković L. Structural Properties of Small Single-Stranded Circular Nucleic Acids. J Phys Chem B 2019; 123:8216-8221. [PMID: 31498637 DOI: 10.1021/acs.jpcb.9b06831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
One strategy to avoid rapid degradation of small nucleic acids in biomedical applications is to covalently link their 3'- and 5'-ends, turning them into circular nucleic acids (circNAs). Here, we examine structural properties of flexible non-base-paired circNAs, containing 6-48 nucleotides, in aqueous solution, using microsecond long molecular dynamics simulations. Analyses of conformational ensembles of circular DNA (circDNA) and RNA (circRNA) molecules of different lengths and sequences reveal how their structures and dynamics are affected by the constraints of their geometries. The circDNAs are more bent and flexible than circRNAs, with distinctly different arrangements of phosphate backbones and bases. Small circNAs can sequester counterions in conformations that resemble crown ethers for the smallest (6-8 nucleotide long) molecules examined, in contrast to their linear counterparts. At millimolar concentrations (7.9 mM), circNA molecules were observed to aggregate, adopting linear chain shapes at physiological ionic strengths.
Collapse
Affiliation(s)
- Parth Chaturvedi
- Department of Chemistry and Biochemistry , University of Texas at El Paso , El Paso , Texas 79968 , United States
| | - Lela Vuković
- Department of Chemistry and Biochemistry , University of Texas at El Paso , El Paso , Texas 79968 , United States
| |
Collapse
|
24
|
Dual Aptamer-Functionalized 3D Plasmonic Metamolecule for Thrombin Sensing. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9153006] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
DNA nanotechnology offers the possibility to rationally design structures with emergent properties by precisely controlling their geometry and functionality. Here, we demonstrate a DNA-based plasmonic metamolecule that is capable of sensing human thrombin proteins. The chiral reconfigurability of a DNA origami structure carrying two gold nanorods was used to provide optical read-out of thrombin binding through changes in the displayed plasmonic circular dichroism. In our experiments, each arm of the structure was modified with one of two different thrombin-binding aptamers—thrombin-binding aptamer (TBA) and HD22—in such a way that a thrombin molecule could be sandwiched by the aptamers to lock the metamolecule in a state of defined chirality. Our structure exhibited a Kd of 1.4 nM, which was an order of magnitude lower than those of the individual aptamers. The increased sensitivity arose from the avidity gained by the cooperative binding of the two aptamers, which was also reflected by a Hill coefficient of 1.3 ± 0.3. As we further exploited the strong plasmonic circular dichroism (CD) signals of the metamolecule, our method allowed one-step, high sensitivity optical detection of human thrombin proteins in solution.
Collapse
|
25
|
Liu M, Yin Q, Chang Y, Zhang Q, Brennan JD, Li Y. In Vitro Selection of Circular DNA Aptamers for Biosensing Applications. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901192] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Meng Liu
- School of Environmental Science and Technology Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) Dalian University of Technology Dalian 116024 China
| | - Qingxin Yin
- School of Environmental Science and Technology Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) Dalian University of Technology Dalian 116024 China
| | - Yangyang Chang
- School of Environmental Science and Technology Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) Dalian University of Technology Dalian 116024 China
| | - Qiang Zhang
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton Ontario L8S4O3 Canada
- School of Life Science and Biotechnology Dalian University of Technology Dalian 116024 China
| | - John D. Brennan
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton Ontario L8S4K1 Canada
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| |
Collapse
|
26
|
Liu M, Yin Q, Chang Y, Zhang Q, Brennan JD, Li Y. In Vitro Selection of Circular DNA Aptamers for Biosensing Applications. Angew Chem Int Ed Engl 2019; 58:8013-8017. [PMID: 31020784 DOI: 10.1002/anie.201901192] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/17/2019] [Indexed: 01/01/2023]
Abstract
We report on the first effort to select DNA aptamers from a circular DNA library, which resulted in the discovery of two high-affinity circular DNA aptamers that recognize the glutamate dehydrogenase (GDH) from Clostridium difficile, an established antigen for diagnosing Clostridium difficile infection (CDI). One aptamer binds effectively in both the circular and linear forms, the other is functional only in the circular configuration. Interestingly, these two aptamers recognize different epitopes on GDH, demonstrating the advantage of selecting aptamers from circular DNA libraries. A sensitive diagnostic test was developed to take advantage of the high stability of circular DNA aptamers in biological samples and their compatibility with rolling circle amplification. This test is capable of identifying patients with active CDI using stool samples. This work represents a significant step forward towards demonstrating the practical utility of DNA aptamers in clinical diagnosis.
Collapse
Affiliation(s)
- Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Qingxin Yin
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Qiang Zhang
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada.,School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| |
Collapse
|
27
|
Chylewska A, Ogryzek M, Makowski M. Modern Approach to Medical Diagnostics - the Use of Separation Techniques in Microorganisms Detection. Curr Med Chem 2019; 26:121-165. [DOI: 10.2174/0929867324666171023164813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 04/20/2017] [Accepted: 05/20/2016] [Indexed: 11/22/2022]
Abstract
Background:Analytical chemistry and biotechnology as an interdisciplinary fields of science have been developed during many years and are experiencing significant growth, to cover a wide range of microorganisms separation techniques and methods, utilized for medical therapeutic and diagnostic purposes. Currently scientific reports contribute by introducing electrophoretical and immunological methods and formation of devices applied in food protection (avoiding epidemiological diseases) and healthcare (safety ensuring in hospitals).Methods:Electrophoretic as well as nucleic-acid-based or specific immunological methods have contributed tremendously to the advance of analyses in recent three decades, particularly in relation to bacteria, viruses and fungi identifications, especially in medical in vitro diagnostics, as well as in environmental or food protection.Results:The paper presents the pathogen detection competitiveness of these methods against conventional ones, which are still too time consuming and also labor intensive. The review is presented in several parts following the current trends in improved pathogens separation and detection methods and their subsequent use in medical diagnosis.Discussion:Part one, consists of elemental knowledge about microorganisms as an introduction to their characterization: descriptions of divisions, sizes, membranes (cells) components. Second section includes the development, new technological and practical solution descriptions used in electrophoretical procedures during microbes analyses, with special attention paid to bio-samples analyses like blood, urine, lymph or wastewater. Third part covers biomolecular areas that have created a basis needed to identify the progress, limitations and challenges of nucleic-acid-based and immunological techniques discussed to emphasize the advantages of new separative techniques in selective fractionating of microorganisms.
Collapse
Affiliation(s)
- Agnieszka Chylewska
- Laboratory of Intermolecular Interactions, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80- 308 Gdansk, Poland
| | - Małgorzata Ogryzek
- Laboratory of Intermolecular Interactions, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80- 308 Gdansk, Poland
| | - Mariusz Makowski
- Laboratory of Intermolecular Interactions, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80- 308 Gdansk, Poland
| |
Collapse
|
28
|
Zhang Y, Huang X, Luo F, Lei Y, Chen L, Weng Z, Guo L, Lin Z. Highly sensitive electrochemical immunosensor for golgi protein 73 based on proximity ligation assay and enzyme-powered recycling amplification. Anal Chim Acta 2018; 1040:150-157. [DOI: 10.1016/j.aca.2018.08.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/26/2018] [Accepted: 08/09/2018] [Indexed: 10/28/2022]
|
29
|
Huang Z, Luo Z, Chen J, Xu Y, Duan Y. A Facile, Label-Free, and Universal Biosensor Platform Based on Target-Induced Graphene Oxide Constrained DNA Dissociation Coupling with Improved Strand Displacement Amplification. ACS Sens 2018; 3:2423-2431. [PMID: 30335968 DOI: 10.1021/acssensors.8b00935] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In this work, we report a low-cost and easy operation biosensor platform capable of detection of various analytes with high sensitivity and good selectivity. By ingeniously assigning the specific aptamer into a primer-template integrated DNA template, and using monolayer graphene oxide as a reversible and nonspecific inhibitor, the simple biosensor platform is set up. Without a target, the DNA template is constrained by the graphene oxide sheet and results in low signal. In the presence of a target, the constrained DNA template is released from the graphene oxide surface via a target-induced aptamer conformational change, and further amplified through the improved strand displacement amplification reaction. Therefore, the target detection is simply converted to DNA detection, and a correlation between target concentration and fluorescence signal can be set up. As a result, dozens-fold signal enhancement, high sensitivity, good selectivity, and potential practicability are achieved in target detection. More importantly, the proposed biosensor platform is versatile, meaning that it can greatly facilitate the detection of a variety of analytes. Due to the low cost and easy availability of sensing materials, and the elimination of tedious detection operations, we believe that this simple and universal biosensor platform can find wide applications in biological assay and environment monitoring.
Collapse
Affiliation(s)
- Zhijun Huang
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
| | - Zewei Luo
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
| | - Junman Chen
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
| | - Ya Xu
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
| |
Collapse
|
30
|
Canoura J, Wang Z, Yu H, Alkhamis O, Fu F, Xiao Y. No Structure-Switching Required: A Generalizable Exonuclease-Mediated Aptamer-Based Assay for Small-Molecule Detection. J Am Chem Soc 2018; 140:9961-9971. [PMID: 30011200 PMCID: PMC6133295 DOI: 10.1021/jacs.8b04975] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The binding of small molecules to double-stranded DNA can modulate its susceptibility to digestion by exonucleases. Here, we show that the digestion of aptamers by exonuclease III can likewise be inhibited upon binding of small-molecule targets and exploit this finding for the first time to achieve sensitive, label-free small-molecule detection. This approach does not require any sequence engineering and employs prefolded aptamers which have higher target-binding affinities than structure-switching aptamers widely used in current small-molecule detecting assays. We first use a dehydroisoandrosterone-3-sulfate-binding aptamer to show that target binding halts exonuclease III digestion four bases prior to the binding site. This leaves behind a double-stranded product that retains strong target affinity, whereas digestion of nontarget-bound aptamer produces a single-stranded product incapable of target binding. Exonuclease I efficiently eliminates these single-stranded products but is unable to digest the target-bound double-stranded product. The remaining products can be fluorescently quantified with SYBR Gold to determine target concentrations. We demonstrate that this dual-exonuclease-mediated approach can be broadly applied to other aptamers with differing secondary structures to achieve sensitive detection of various targets, even in biological matrices. Importantly, each aptamer digestion product has a unique sequence, enabling the creation of multiplex assays, and we successfully demonstrate simultaneous detection of cocaine and ATP in a single microliter volume sample in 25 min via sequence-specific molecular beacons. Due to the generality and simplicity of this assay, we believe that different DNA signal-reporting or amplification strategies can be adopted into our assay for target detection in diverse analytical contexts.
Collapse
Affiliation(s)
- Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 Southwest Eighth Street, Miami, Florida 33199, United States
| | - Zongwen Wang
- Department of Chemistry and Biochemistry, Florida International University, 11200 Southwest Eighth Street, Miami, Florida 33199, United States
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 Southwest Eighth Street, Miami, Florida 33199, United States
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 Southwest Eighth Street, Miami, Florida 33199, United States
| | - Fengfu Fu
- Key Laboratory for Analytical Science of Food Safety and Biology of MOE, Fujian Provincial Key Lab of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 Southwest Eighth Street, Miami, Florida 33199, United States
| |
Collapse
|
31
|
Yang D, Tang Y, Guo Z, Chen X, Miao P. Proximity aptasensor for protein detection based on an enzyme-free amplification strategy. MOLECULAR BIOSYSTEMS 2018; 13:1936-1939. [PMID: 28796267 DOI: 10.1039/c7mb00458c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A novel electrochemical aptasensor for the detection of trace protein is proposed based on proximity binding-induced strand displacement and hybridization chain reaction. This method is proven to be highly selective and has potential practical utility, and offers new opportunities for the convenient detection of proteins with an enzyme-free amplification process.
Collapse
Affiliation(s)
- Dawei Yang
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China.
| | | | | | | | | |
Collapse
|
32
|
Huang Y, Zheng W, Li X. Detection of protein targets with a single binding epitope using DNA-templated photo-crosslinking and strand displacement. Anal Biochem 2018; 545:84-90. [DOI: 10.1016/j.ab.2018.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/10/2018] [Accepted: 01/12/2018] [Indexed: 12/17/2022]
|
33
|
Streamlined circular proximity ligation assay provides high stringency and compatibility with low-affinity antibodies. Proc Natl Acad Sci U S A 2018; 115:E925-E933. [PMID: 29339495 DOI: 10.1073/pnas.1718283115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proximity ligation assay (PLA) is a powerful tool for quantitative detection of protein biomarkers in biological fluids and tissues. Here, we present the circular proximity ligation assay (c-PLA), a highly specific protein detection method that outperforms traditional PLA in stringency, ease of use, and compatibility with low-affinity reagents. In c-PLA, two proximity probes bind to an analyte, providing a scaffolding that positions two free oligonucleotides such that they can be ligated into a circular DNA molecule. This assay format stabilizes antigen proximity probe complexes and enhances stringency by reducing the probability of random background ligation events. Circle formation also increases selectivity, since the uncircularized DNA can be removed enzymatically. We compare this method with traditional PLA on several biomarkers and show that the higher stringency for c-PLA improves reproducibility and enhances sensitivity in both buffer and human plasma. The limit of detection ranges from femtomolar to nanomolar concentrations for both methods. Kinetic analyses using surface plasmon resonance (SPR) and biolayer interferometry (BLI) reveal that the variation in limit of detection is due to the variation in antibody affinity and that c-PLA outperforms traditional PLA for low-affinity antibodies. The lower background signal can be used to increase proximity probe concentration while maintaining a high signal-to-noise ratio, thereby enabling the use of low-affinity reagents in a homogeneous assay format. We anticipate that the advantages of c-PLA will be useful in a variety of clinical protein detection applications where high-affinity reagents are lacking.
Collapse
|
34
|
Li J, Zhou J, Liu T, Chen S, Li J, Yang H. Circular DNA: a stable probe for highly efficient mRNA imaging and gene therapy in living cells. Chem Commun (Camb) 2018; 54:896-899. [DOI: 10.1039/c7cc08906f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We integrated circular DNA with graphene oxide to fabricate improved platforms for highly efficient imaging and therapy in living cells.
Collapse
Affiliation(s)
- Jingying Li
- College of Biological Science and Engineering, Fuzhou University
- Fuzhou 350116
- P. R. China
| | - Jie Zhou
- College of Biological Science and Engineering, Fuzhou University
- Fuzhou 350116
- P. R. China
| | - Tong Liu
- College of Biological Science and Engineering, Fuzhou University
- Fuzhou 350116
- P. R. China
| | - Shan Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
- Fuzhou 350116
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
- Fuzhou 350116
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
- Fuzhou 350116
| |
Collapse
|
35
|
Gong H, Wang X, Liu B, Boutet S, Holcomb I, Dakshinamoorthy G, Ooi A, Sanada C, Sun G, Ramakrishnan R. Single-cell protein-mRNA correlation analysis enabled by multiplexed dual-analyte co-detection. Sci Rep 2017; 7:2776. [PMID: 28584233 PMCID: PMC5459813 DOI: 10.1038/s41598-017-03057-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 04/24/2017] [Indexed: 01/01/2023] Open
Abstract
We have investigated the correlation between proteins and mRNAs in single cells employing an integrated workflow for dual-analyte co-detection. This is achieved by combining the oligo extension reaction (OER), which converts protein levels to DNA levels, with reverse transcription for mRNA detection. Unsupervised gene expression profiling analysis, including principal component analysis and hierarchical clustering, revealed different aspects of the protein-mRNA relationship. Violin plot analysis showed that some genes exhibited similar distribution patterns for proteins and mRNAs. We also demonstrate that cells can be separated into subpopulations based on their protein-mRNA expression profiles, and that different subpopulations have distinct correlation coefficient values. Our results demonstrated that integrated investigations of mRNA and protein levels in single cells allows comprehensive analysis not attainable at bulk levels.
Collapse
Affiliation(s)
- Haibiao Gong
- Fluidigm Corporation, South San Francisco, CA, 94080, USA.
| | - Xiaohui Wang
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | - Benjamin Liu
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | | | - Ilona Holcomb
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | | | - Aik Ooi
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | - Chad Sanada
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | - Gang Sun
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | | |
Collapse
|
36
|
Zhu D, Wang L, Xu X, Jiang W. Colocalization recognition-activated cascade signal amplification strategy for ultrasensitive detection of transcription factors. Biosens Bioelectron 2017; 89:978-983. [DOI: 10.1016/j.bios.2016.09.073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/15/2016] [Accepted: 09/21/2016] [Indexed: 01/10/2023]
|
37
|
Liu S, Fang L, Wang Y, Wang L. Universal Dynamic DNA Assembly-Programmed Surface Hybridization Effect for Single-Step, Reusable, and Amplified Electrochemical Nucleic Acid Biosensing. Anal Chem 2017; 89:3108-3115. [DOI: 10.1021/acs.analchem.6b04871] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Shufeng Liu
- Key Laboratory of Sensor
Analysis of Tumor Marker, Ministry of Education, College of Chemistry
and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Rd. Zhengzhou, Qingdao, Shandong 266042, China
| | - Li Fang
- Key Laboratory of Sensor
Analysis of Tumor Marker, Ministry of Education, College of Chemistry
and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Rd. Zhengzhou, Qingdao, Shandong 266042, China
| | - Yanqun Wang
- Key Laboratory of Sensor
Analysis of Tumor Marker, Ministry of Education, College of Chemistry
and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Rd. Zhengzhou, Qingdao, Shandong 266042, China
| | - Li Wang
- Key Laboratory of Sensor
Analysis of Tumor Marker, Ministry of Education, College of Chemistry
and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Rd. Zhengzhou, Qingdao, Shandong 266042, China
| |
Collapse
|
38
|
Wei L, Wang X, Wu D, Li C, Yin Y, Li G. Proximity ligation-induced assembly of DNAzymes for simple and cost-effective colourimetric detection of proteins with high sensitivity. Chem Commun (Camb) 2016; 52:5633-6. [PMID: 27032382 DOI: 10.1039/c6cc00205f] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A novel colourimetric method for protein assays is proposed based on proximity ligation induced assembly of Mg(2+)-dependent DNAzymes, which may offer simple, cost-effective, sensitive and selective detection of the target protein.
Collapse
Affiliation(s)
- Luming Wei
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China.
| | - Xiaoying Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Dan Wu
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China.
| | - Chao Li
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China.
| | - Yongmei Yin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China. and Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| |
Collapse
|
39
|
Chu-mong K, Thammakhet C, Thavarungkul P, Kanatharana P, Buranachai C. A FRET based aptasensor coupled with non-enzymatic signal amplification for mercury (II) ion detection. Talanta 2016; 155:305-13. [DOI: 10.1016/j.talanta.2016.05.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 04/30/2016] [Accepted: 05/02/2016] [Indexed: 12/30/2022]
|
40
|
Hollenstein M. Generation of long, fully modified, and serum-resistant oligonucleotides by rolling circle amplification. Org Biomol Chem 2016; 13:9820-4. [PMID: 26273951 DOI: 10.1039/c5ob01540e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Rolling Circle Amplification (RCA) is an isothermal enzymatic method generating single-stranded DNA products consisting of concatemers containing multiple copies of the reverse complement of the circular template precursor. Little is known on the compatibility of modified nucleoside triphosphates (dN*TPs) with RCA, which would enable the synthesis of long, fully modified ssDNA sequences. Here, dNTPs modified at any position of the scaffold were shown to be compatible with rolling circle amplification, yielding long (>1 kb), and fully modified single-stranded DNA products. This methodology was applied for the generation of long, cytosine-rich synthetic mimics of telomeric DNA. The resulting modified oligonucleotides displayed an improved resistance to fetal bovine serum.
Collapse
Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| |
Collapse
|
41
|
Lin X, Sun X, Luo S, Liu B, Yang C. Development of DNA-based signal amplification and microfluidic technology for protein assay: A review. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.02.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
42
|
Tang S, Wei H, Hu T, Jiang J, Chang J, Guan Y, Zhao G. Suppression of rolling circle amplification by nucleotide analogs in circular template for three DNA polymerases. Biosci Biotechnol Biochem 2016; 80:1555-61. [PMID: 27151504 DOI: 10.1080/09168451.2016.1171699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Among wide applications of nucleotide analogs, their roles in enzyme catalytic reactions are significant in both fundamental and medical researches. By introducing analogs into circular templates, we succeeded in determining effects of four analogs on RCA efficiency for three different DNA polymerases. Results showed an obvious suppression effect for 2'-OMeRNA modification, which might be due to the size of the C2'-modified moieties. 2'-F RNA, LNA and PS had little interference, suggesting good analog candidates for application in RCA. Different polymerases and nucleobases made a little difference according to analogs we used. These results are useful for understanding polymerase catalytic mechanism and analogs applications in RCA reaction.
Collapse
Affiliation(s)
- Suming Tang
- a Department of Biochemistry and Molecular Biology , China Medical University , Shenyang , China
| | - Hua Wei
- a Department of Biochemistry and Molecular Biology , China Medical University , Shenyang , China.,b Department of Aquaculture , Animal Science and Veterinary Medicine College, Shenyang Agricultural University , Shenyang , China
| | - Tianyu Hu
- a Department of Biochemistry and Molecular Biology , China Medical University , Shenyang , China
| | - Jiquan Jiang
- a Department of Biochemistry and Molecular Biology , China Medical University , Shenyang , China
| | - Jinglin Chang
- a Department of Biochemistry and Molecular Biology , China Medical University , Shenyang , China
| | - Yifu Guan
- a Department of Biochemistry and Molecular Biology , China Medical University , Shenyang , China
| | - Guojie Zhao
- a Department of Biochemistry and Molecular Biology , China Medical University , Shenyang , China
| |
Collapse
|
43
|
Wu YX, Kwon YJ. Aptamers: The "evolution" of SELEX. Methods 2016; 106:21-8. [PMID: 27109056 DOI: 10.1016/j.ymeth.2016.04.020] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 01/09/2023] Open
Abstract
It has been more than two decades since the first aptamer molecule was discovered. Since then, aptamer molecules have gain much attention in the scientific field. This increasing traction can be attributed to their many desirable traits, such as 1) their potentials to bind a wide range of molecules, 2) their malleability, and 3) their low cost of production. These traits have made aptamer molecules an ideal platform to pursue in the realm of pharmaceuticals and bio-sensors. Despite the broad applications of aptamers, tedious procedure, high resource consumption, and limited nucleobase repertoire have hindered aptamer in application usage. To address these issues, new innovative methodologies, such as automation and single round SELEX, are being developed to improve the outcomes and rates in which aptamers are discovered.
Collapse
Affiliation(s)
- Yi Xi Wu
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, United States
| | - Young Jik Kwon
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, United States; Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697, United States; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, United States; Department of Biomedical Engineering, University of California, Irvine, CA 92697, United States.
| |
Collapse
|
44
|
Jung IY, Lee EH, Suh AY, Lee SJ, Lee H. Oligonucleotide-based biosensors for in vitro diagnostics and environmental hazard detection. Anal Bioanal Chem 2016; 408:2383-406. [PMID: 26781106 DOI: 10.1007/s00216-015-9212-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/19/2015] [Accepted: 11/23/2015] [Indexed: 02/06/2023]
Abstract
Oligonucleotide-based biosensors have drawn much attention because of their broad applications in in vitro diagnostics and environmental hazard detection. They are particularly of interest to many researchers because of their high specificity as well as excellent sensitivity. Recently, oligonucleotide-based biosensors have been used to achieve not only genetic detection of targets but also the detection of small molecules, peptides, and proteins. This has further broadened the applications of these sensors in the medical and health care industry. In this review, we highlight various examples of oligonucleotide-based biosensors for the detection of diseases, drugs, and environmentally hazardous chemicals. Each example is provided with detailed schematics of the detection mechanism in addition to the supporting experimental results. Furthermore, future perspectives and new challenges in oligonucleotide-based biosensors are discussed.
Collapse
Affiliation(s)
- Il Young Jung
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Eun Hee Lee
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Ah Young Suh
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Seung Jin Lee
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Hyukjin Lee
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea.
| |
Collapse
|
45
|
Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
Collapse
Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
| |
Collapse
|
46
|
Highly Sensitive Fluorescent Aptasensor for Thrombin Detection Based on Competition Triggered Rolling Circle Amplification. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1016/s1872-2040(15)60880-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
47
|
Zeng Y, Zheng A, Wu J, Cai Z, Huang A, Liu X. Horseradish peroxidase and aptamer dual-functionalized nanoprobe for the amplification detection of alpha-methylacyl-CoA racemase. Anal Chim Acta 2015; 899:100-5. [DOI: 10.1016/j.aca.2015.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/09/2015] [Accepted: 10/08/2015] [Indexed: 12/14/2022]
|
48
|
Hu J, Kim J, Easley CJ. Quantifying Aptamer-Protein Binding via Thermofluorimetric Analysis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2015; 7:7358-7362. [PMID: 26366207 PMCID: PMC4562029 DOI: 10.1039/c5ay00837a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Effective aptamer-based protein assays require coupling to a quantitative reporter of aptamer-protein binding. Typically, this involves a direct optical or electrochemical readout of DNA hybridization or an amplification step coupled to the readout. However, method development is often hampered by the multiplicity of aptamer-target binding mechanisms, which can interfere with the hybridization step. As a simpler and more generalizable readout of aptamer-protein binding, we report that thermofluorimetric analysis (TFA) can be used to quantitatively assay protein levels. Sub-nanomolar detection (0.74 nM) of platelet-derived growth factor (PDGF) with its corresponding aptamer is shown as a test case. In the presence of various DNA intercalating dyes, protein-bound aptamers exhibit a change in fluorescence intensity compared to the intercalated, unbound aptamer. This allows thermal resolution of bound and unbound aptamers using fluorescence melting analysis (-dF/dT curves). Remarkably, the homogeneous optical method allows subtraction of autofluorescence in human serum, giving PDGF detection limits of 1.8 and 10.7 nM in serum diluted 1:7 and 1:3, respectively. We have thus demonstrated that bound and unbound aptamers can be thermally resolved in a homogeneous format using a simple qPCR instrument-even in human serum. The simplicity of this approach provides an important step toward a robust, generalizable readout of aptamer-protein binding.
Collapse
Affiliation(s)
- Juan Hu
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, AL 36849
| | - Joonyul Kim
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, AL 36849
| | - Christopher J. Easley
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, AL 36849
| |
Collapse
|
49
|
Zhou W, Huang PJJ, Ding J, Liu J. Aptamer-based biosensors for biomedical diagnostics. Analyst 2015; 139:2627-40. [PMID: 24733714 DOI: 10.1039/c4an00132j] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aptamers are single-stranded nucleic acids that selectively bind to target molecules. Most aptamers are obtained through a combinatorial biology technique called SELEX. Since aptamers can be isolated to bind to almost any molecule of choice, can be readily modified at arbitrary positions and they possess predictable secondary structures, this platform technology shows great promise in biosensor development. Over the past two decades, more than one thousand papers have been published on aptamer-based biosensors. Given this progress, the application of aptamer technology in biomedical diagnosis is still in a quite preliminary stage. Most previous work involves only a few model aptamers to demonstrate the sensing concept with limited biomedical impact. This Critical Review aims to summarize progress that might enable practical applications of aptamers for biological samples. First, general sensing strategies based on the unique properties of aptamers are summarized. Each strategy can be coupled to various signaling methods. Among these, a few detection methods including fluorescence lifetime, flow cytometry, upconverting nanoparticles, nanoflare technology, magnetic resonance imaging, electronic aptamer-based sensors, and lateral flow devices have been discussed in more detail since they are more likely to work in a complex sample matrix. The current limitations of this field include the lack of high quality aptamers for clinically important targets. In addition, the aptamer technology has to be extensively tested in a clinical sample matrix to establish reliability and accuracy. Future directions are also speculated to overcome these challenges.
Collapse
Affiliation(s)
- Wenhu Zhou
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Central South University, Tongzipo Road #172, Changsha 410013, Hunan, PR China.
| | | | | | | |
Collapse
|
50
|
Liu M, Zhang W, Zhang Q, Brennan JD, Li Y. Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503182] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|