1
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Chowdhury R, Eslami S, Pham CV, Rai A, Lin J, Hou Y, Greening DW, Duan W. Role of aptamer technology in extracellular vesicle biology and therapeutic applications. NANOSCALE 2024; 16:11457-11479. [PMID: 38856692 DOI: 10.1039/d4nr00207e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Extracellular vesicles (EVs) are cell-derived nanosized membrane-bound vesicles that are important intercellular signalling regulators in local cell-to-cell and distant cell-to-tissue communication. Their inherent capacity to transverse cell membranes and transfer complex bioactive cargo reflective of their cell source, as well as their ability to be modified through various engineering and modification strategies, have attracted significant therapeutic interest. Molecular bioengineering strategies are providing a new frontier for EV-based therapy, including novel mRNA vaccines, antigen cross-presentation and immunotherapy, organ delivery and repair, and cancer immune surveillance and targeted therapeutics. The revolution of EVs, their diversity as biocarriers and their potential to contribute to intercellular communication, is well understood and appreciated but is ultimately dependent on the development of methods and techniques for their isolation, characterization and enhanced targeting. As single-stranded oligonucleotides, aptamers, also known as chemical antibodies, offer significant biological, chemical, economic, and therapeutic advantages in terms of their size, selectivity, versatility, and multifunctional programming. Their integration into the field of EVs has been contributing to the development of isolation, detection, and analysis pipelines associated with bioengineering strategies for nano-meets-molecular biology, thus translating their use for therapeutic and diagnostic utility.
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Affiliation(s)
- Rocky Chowdhury
- School of Medicine, Deakin University, and IMPACT Strategic Research Centre, Waurn Ponds, VIC, 3216, Australia.
| | - Sadegh Eslami
- Molecular Proteomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
| | - Cuong Viet Pham
- Molecular Imaging and Theranostics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
| | - Alin Rai
- Molecular Proteomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- Department of Cardiovascular Research, Translation and Implementation, and La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Jia Lin
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yingchu Hou
- Laboratory of Tumor Molecular and Cellular Biology College of Life Sciences, Shaanxi Normal University 620 West Chang'an Avenue, Xi'an, Shaanxi, 710119, China
| | - David W Greening
- Molecular Proteomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- Department of Cardiovascular Research, Translation and Implementation, and La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Wei Duan
- School of Medicine, Deakin University, and IMPACT Strategic Research Centre, Waurn Ponds, VIC, 3216, Australia.
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2
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Huang LH, Hsieh YY, Yang FA, Liao WC. DNA-modified Prussian blue nanozymes for enhanced electrochemical biosensing. NANOSCALE 2024; 16:9770-9780. [PMID: 38597919 DOI: 10.1039/d4nr00387j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Prussian blue nanoparticles exhibit the potential to be employed in bioanalytical applications due to their robust stability, peroxidase-like catalytic functionality, straightforward synthesis, and biocompatibility. An efficient approach is presented for the synthesis of nucleic acid-modified Prussian blue nanoparticles (DNA-PBNPs), utilizing nanoparticle porosity to adsorb nucleic acids (polyT). This strategic adsorption leads to the exposure of nucleic acid sequences on the particle surface while retaining catalytic activity. DNA-PBNPs further couple with functional nucleic acid sequences and aptamers through complementary base pairing to act as transducers in biosensors and amplify signal acquisition. Subsequently, we integrated a copper ion-dependent DNAzyme (Cu2+-DNAzyme) and a vascular endothelial growth factor aptamer (VEGF aptamer) onto screen-printed electrodes to serve as recognition elements for analytes. Significantly, our approach leverages DNA-PBNPs as a superior alternative to traditional enzyme-linked antibodies in electrochemical biosensors, thereby enhancing both the efficiency and adaptability of these devices. Our study conclusively demonstrates the application of DNA-PBNPs in two different biosensing paradigms: the sensitive detection of copper ions and vascular endothelial growth factor (VEGF). These results indicate the promising potential of DNA-modified Prussian blue nanoparticles in advancing bioanalytical sensing technologies.
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Affiliation(s)
- Lin-Hui Huang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
| | - Yu-Yu Hsieh
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
| | - Fu-An Yang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
| | - Wei-Ching Liao
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
- Medical Device Innovation and Translation Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
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3
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Duan H, Tang SY, Goda K, Li M. Enhancing the sensitivity and stability of electrochemical aptamer-based sensors by AuNPs@MXene nanocomposite for continuous monitoring of biomarkers. Biosens Bioelectron 2024; 246:115918. [PMID: 38086309 DOI: 10.1016/j.bios.2023.115918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/21/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023]
Abstract
Electrochemical aptamer-based (E-AB) sensors offer exciting potential for real-time tracking of various biomarkers, such as proteins and small molecules, due to their exceptional selectivity and adaptability. However, most E-AB sensors rely on planar gold structures, which inherently limit their sensitivity and operational stability for continuous monitoring of biomarkers. Although gold nanostructures have recently enhanced E-AB sensor performance, no studies have explored the combination of gold nanostructure with other types of nanomaterials for continuous molecular monitoring. To fill this gap, we employed gold nanoparticles and MXene Ti3C2 (AuNPs@MXene), a versatile nanocomposite, in designing an E-AB sensor targeted at vascular endothelial growth factor (VEGF), a crucial human signaling protein. Remarkably, the AuNPs@MXene nanocomposite achieved over thirty-fold and half-fold increases in active surface area compared to bare and AuNPs-modified gold electrodes, respectively, significantly elevating the analytical capabilities of E-AB sensors during continuous operation. After a systematic optimization and characterization process, the newly developed E-AB sensor, powered by AuNPs@MXene nanocomposite, demonstrated both enhanced stability and heightened sensitivity. Overall, our findings open new avenues for the incorporation of nanocomposites in E-AB sensor design, enabling the creation of more sensitive and durable real-time monitoring systems.
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Affiliation(s)
- Haowei Duan
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shi-Yang Tang
- School of Electronics and Computer Science, University of Southampton, Southampton, SO16 1BJ, UK
| | - Keisuke Goda
- Department of Chemistry, University of Tokyo, Tokyo, 113-0033, Japan; Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA; Institute of Technological Sciences, Wuhan University, Hubei, 430072, China
| | - Ming Li
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia; School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, 2052, Australia.
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4
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Kalathingal M, Rhee YM. Molecular mechanism of binding between a therapeutic RNA aptamer and its protein target VEGF: A molecular dynamics study. J Comput Chem 2023; 44:1129-1137. [PMID: 36625560 DOI: 10.1002/jcc.27070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 11/18/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023]
Abstract
Macugen is a therapeutic RNA aptamer against vascular endothelial growth factor (VEGF)-165, the VEGF isoform primarily responsible for angiogenesis. It has been reported that Macugen inhibits angiogenesis by specifically binding to the heparin binding domain (HBD) of VEGF165. The mechanism of the molecular recognition between HBD and Macugen is investigated here using all-atom molecular dynamics simulations. We find that Macugen recognizes HBD by an induced-fit mechanism with major conformational changes in Macugen and almost no changes in the structure of HBD, whereas HBD recognizes Macugen by a conformational selection mechanism.
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Affiliation(s)
- Mahroof Kalathingal
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
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5
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Abstract
SELEX has enabled the selection of aptamers, nucleic acids that can bind a defined ligand, in some cases with exceptionally high affinity and specificity. The SELEX protocol has been adapted many times to fit a variety of needs. This protocol describes such an adaptation, namely, RNA-Capture SELEX that we have used to successfully develop small molecule-binding RNA aptamers. Our proposed method specifically selects not only for excellent binding but also for conformational switching. In consequence, we found this SELEX method to be particularly suitable for identifying aptamers for further application in synthetic riboswitch engineering.
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Affiliation(s)
- Leon Kraus
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany.
- Center for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany.
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6
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Moreno M, García-Sacristán A, Martín ME, González VM. Enzyme-Linked Oligonucleotide Assay (ELONA). Methods Mol Biol 2023; 2570:235-242. [PMID: 36156787 DOI: 10.1007/978-1-0716-2695-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Aptamers are single-stranded oligonucleotides able to recognize a target with high affinity and specificity. Aptamers are used in different diagnostics applications, highlighting, among all, variations of the traditional enzyme-linked immunosorbent assay (ELISA). In this chapter, we show the procedures for the development of two types of indirect ELONA: a sandwich ELONA and a direct ELONA coupled to either real-time quantitative PCR as a direct and sensitive readout.
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Affiliation(s)
| | | | - M Elena Martín
- Grupo de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Víctor M González
- Aptus Biotech SL, Madrid, Spain. .,Grupo de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Universitario Ramón y Cajal, Madrid, Spain.
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7
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Freund N, Taylor AI, Arangundy-Franklin S, Subramanian N, Peak-Chew SY, Whitaker AM, Freudenthal BD, Abramov M, Herdewijn P, Holliger P. A two-residue nascent-strand steric gate controls synthesis of 2'-O-methyl- and 2'-O-(2-methoxyethyl)-RNA. Nat Chem 2023; 15:91-100. [PMID: 36229679 PMCID: PMC7614059 DOI: 10.1038/s41557-022-01050-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 08/29/2022] [Indexed: 01/17/2023]
Abstract
Steric exclusion is a key element of enzyme substrate specificity, including in polymerases. Such substrate specificity restricts the enzymatic synthesis of 2'-modified nucleic acids, which are of interest in nucleic-acid-based drug development. Here we describe the discovery of a two-residue, nascent-strand, steric control 'gate' in an archaeal DNA polymerase. We show that engineering of the gate to reduce steric bulk in the context of a previously described RNA polymerase activity unlocks the synthesis of 2'-modified RNA oligomers, specifically the efficient synthesis of both defined and random-sequence 2'-O-methyl-RNA (2'OMe-RNA) and 2'-O-(2-methoxyethyl)-RNA (MOE-RNA) oligomers up to 750 nt. This enabled the discovery of RNA endonuclease catalysts entirely composed of 2'OMe-RNA (2'OMezymes) for the allele-specific cleavage of oncogenic KRAS (G12D) and β-catenin CTNNB1 (S33Y) mRNAs, and the elaboration of mixed 2'OMe-/MOE-RNA aptamers with high affinity for vascular endothelial growth factor. Our results open up these 2'-modified RNAs-used in several approved nucleic acid therapeutics-for enzymatic synthesis and a wider exploration in directed evolution and nanotechnology.
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Affiliation(s)
- Niklas Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Alexander I Taylor
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.
| | | | - Nithya Subramanian
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Sew-Yeu Peak-Chew
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Amy M Whitaker
- Laboratory of Genome Maintenance and Structural Biology, Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Bret D Freudenthal
- Laboratory of Genome Maintenance and Structural Biology, Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Mikhail Abramov
- Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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8
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Rana D, Kandar A, Salehi-Nik N, Inci I, Koopman B, Rouwkema J. Spatiotemporally controlled, aptamers-mediated growth factor release locally manipulates microvasculature formation within engineered tissues. Bioact Mater 2022; 12:71-84. [PMID: 35087964 PMCID: PMC8777207 DOI: 10.1016/j.bioactmat.2021.10.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 12/14/2022] Open
Affiliation(s)
- Deepti Rana
- Department of Biomechanical Engineering, Technical Medical Centre, Faculty of Engineering Technology, University of Twente, 7500, AE, Enschede, the Netherlands
| | - Ajoy Kandar
- Department of Biomechanical Engineering, Technical Medical Centre, Faculty of Engineering Technology, University of Twente, 7500, AE, Enschede, the Netherlands
| | - Nasim Salehi-Nik
- Department of Biomechanical Engineering, Technical Medical Centre, Faculty of Engineering Technology, University of Twente, 7500, AE, Enschede, the Netherlands
| | - Ilyas Inci
- Izmir Democracy University, Vocational School of Health Services, Department of Dentistry Services, Dental Prosthetics Technology, Izmir, 35140, Turkey
| | - Bart Koopman
- Department of Biomechanical Engineering, Technical Medical Centre, Faculty of Engineering Technology, University of Twente, 7500, AE, Enschede, the Netherlands
| | - Jeroen Rouwkema
- Department of Biomechanical Engineering, Technical Medical Centre, Faculty of Engineering Technology, University of Twente, 7500, AE, Enschede, the Netherlands
- Corresponding author.
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9
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Aptamer–Gemcitabine Conjugates with Enzymatically Cleavable Linker for Targeted Delivery and Intracellular Drug Release in Cancer Cells. Pharmaceuticals (Basel) 2022; 15:ph15050558. [PMID: 35631384 PMCID: PMC9147807 DOI: 10.3390/ph15050558] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Gemcitabine is a chemotherapeutic used clinically to treat a variety of cancers. However, because it lacks tumor cell specificity, gemcitabine may cause off-target cytotoxicity and adversely impact patients. To impart cancer cell specificity to gemcitabine and improve its therapeutic efficacy, we synthesized a unique aptamer–drug conjugate that carries a high gemcitabine payload (three molecules) via a dendrimer structure and enzymatically cleavable linkers for controlled intracellular drug release. First, linker–gemcitabinedendrimer–linker–gemcitabine products were produced, which had significantly lower cytotoxicity than an equimolar amount of free drug. Biochemical analysis revealed that lysosomal cathepsin B protease rapidly cleaved the dendritic linkers and released the conjugated gemcitabine as a free drug. Subsequently, the dendrimer–linker–gemcitabine was coupled with a cell-specific aptamer to form aptamer–gemcitabine conjugates. Functional assays confirmed that, under aptamer guidance, aptamer–gemcitabine conjugates were selectively bound to and then internalized by triple-negative breast cancer cells. Cellular therapy studies indicated that the aptamer–gemcitabine conjugates potentiated cytotoxic activity to targeted cancer cells but did not affect off-target control cells. Our study demonstrates a novel approach to aptamer-mediated targeted drug delivery that combines a high drug payload and an enzymatically controlled drug release switch to achieve higher therapeutic efficacy and fewer off-target effects relative to free-drug chemotherapy.
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10
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Pal R, Deb I, Sarzynska J, Lahiri A. LNA-induced dynamic stability in a therapeutic aptamer: insights from molecular dynamics simulations. J Biomol Struct Dyn 2022; 41:2221-2230. [PMID: 35100936 DOI: 10.1080/07391102.2022.2029567] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Modulation of structural and thermodynamic properties of nucleic acids with synthetic modifications is a promising area of research with possible applications in nanotechnology and nanotherapeutics. Locked nucleic acid (LNA) is one such modification in which the C4' and O2' atoms of the sugar moiety are connected through a methylene bridge. The LNA modified DNA aptamer RNV66, and its unmodified counterpart V7t1, both of which target the vascular endothelial growth factor (VEGF) implicated in oncogenic angiogenesis, have a G-rich tract that can fold into G-quadruplex structures. However, it is not understood why V7t1 has a polymorphic structure while its LNA modified counterpart RNV66 has a unique quadruplex fold with higher nuclease resistance, thermal stability and greater binding affinity for VEGF. In this work, we have performed extensive molecular dynamics simulations of RNV66 and V7t1 to study and compare the structural and dynamic consequences of the insertion of LNAs. It was observed that the increase in dynamic stability was significant in the presence of LNA residues and our protocol for combining different torsional parameters using OL15 for the DNA aptamer and parm99_LNA along with parmbsc0 and βOL15 for the LNAs nicely reproduced the experimentally observed conformational features of RNV66. Our observations would help in further theoretical studies in understanding the lack of frustration in the folding of the LNA modified aptamer and its higher affinity for VEGF.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rupak Pal
- Department of Biophysics, Molecular Biology, and Bioinformatics, University of Calcutta, Kolkata, India
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology, and Bioinformatics, University of Calcutta, Kolkata, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology, and Bioinformatics, University of Calcutta, Kolkata, India
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11
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Zhang J, Huang Y, Sun M, Wan S, Yang C, Song Y. Recent Advances in Aptamer-Based Liquid Biopsy. ACS APPLIED BIO MATERIALS 2022; 5:1954-1979. [PMID: 35014838 DOI: 10.1021/acsabm.1c01202] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Liquid biopsy capable of noninvasive and real-time molecular profiling is considered as a breakthrough technology, endowing an opportunity for precise diagnosis of individual patients. Extracellular vesicles (EVs) and circulating tumor cells (CTCs) consisting of substantial disease-related molecular information play an important role in liquid biopsy. Therefore, it is critically significant to exploit high-performance recognition ligands for efficient isolation and analysis of EVs and CTCs from complex body fluids. Aptamers exhibit extraordinary merits of high specificity and affinity, which are considered as superior recognition ligands for liquid biopsy. In this review, we first summarize recent advanced strategies for the evolution of high-performance aptamers and the construction of various aptamer-based recognition elements. Subsequently, we mainly discuss the isolation and analysis of EVs and CTCs based on the aptamer functioned biomaterials/biointerface. Ultimately, we envision major challenges and future direction of aptamer-based liquid biopsy for clinical utilities.
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Affiliation(s)
- Jialu Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yihao Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Miao Sun
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shuang Wan
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.,Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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12
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Kramat J, Suess B. Efficient Method to Identify Synthetic Riboswitches Using RNA-Based Capture-SELEX Combined with In Vivo Screening. Methods Mol Biol 2022; 2518:157-177. [PMID: 35666445 DOI: 10.1007/978-1-0716-2421-0_10] [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: 06/15/2023]
Abstract
Synthetic riboswitches are a promising tool for conditional gene expression. In vitro selected aptamers used as binding domains for the design of RNA-based switches have to exhibit excellent binding affinity as well as ligand binding-induced structural changes. Selection via Capture-SELEX favors the enrichment of aptamers which exhibit both characteristics. For the Capture-SELEX, an RNA pool is used that gets immobilized onto a capture oligonucleotide by hybridization. Addition of the ligand frees the aptamers by their binding to the ligand, resulting in the release from the capture oligonucleotide through structural changes. These sequences get reverse transcribed, PCR amplified, and used for the following selection rounds. In this publication, we present a detailed protocol for Capture-SELEX, followed by screening in yeast to identify aptamers suitable for the design of synthetic riboswitches.
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Affiliation(s)
- Janice Kramat
- Department of Biology, Technical University Darmstadt, Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Darmstadt, Germany.
- Centre of Synthetic Biology, Technical University Darmstadt, Darmstadt, Germany.
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13
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Zheng X, Gao S, Wu J, Hu X. A Fluorescent Aptasensor Based on Assembled G-Quadruplex and Thioflavin T for the Detection of Biomarker VEGF165. Front Bioeng Biotechnol 2021; 9:764123. [PMID: 34869275 PMCID: PMC8636943 DOI: 10.3389/fbioe.2021.764123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/29/2021] [Indexed: 01/05/2023] Open
Abstract
VEGF165, a regulator of angiogenesis, has been widely used as a serum biomarker for a number of human diseases, including cancer, rheumatoid arthritis, bronchial asthma, and diabetic eye disease. The rapid, accurate, and convenient detection of VEGF165 is a crucial step in effective healthcare monitoring, disease diagnosis, and prognosis assessment. In this study, a fluorescent aptasensor based on an assembled G-quadruplex and the signal molecule ThT was developed for VEGF165 detection. First, G-rich DNA fragments were assembled at both ends of the anti-VEGF165 aptamer, and the B-DNA form was converted into a G-quadruplex structure aptamer (G4-Apt). Then, ThT was introduced, and the G-quadruplex significantly enhanced the fluorescence intensity of the bound ThT. When VEGF165 was present, the higher affinity of the aptamer to the target protein allowed the G4-Apt/VEGF165 complex to form and release ThT, which emitted only weak fluorescence in the free state. Therefore, the aptasensor exhibited a good linear detection window from 1.56 to 25 nM VEGF165, with a limit of detection of 0.138 nM. In addition, the aptasensor was applied to detect VEGF165 in clinical serum samples, showing good accuracy, reproducibility, and stability. These results indicate that our developed fluorescent aptasensor can potentially be a reliable, convenient, and cost-effective approach for the sensitive, specific, and rapid detection of the VEGF165 biomarker.
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Affiliation(s)
- Xin Zheng
- Department of Clinical Laboratory, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shunxiang Gao
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Jihong Wu
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Xiaobo Hu
- Department of Clinical Laboratory, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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14
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Patil U, Goyal A, Vu B, Liu Y, Maranholkar V, Kourentzi K, Briggs JM, Willson RC. Antibody mix-and-read assays based on fluorescence intensity probes. MAbs 2021; 13:1980178. [PMID: 34662534 PMCID: PMC8525972 DOI: 10.1080/19420862.2021.1980178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Antibodies and Fc fusion proteins are a rapidly growing class of pharmaceuticals. Cell culture and purification process development and operation require frequent measurement of product concentrations, commonly by complex enzyme-linked immunosorbent assay and high-performance liquid chromatography methods. Here we report a fast (<30 s), and simple antibody Fc assay based on mix-and-read reporting by fluorescence emission. A soluble fluorescein-labeled Fc-affinity reporter produced by standard peptide synthesis is mixed with an Fc-containing sample to produce an immediate shift in both fluorescence polarization and intensity, compatible with on- and at-line measurements and microbioreactor monitoring. We observed significant shifts in fluorescence intensity in Chinese hamster ovary cell culture fluid spiked with IgG and detected an adalimumab biosimilar down to 100 ng/mL (10-4 g/L), despite the interferents in the complex sample matrix. Neither the fluorescence polarization nor the fluorescence intensity assay is significantly affected by the addition of clarified lysate of 2 million CHO-k1 cells/mL, suggesting applicability even to cultures of low viability. Biochemical and molecular docking approaches suggest that the fluorescence intensity enhancement is caused by changes in the fluorophore's local microenvironment upon binding to IgG Fc, especially by interactions with Fc His433.Abbreviations: CCF: Cell Culture Fluid; CHO: Chinese Hamster Ovary cells; ELISA: Enzyme Linked Immunosorbent Assay; Fc: Fragment Crystallizable of antibody; HPLC: High-Performance Liquid Chromatography; HPβCD: hydroxypropyl-β-cyclodextrin; IgG: ImmunoglobulinG; mAb: Monoclonal Antibody; PBS: Phosphate-Buffered Saline; PDB: Protein Data Bank; SpA: Staphylococcal protein A; SpG: Staphylococcal protein G.
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Affiliation(s)
- Ujwal Patil
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Atul Goyal
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Binh Vu
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Yanyun Liu
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Vijay Maranholkar
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Katerina Kourentzi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - James M Briggs
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA.,William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Richard C Willson
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA.,William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA.,Escuela De Medicina Y Ciencias De La Salud TecSalud, Monterrey, Nuevo León, Mexico
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15
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Stawicki CM, Rinker TE, Burns M, Tonapi SS, Galimidi RP, Anumala D, Robinson JK, Klein JS, Mallick P. Modular fluorescent nanoparticle DNA probes for detection of peptides and proteins. Sci Rep 2021; 11:19921. [PMID: 34620912 PMCID: PMC8497506 DOI: 10.1038/s41598-021-99084-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/20/2021] [Indexed: 02/08/2023] Open
Abstract
Fluorescently labeled antibody and aptamer probes are used in biological studies to characterize binding interactions, measure concentrations of analytes, and sort cells. Fluorescent nanoparticle labels offer an excellent alternative to standard fluorescent labeling strategies due to their enhanced brightness, stability and multivalency; however, challenges in functionalization and characterization have impeded their use. This work introduces a straightforward approach for preparation of fluorescent nanoparticle probes using commercially available reagents and common laboratory equipment. Fluorescent polystyrene nanoparticles, Thermo Fisher Scientific FluoSpheres, were used in these proof-of-principle studies. Particle passivation was achieved by covalent attachment of amine-PEG-azide to carboxylated particles, neutralizing the surface charge from - 43 to - 15 mV. A conjugation-annealing handle and DNA aptamer probe were attached to the azide-PEG nanoparticle surface either through reaction of pre-annealed handle and probe or through a stepwise reaction of the nanoparticles with the handle followed by aptamer annealing. Nanoparticles functionalized with DNA aptamers targeting histidine tags and VEGF protein had high affinity (EC50s ranging from 3 to 12 nM) and specificity, and were more stable than conventional labels. This protocol for preparation of nanoparticle probes relies solely on commercially available reagents and common equipment, breaking down the barriers to use nanoparticles in biological experiments.
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Affiliation(s)
| | - Torri E Rinker
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA.
| | - Markus Burns
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Sonal S Tonapi
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Rachel P Galimidi
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Deepthi Anumala
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Julia K Robinson
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Joshua S Klein
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
| | - Parag Mallick
- Nautilus Biotechnology, 201 Industrial Rd #310, San Carlos, CA, 94070, USA
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16
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Tapp M, Dennis P, Naik RR, Milam VT. Competition-Enhanced Ligand Selection to Screen for DNA Aptamers for Spherical Gold Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9043-9052. [PMID: 34279112 DOI: 10.1021/acs.langmuir.1c01053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Competition-Enhanced Ligand Selection (CompELS) approach was used to identify aptamer candidates for spherical gold nanoparticles (AuNPs). This approach differs from conventional Systematic Evolution of Ligands by EXponential enrichment (SELEX)-based aptamer screening by eliminating repeated elution and polymerase chain reaction (PCR) amplification steps of bound candidate sequences between each selection round to continually enrich the candidate aptamer pool with oligonucleotides remaining from an earlier SELEX selection round. Instead, a new pool of unenriched oligonucleotides is added during each CompELS selection round to compete with existing target-bound oligonucleotides species for target binding sites. In this study, 24 aptamer candidates for AuNPs were identified using the CompELS approach and then compared to reveal similarities in their primary structures and their predicted secondary structures. No strong patterns in individual base identities (position-dependent) nor in segments of consecutive bases (independent of position) prevailed among the identified sequences. Motifs in predicted secondary structures, on the other hand, were shared among otherwise unrelated aptamer sequences. These motifs were revealed using a systematic classification and enumeration of distinct secondary structure elements, namely, hairpins, duplexes, single-stranded segments, interior loops, bulges, and multibranched loops.
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Affiliation(s)
| | - Patrick Dennis
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Rajesh R Naik
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
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17
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Kim J, Park H, Saravanakumar G, Kim WJ. Polymer/Aptamer-Integrated Gold Nanoconstruct Suppresses the Inflammatory Process by Scavenging ROS and Capturing Pro-inflammatory Cytokine TNF-α. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9390-9401. [PMID: 33155813 DOI: 10.1021/acsami.0c15727] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In the present study, we report a rationally designed polymer/aptamer-integrated gold (Au) nanoconstruct capable of scavenging reactive oxygen species (ROS) and capturing tumor necrosis factor alpha (TNF-α) and investigate its potential as an anti-inflammatory agent for the treatment of peritonitis. By taking advantage of specific interactions between ATP and both ATP aptamer and polymeric phenylboronic acid (pPBA), we construct a unique polymer-coated Au nanoconstruct equipped with TNF-α aptamer and ATP aptamer. The formed phenylboronic ester and TNF-α aptamer in the nanoconstruct is capable of scavenging ROS and capturing of TNF-α, respectively. Thus, this combined characteristics enable the nanoconstruct an additive anti-inflammatory effect. Furthermore, we demonstrate the high anti-inflammatory effect of the nanoconstruct in vitro and in vivo using the peritonitis model by monitoring ROS and pro-inflammatory cytokine levels.
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Affiliation(s)
- Jinseong Kim
- Department of Chemistry, POSTECH-CATHOLIC Biomedical Engineering Institute, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Hyeongmok Park
- Department of Chemistry, POSTECH-CATHOLIC Biomedical Engineering Institute, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Gurusamy Saravanakumar
- Department of Chemistry, POSTECH-CATHOLIC Biomedical Engineering Institute, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Won Jong Kim
- Department of Chemistry, POSTECH-CATHOLIC Biomedical Engineering Institute, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
- OmniaMed Co., Ltd, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
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18
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Lee W, Park JW, Go YJ, Kim WJ, Rhee YM. Considering both small and large scale motions of vascular endothelial growth factor (VEGF) is crucial for reliably predicting its binding affinities to DNA aptamers. RSC Adv 2021; 11:9315-9326. [PMID: 35423456 PMCID: PMC8695334 DOI: 10.1039/d0ra10106k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/23/2021] [Indexed: 11/21/2022] Open
Abstract
Considering both small and large scale motions of VEGF is crucial to predict its relative binding affinities to DNA aptamer variants with docking.
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Affiliation(s)
- Wook Lee
- Department of Chemistry
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Korea
- Department of Chemistry
| | - Jae Whee Park
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 34141
- Korea
| | - Yeon Ju Go
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 34141
- Korea
| | - Won Jong Kim
- Department of Chemistry
- Pohang University of Science and Technology (POSTECH)
- Pohang 37673
- Korea
| | - Young Min Rhee
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 34141
- Korea
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19
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Riccardi C, Napolitano E, Musumeci D, Montesarchio D. Dimeric and Multimeric DNA Aptamers for Highly Effective Protein Recognition. Molecules 2020; 25:E5227. [PMID: 33182593 PMCID: PMC7698228 DOI: 10.3390/molecules25225227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/14/2022] Open
Abstract
Multivalent interactions frequently occur in biological systems and typically provide higher binding affinity and selectivity in target recognition than when only monovalent interactions are operative. Thus, taking inspiration by nature, bivalent or multivalent nucleic acid aptamers recognizing a specific biological target have been extensively studied in the last decades. Indeed, oligonucleotide-based aptamers are suitable building blocks for the development of highly efficient multivalent systems since they can be easily modified and assembled exploiting proper connecting linkers of different nature. Thus, substantial research efforts have been put in the construction of dimeric/multimeric versions of effective aptamers with various degrees of success in target binding affinity or therapeutic activity enhancement. The present review summarizes recent advances in the design and development of dimeric and multimeric DNA-based aptamers, including those forming G-quadruplex (G4) structures, recognizing different key proteins in relevant pathological processes. Most of the designed constructs have shown improved performance in terms of binding affinity or therapeutic activity as anti-inflammatory, antiviral, anticoagulant, and anticancer agents and their number is certainly bound to grow in the next future.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
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20
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Bottari F, Daems E, de Vries AM, Van Wielendaele P, Trashin S, Blust R, Sobott F, Madder A, Martins JC, De Wael K. Do Aptamers Always Bind? The Need for a Multifaceted Analytical Approach When Demonstrating Binding Affinity between Aptamer and Low Molecular Weight Compounds. J Am Chem Soc 2020; 142:19622-19630. [DOI: 10.1021/jacs.0c08691] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Fabio Bottari
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium
| | - Elise Daems
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium
- BAMS Research Group, Department of Chemistry, University of Antwerp, Antwerp, 2020, Belgium
| | - Anne-Mare de Vries
- NMR and Structure Analysis Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
| | - Pieter Van Wielendaele
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, 2610, Belgium
| | - Stanislav Trashin
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium
| | - Ronny Blust
- Sphere Research Group, Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Frank Sobott
- BAMS Research Group, Department of Chemistry, University of Antwerp, Antwerp, 2020, Belgium
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
| | - José C. Martins
- NMR and Structure Analysis Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
| | - Karolien De Wael
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium
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21
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Riccardi C, Napolitano E, Platella C, Musumeci D, Melone MAB, Montesarchio D. Anti-VEGF DNA-based aptamers in cancer therapeutics and diagnostics. Med Res Rev 2020; 41:464-506. [PMID: 33038031 DOI: 10.1002/med.21737] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/12/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022]
Abstract
The vascular endothelial growth factor (VEGF) family and its receptors play fundamental roles not only in physiological but also in pathological angiogenesis, characteristic of cancer progression. Aiming at finding putative treatments for several malignancies, various small molecules, antibodies, or protein-based drugs have been evaluated in vitro and in vivo as VEGF inhibitors, providing efficient agents approved for clinical use. Due to the high clinical importance of VEGF, also a great number of anti-VEGF nucleic acid-based aptamers-that is, oligonucleotides able to bind with high affinity and specificity a selected biological target-have been developed as promising agents in anticancer strategies. Notable research efforts have been made in optimization processes of the identified aptamers, searching for increased target affinity and/or bioactivity by exploring structural analogues of the lead compounds. This review is focused on recent studies devoted to the development of DNA-based aptamers designed to target VEGF. Their therapeutic potential as well as their significance in the construction of highly selective biosensors is here discussed.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.,Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and Inter-University Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.,Institute of Biostructures and Bioimages, Naples, Italy
| | - Mariarosa A B Melone
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and Inter-University Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, Naples, Italy.,Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
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22
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Şahin S, Caglayan MO, Üstündağ Z. Recent advances in aptamer-based sensors for breast cancer diagnosis: special cases for nanomaterial-based VEGF, HER2, and MUC1 aptasensors. Mikrochim Acta 2020; 187:549. [PMID: 32888061 DOI: 10.1007/s00604-020-04526-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/20/2020] [Indexed: 02/07/2023]
Abstract
Cancer is one of the most common and important diseases with a high mortality rate. Breast cancer is among the three most common types of cancer in women, and the mortality rate has reached 0.024% in some countries. For early-stage preclinical diagnosis of breast cancer, sensitive and reliable tools are needed. Today, there are many types of biomarkers that have been identified for cancer diagnosis. A wide variety of detection strategies have also been developed for the detection of these biomarkers from serum or other body fluids at physiological concentrations. Aptamers are single-stranded DNA or RNA oligonucleotides and promising in the production of more sensitive and reliable biosensor platforms in combination with a wide range of nanomaterials. Conformational changes triggered by the target analyte have been successfully applied in fluorometric, colorimetric, plasmonic, and electrochemical-based detection strategies. This review article presents aptasensor approaches used in the detection of vascular endothelial growth factor (VEGF), human epidermal growth factor receptor 2 (HER2), and mucin-1 glycoprotein (MUC1) biomarkers, which are frequently studied in the diagnosis of breast cancer. The focus of this review article is on developments of the last decade for detecting these biomarkers using various sensitivity enhancement techniques and nanomaterials.
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Affiliation(s)
- Samet Şahin
- Department of Bioengineering, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey.
| | | | - Zafer Üstündağ
- Department of Chemistry, Kütahya Dumlupınar University, 43100, Kütahya, Turkey
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23
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Aptamer binding assays and molecular interaction studies using fluorescence anisotropy - A review. Anal Chim Acta 2020; 1125:267-278. [PMID: 32674773 DOI: 10.1016/j.aca.2020.05.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/16/2020] [Accepted: 05/23/2020] [Indexed: 12/26/2022]
Abstract
Binding of nucleic acid aptamers to specific targets and detection with fluorescence anisotropy (FA) or fluorescence polarization (FP) take advantage of the complementary features of aptamers and the fluorescence techniques. We review recent advances in affinity binding assays using aptamers and FA/FP, with an emphasis on studies of molecular interactions and identification of binding sites. Aptamers provide several benefits, including the ease of labelling fluorophores on specific sites, binding-induced changes in aptamer structures, hybridization of the aptamers to complementary sequences, changes in molecular volume upon binding of the aptamer to its target, and adsorption of aptamers onto nanomaterials. Some of these benefits have been utilized for FA/FP assays. Once the aptamer binds to its target, the resulting changes in molecular volume (size), structure, local rotation of the fluorophore, and/or the fluorescence lifetime influence changes to the FA/FP values. Measurements of these fluorescence anisotropy/polarization changes have provided insights into the molecular interactions, such as the binding affinity and the site of binding. Studies of molecular interactions conducted in homogeneous solutions, as well as those with separations, e.g., capillary electrophoresis, have been summarized in this review. Studies on mapping the position of binding in aptamers at the single nucleotide level have demonstrated a unique benefit of the FA/FP techniques and pointed to an exciting direction for future research.
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24
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Kammer M, Kussrow AK, Olmsted IR, Jackson GW, Bornhop DJ. Free Solution Assay Signal Modulation in Variable-Stem-Length Hairpin Aptamers. ACS OMEGA 2020; 5:11308-11313. [PMID: 32478218 PMCID: PMC7254501 DOI: 10.1021/acsomega.9b04341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Interferometric measurements of free solution assays (FSAs) quantify changes in molecular conformation and hydration upon binding. Here, we demonstrate that aptamer probes designed to undergo varying levels of conformational change upon binding produce corresponding variations in FSA signals. A series of hairpin aptamers were synthesized for the small molecule (tenofovir) with identical loop regions that contain the binding pocket, with between 2 and 10 self-associating base pairings in the stem region. Aptamers selected for tenofovir showed a decrease in the FSA signal and binding affinity (increase in K D) with increasing stem length. Thermodynamic calculations of the Gibbs free energy (ΔG) reported a decrease in ΔG with respect to a corresponding increase in the aptamer stem length. Collectively, these observations provide an expanded understanding of FSA and demonstrate the potential for the rational design of label-free aptamer beacons using FSA as readout.
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Affiliation(s)
- Michael
N. Kammer
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Amanda K. Kussrow
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ian R. Olmsted
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - George W. Jackson
- Base
Pair Biotechnologies, Inc., Pearland, Texas 77584, United States
| | - Darryl J. Bornhop
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
University Institute of Chemical Biology, Nashville, Tennessee 37232-6304, United States
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25
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Manochehry S, Gu J, McConnell EM, Salena BJ, Li Y. In Vitro Selection of New DNA Aptamers for Human Vascular Endothelial Growth Factor 165. Chembiochem 2020; 21:2029-2036. [PMID: 32180322 DOI: 10.1002/cbic.202000024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/26/2020] [Indexed: 11/06/2022]
Abstract
Two DNA aptamers that bind the heparin-binding domain (HBD) of the human vascular endothelial growth factor 165 (VEGF-165) have been previously reported. Although VEGF-165 is a homodimeric protein and the two aptamers have different sequences and secondary structures, the aptamers appear to occupy the same binding site and cannot form a 2 : 1 aptamer/protein complex, thus making them unsuitable for creating a higher-affinity dimeric DNA aptamer. This has motivated us to conduct a new in vitro selection experiment to search for new VEGF-165-binding DNA aptamers with different properties. We undertook a multistream selection strategy in which the concentration of VEGF-165 was varied significantly. We carried out 11 rounds of selection, and next-generation sequencing was conducted for every round in each stream. From comprehensive sequence analysis, we identified four classes of DNA aptamers, of which two were reported before, but two are new DNA aptamers. One of the new aptamers exhibits a unique property that has never been observed before: it is capable of forming the 2 : 1 aptamer/protein complex with VEGF-165. This work has expanded the repertoire of VEGF-165-binding DNA aptamers and creates a possibility to engineer a higher affinity homodimeric aptamer for VEGF-165.
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Affiliation(s)
- Sepehr Manochehry
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 K1, Canada
| | - Jimmy Gu
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 K1, Canada
| | - Erin M McConnell
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 K1, Canada
| | - Bruno J Salena
- Department of Medicine DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4 K1, Canada
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26
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Dong J, He L, Wang Y, Yu F, Yu S, Liu L, Wang J, Tian Y, Qu L, Han R, Wang Z, Wu Y. A highly sensitive colorimetric aptasensor for the detection of the vascular endothelial growth factor in human serum. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 226:117622. [PMID: 31606672 DOI: 10.1016/j.saa.2019.117622] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/23/2019] [Accepted: 10/06/2019] [Indexed: 06/10/2023]
Abstract
Early detection of cancer is of great significance for disease prevention and diagnosis. However, the levels of most cancer markers are quite low in the early stages of disease, so it is urgent to develop a highly sensitive detection method. In this study, a label-free and highly sensitive colorimetric strategy was developed for the detection of the vascular endothelial growth factor165 (VEGF165) in human serum. First, a convenient biosensor was constructed by immobilizing VEGF165 on a microplate, where aptamers bound with VEGF165 to form a complex. Then, streptavidin labeled-horseradish peroxidase (HRP-SA) combined with the complex via the interaction between streptavidin and biotin, thus catalyzing the 3,3',5,5'-tetramethylbenzidine (TMB) and H2O2 system to produce colored products. In the presence of target, immobilized VEGF165 and target competitively bound with the aptamers, resulting in a reduction of the colorimetric signal. Moreover, the optical density (OD) signal decreased with the increase of target concentration. The strategy showed a broad linear range (0.1-100 ng/mL) and a rather low detection limit of 10 pg/mL with good precision and selectivity. Further, the proposed method was successfully applied in detecting VEGF165 in human serum. The detection results of serum samples showed that the proposed assay had a high correlation with CLEIA kits (r = 0.971, P = 0.001). It has potential for application in clinical research and diagnosis.
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Affiliation(s)
- Jiajia Dong
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China; College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, 450001, China
| | - Leiliang He
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yilin Wang
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Fei Yu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Songcheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Lie Liu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Jia Wang
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yongmei Tian
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Lingbo Qu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, 450001, China
| | - Runping Han
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, 450001, China
| | - Ziling Wang
- Henan Provincial Chest Hospital, Zhengzhou, 450001, China.
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China; The Key Laboratory of Nanomedicine and Health Inspection of Zhengzhou, Zhengzhou, 450001, China.
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27
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Manochehry S, McConnell EM, Li Y. Unraveling Determinants of Affinity Enhancement in Dimeric Aptamers for a Dimeric Protein. Sci Rep 2019; 9:17824. [PMID: 31780794 PMCID: PMC6883073 DOI: 10.1038/s41598-019-54005-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/20/2019] [Indexed: 11/09/2022] Open
Abstract
High-affinity aptamers can be derived de novo by using stringent conditions in SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments or can be engineered post SELEX via dimerization of selected aptamers. Using electrophoretic mobility shift assays, we studied a series of heterodimeric and homodimeric aptamers, constructed from two DNA aptamers with distinct primary sequences and secondary structures, previously isolated for VEGF-165, a homodimeric protein. We investigated four factors envisaged to impact the affinity of a dimeric aptamer to a dimeric protein: (1) length of the linker between two aptamer domains, (2) linking orientation, (3) binding-site compatibility of two component aptamers in a heterodimeric aptamer, and (4) steric acceptability of the two identical aptamers in a homodimeric aptamer. All heterodimeric aptamers for VEGF-165 were found to exhibit monomeric aptamer-like affinity and the lack of affinity enhancement was attributed to binding-site overlap by the constituent aptamers. The best homodimeric aptamer showed 2.8-fold better affinity than its monomeric unit (Kd = 13.6 ± 2.7 nM compared to 37.9 ± 14 nM), however the barrier to further affinity enhancement was ascribed to steric interference of the constituent aptamers. Our findings point to the need to consider the issues of binding-site compatibility and spatial requirement of aptamers for the development of dimeric aptamers capable of bivalent recognition. Thus, determinants highlighted herein should be assessed in future multimerization efforts.
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Affiliation(s)
- Sepehr Manochehry
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4K1, Canada
| | - Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4K1, Canada. .,Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4K1, Canada.
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28
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Eremeeva E, Fikatas A, Margamuljana L, Abramov M, Schols D, Groaz E, Herdewijn P. Highly stable hexitol based XNA aptamers targeting the vascular endothelial growth factor. Nucleic Acids Res 2019; 47:4927-4939. [PMID: 30968117 PMCID: PMC6547419 DOI: 10.1093/nar/gkz252] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 01/22/2023] Open
Abstract
Biomedical applications of nucleic acid aptamers are limited by their rapid degradation in biological fluids and generally demand tedious post-selection modifications that might compromise binding. One possible solution to warrant biostability is to directly evolve chemically modified aptamers from xenobiotic nucleic acids (XNAs). We have isolated fully modified 2'-O-methyl-ribose-1,5-anhydrohexitol nucleic acid (MeORNA-HNA) aptamers targeting the rat vascular endothelial growth factor 164 (rVEGF164). Three sequences have been identified that interact with the target protein with affinities in the low-nanomolar range and HNA modifications appeared to be mandatory for their tight binding. The evolution of these XNA aptamers was accomplished using an in vitro selection procedure starting from a fully sugar-modified library containing a 20mer 2'-OMe-ribonucleotide region followed by a 47mer HNA sequence. The high binding affinity and selectivity of the selected aptamers were confirmed by several methods including gel-shift, fluorescence polarisation, and enzyme-linked oligonucleotide assays. The isolated HNA ligands exhibited higher specificity to the rVEGF164 and human VEGF165 isoforms compared to rat VEGF120, while very low binding efficiencies were observed to streptavidin and thrombin. Furthermore, it was clearly demonstrated that the resulting aptamers possessed a superior stability to degradation in human serum and DNase I solutions.
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Affiliation(s)
- Elena Eremeeva
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Antonios Fikatas
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1043, 3000 Leuven, Belgium
| | - Lia Margamuljana
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Mikhail Abramov
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1043, 3000 Leuven, Belgium
| | - Elisabetta Groaz
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
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Development of electrochemical biosensors for tumor marker determination towards cancer diagnosis: Recent progress. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.05.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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30
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Hirasawa S, Kitahara Y, Okamatsu Y, Fujii T, Nakayama A, Ueno S, Ijichi C, Futaki F, Nakata K, Taki M. Facile and Efficient Chemoenzymatic Semisynthesis of Fc-Fusion Compounds for Half-Life Extension of Pharmaceutical Components. Bioconjug Chem 2019; 30:2323-2331. [PMID: 31038930 DOI: 10.1021/acs.bioconjchem.9b00235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The formation of Fc-fusions, in which biologically active molecules and the Fc fragment of antibodies are linked to each other, is one of the most efficient and successful half-life extension technologies to be developed and applied to peptide and protein pharmaceuticals thus far. Fc-fusion compounds are generally produced by recombinant methods. However, these cannot be applied to artificial middle molecules, such as peptides with non-natural amino acids, unnatural cyclic peptides, or pharmaceutical oligonucleotides. Here, we developed a simple, efficient, semisynthetic method for Fc-fusion production involving our previously developed enzymatic N-terminal extension reaction (i.e., NEXT-A reaction) and strain-promoted azide-alkyne cycloaddition, achieving quantitative conversion and high selectivity for the N-terminus of the Fc protein. An Fc-fusion compound prepared by this method showed comparable biological activity to that of the original peptide and a long-circulating plasma half-life. Thus, the proposed method is potentially applicable for the conjugation of a wide range of pharmaceutical components.
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Affiliation(s)
- Shigeo Hirasawa
- Department of Engineering Science, Graduate School of Informatics and Engineering , The University of Electro-Communications (UEC) , 1-5-1 Chofugaoka , Chofu , Tokyo 182-8585 , Japan
| | | | | | | | | | | | | | | | | | - Masumi Taki
- Department of Engineering Science, Graduate School of Informatics and Engineering , The University of Electro-Communications (UEC) , 1-5-1 Chofugaoka , Chofu , Tokyo 182-8585 , Japan
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31
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Moreno M, Fernández-Algar M, Fernández-Chamorro J, Ramajo J, Martínez-Salas E, Briones C. A Combined ELONA-(RT)qPCR Approach for Characterizing DNA and RNA Aptamers Selected against PCBP-2. Molecules 2019; 24:molecules24071213. [PMID: 30925703 PMCID: PMC6480920 DOI: 10.3390/molecules24071213] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/24/2019] [Accepted: 03/26/2019] [Indexed: 11/21/2022] Open
Abstract
Improvements in Systematic Evolution of Ligands by EXponential enrichment (SELEX) technology and DNA sequencing methods have led to the identification of a large number of active nucleic acid molecules after any aptamer selection experiment. As a result, the search for the fittest aptamers has become a laborious and time-consuming task. Herein, we present an optimized approach for the label-free characterization of DNA and RNA aptamers in parallel. The developed method consists in an Enzyme-Linked OligoNucleotide Assay (ELONA) coupled to either real-time quantitative PCR (qPCR, for DNA aptamers) or reverse transcription qPCR (RTqPCR, for RNA aptamers), which allows the detection of aptamer-target interactions in the high femtomolar range. We have applied this methodology to the affinity analysis of DNA and RNA aptamers selected against the poly(C)-binding protein 2 (PCBP-2). In addition, we have used ELONA-(RT)qPCR to quantify the dissociation constant (Kd) and maximum binding capacity (Bmax) of 16 high affinity DNA and RNA aptamers. The Kd values of the high affinity DNA aptamers were compared to those derived from colorimetric ELONA performed in parallel. Additionally, Electrophoretic Mobility Shift Assays (EMSA) were used to confirm the binding of representative PCBP-2-specific RNA aptamers in solution. We propose this ELONA-(RT)qPCR approach as a general strategy for aptamer characterization, with a broad applicability in biotechnology and biomedicine.
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Affiliation(s)
- Miguel Moreno
- Laboratory of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, 28850 Madrid, Spain.
| | - María Fernández-Algar
- Laboratory of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, 28850 Madrid, Spain.
| | | | - Jorge Ramajo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049 Madrid, Spain.
| | | | - Carlos Briones
- Laboratory of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, 28850 Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain.
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Abstract
To explore thermofluorimetric analysis (TFA) in detail, we compared two related aptamers. The first, LINN2, is a DNA aptamer previously selected against EGFR recombinant protein. In this work we selected a second aptamer, KM4, against EGFR-overexpressing A549 cells. The two aptamers were derived from the same pool and bind the same target but behave differently in TFA. Our results suggest four overall conclusions about TFA of aptamers: 1. Some aptamers show reduced fluorescence upon target binding suggesting that target-bound aptamer is not always fluorescent. 2. Many aptamers do not obey the intuitive assumptions that aptamer-target interactions stabilize a folded conformation. 3. TFA may be most appropriate for aptamers with significant double-stranded structure. 4. Kinetic effects may be significant and the order of operations in preparing samples should be carefully optimized.
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Amano R, Furukawa T, Sakamoto T. ITC Measurement for High-Affinity Aptamers Binding to Their Target Proteins. Methods Mol Biol 2019; 1964:119-128. [PMID: 30929239 DOI: 10.1007/978-1-4939-9179-2_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Aptamers are nucleic acid molecules that bind to a target molecule with high affinity and specificity, which are generated by a process known as systematic evolution of ligands by exponential enrichment (SELEX). Because of their high affinity and specificity, aptamers were developed as therapeutic agents. Although aptamers are investigated as promising therapeutic agents, the mechanism of their high affinity and specificity is not clear. Therefore, structural and biophysical studies are important to know that. To date, ITC is increasingly being used to study the thermodynamic basis of aptamer-target protein interactions. Understanding the mechanism of aptamer binding would contribute to their development for therapeutic applications. In this chapter, we describe the protocol to study the thermodynamics of aptamer-protein interactions.
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Affiliation(s)
- Ryo Amano
- Faculty of Advanced Engineering, Department of Life Science, Chiba Institute of Technology, Narashino-shi, Chiba, Japan
| | - Tomohisa Furukawa
- Faculty of Advanced Engineering, Department of Life Science, Chiba Institute of Technology, Narashino-shi, Chiba, Japan
| | - Taiichi Sakamoto
- Faculty of Advanced Engineering, Department of Life Science, Chiba Institute of Technology, Narashino-shi, Chiba, Japan.
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34
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Lee J, Lee J, Ree BJ, Lee YM, Park H, Lee TG, Kim JH, Kim WJ. Self-Assembled Aptamer Nanoconstruct: A Highly Effective Molecule-Capturing Platform Having Therapeutic Applications. ADVANCED THERAPEUTICS 2018. [DOI: 10.1002/adtp.201800111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Jihyun Lee
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
| | - Junseok Lee
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
| | - Brian J. Ree
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
| | - Yeong Mi Lee
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
| | - Hyeongmok Park
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
| | - Tae Geol Lee
- Center for Nano-Bio Measurement; Korea Research Institute of Standards and Science; Daejeon 34113 Republic of Korea
| | - Jeong Hun Kim
- Department of Ophthalmology; Seoul National University Hospital; 101 Daehak-Ro, Jongno-Gu Seoul 03080 Republic of Korea
| | - Won Jong Kim
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
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35
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Dong L, Zhou H, Zhao M, Gao X, Liu Y, Liu D, Guo W, Hu H, Xie Q, Fan J, Lin J, Wu W. Phosphorothioate-Modified AP613-1 Specifically Targets GPC3 when Used for Hepatocellular Carcinoma Cell Imaging. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 13:376-386. [PMID: 30347351 PMCID: PMC6198100 DOI: 10.1016/j.omtn.2018.09.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 01/05/2023]
Abstract
Glypican-3 (GPC3), the cellular membrane proteoglycan, has been established as a tumor biomarker for early diagnosis of hepatocellular carcinoma (HCC). GPC3 is highly expressed in more than 70% HCC tissues detected by antibody-based histopathological systems. Recently, aptamers, a short single-strand DNA or RNA generated from systematic evolution of ligands by exponential enrichment (SELEX), were reported as potential alternatives in tumor-targeted imaging and diagnosis. In this study, a total of 19 GPC3-bound aptamers were successfully screened by capillary electrophoresis (CE)-SELEX technology. After truncated, AP613-1 was confirmed to specifically target GPC3 with a dissociation constant (KD) of 59.85 nM. When modified with a phosphorothioate linkage, APS613-1 targeted GPC3 with a KD of 15.48 nM and could be used as a specific probe in living Huh7 and PLC/PRF/5 imaging, GPC3-positive cell lines, but not in L02 or A549, two GPC3-negative cell lines. More importantly, Alexa Fluor 750-conjugated APS613-1 could be used as a fluorescent probe to subcutaneous HCC imaging in xenograft nude mice. Our results indicated that modified AP613-1, especially APS613-1, was a potential agent in GPC3-positive tumor imaging for HCC early diagnosis.
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Affiliation(s)
- Lili Dong
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Hongxin Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Menglong Zhao
- Department of Radiology and Shanghai Institute of Medical Imaging, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xinghui Gao
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yang Liu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Dongli Liu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China; Department of Radiation Oncology, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai 200080, China
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Hongwei Hu
- Shanghai Aijin Biochemical Science & Technology Co. Ltd., Shanghai 200336, China
| | - Qian Xie
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China; Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jiang Lin
- Department of Radiology and Shanghai Institute of Medical Imaging, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Institute of Functional and Molecular Medical Imaging, Fudan University, Shanghai 200040, China.
| | - Weizhong Wu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China.
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36
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Lyu Y, Teng IT, Zhang L, Guo Y, Cai R, Zhang X, Qiu L, Tan W. Comprehensive Regression Model for Dissociation Equilibria of Cell-Specific Aptamers. Anal Chem 2018; 90:10487-10493. [PMID: 30039967 PMCID: PMC6522138 DOI: 10.1021/acs.analchem.8b02484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A comprehensive nonlinear regression model for dissociation equilibria of cell-specific aptamers is proposed by considering the effect of receptor expression level. Benefiting from the global regression of simultaneous equations, the fitted parameters reach a very significant level, indicating the statistical validity of this updated model. According to the fitting results, we found that dissociation constants fitted using the previous model are obviously larger than the updated values, which can be explained by the effect of receptor number on curve fitting. In addition, equivalent receptor density can be estimated using the updated model, which may lead to some new judgments about reported results of cell-SELEX.
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Affiliation(s)
- Yifan Lyu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - I-Ting Teng
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Liqin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Yian Guo
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Ren Cai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
| | - Weihong Tan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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Abstract
The conjugation of biomolecules can impart materials with the bioactivity necessary to modulate specific cell behaviors. While the biological roles of particular polypeptide, oligonucleotide, and glycan structures have been extensively reviewed, along with the influence of attachment on material structure and function, the key role played by the conjugation strategy in determining activity is often overlooked. In this review, we focus on the chemistry of biomolecule conjugation and provide a comprehensive overview of the key strategies for achieving controlled biomaterial functionalization. No universal method exists to provide optimal attachment, and here we will discuss both the relative advantages and disadvantages of each technique. In doing so, we highlight the importance of carefully considering the impact and suitability of a particular technique during biomaterial design.
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Affiliation(s)
- Christopher D. Spicer
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, Stockholm, Sweden
| | - E. Thomas Pashuck
- NJ
Centre for Biomaterials, Rutgers University, 145 Bevier Road, Piscataway, New Jersey United States
| | - Molly M. Stevens
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, Stockholm, Sweden
- Department
of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, Exhibition Road, London, United Kingdom
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38
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Zhang Z, Liu C, Yang C, Wu Y, Yu F, Chen Y, Du J. Aptamer-Patterned Hydrogel Films for Spatiotemporally Programmable Capture and Release of Multiple Proteins. ACS APPLIED MATERIALS & INTERFACES 2018; 10:8546-8554. [PMID: 29465230 DOI: 10.1021/acsami.8b00191] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Various hydrogels have been used for protein delivery in the treatment of human diseases. Nevertheless, it is always difficult to control the capture and release of multiple proteins in different regions and periods. This research successfully proves that multiple proteins can be captured and released from the aptamer-patterned hydrogel films with an adjustable release rate at a prospective time and in specific regions utilizing the complementary DNA strand of aptamers via photoclick chemistry and DNA hybridization. The hydrogel film is successfully applied to complex matrixes such as human serum and has excellent cytocompatibility. Thus, the aptamer-patterned hydrogel film will be a good candidate for controlled delivery of multiple proteins.
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Affiliation(s)
- Zheng Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Materials and Chemical Engineering , Hainan University , Haikou 570228 , PR China
| | - Chen Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Materials and Chemical Engineering , Hainan University , Haikou 570228 , PR China
| | - Chunzheng Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Materials and Chemical Engineering , Hainan University , Haikou 570228 , PR China
| | - Yuyang Wu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Materials and Chemical Engineering , Hainan University , Haikou 570228 , PR China
| | - Feng Yu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Materials and Chemical Engineering , Hainan University , Haikou 570228 , PR China
| | - Yong Chen
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Materials and Chemical Engineering , Hainan University , Haikou 570228 , PR China
| | - Jie Du
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Materials and Chemical Engineering , Hainan University , Haikou 570228 , PR China
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39
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Sakamoto T, Ennifar E, Nakamura Y. Thermodynamic study of aptamers binding to their target proteins. Biochimie 2017; 145:91-97. [PMID: 29054802 DOI: 10.1016/j.biochi.2017.10.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/12/2017] [Indexed: 01/30/2023]
Abstract
Aptamers are nucleic acids that bind to a target molecule with high affinity and specificity, which are selected from systematic evolution of ligands by exponential enrichment (SELEX). Aptamers feature high affinity and specificity to their target molecule and a large structural diversity; biophysical tools, together with structural studies, are essential to reveal the mechanism of aptamers recognition. Furthermore, understanding the mechanism of action would also contribute to their development for therapeutic applications. Isothermal titration calorimetry (ITC) is a fast and robust method to study the physical basis of molecular interactions. In a single experiment, it provides all thermodynamic parameters of a molecular interaction, including dissociation constant, Kd; Gibbs free energy change, ΔG; enthalpy change, ΔH; entropy change, ΔS; and stoichiometry, N. The development of modern microcalorimeters significantly contributed to the expansion of the ITC use in biological systems. Therefore, ITC has been applied to the development of small therapeutic agents that bind to target proteins and is increasingly being used to study aptamer-target protein interactions. This review focuses on thermodynamic approaches for understanding the molecular principles of aptamer-target interactions.
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Affiliation(s)
- Taiichi Sakamoto
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan.
| | - Eric Ennifar
- Structure and Dynamics of Biomolecular Machines, Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire, 15 Rue René Descartes, F-67000 Strasbourg, France
| | - Yoshikazu Nakamura
- RIBOMIC Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan; The Institute of Medical Science, The University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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40
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Meirinho SG, Dias LG, Peres AM, Rodrigues LR. Electrochemical aptasensor for human osteopontin detection using a DNA aptamer selected by SELEX. Anal Chim Acta 2017; 987:25-37. [PMID: 28916037 DOI: 10.1016/j.aca.2017.07.071] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 05/30/2017] [Accepted: 07/27/2017] [Indexed: 02/07/2023]
Abstract
A DNA aptamer with affinity and specificity for human osteopontin (OPN), a potential breast cancer biomarker, was selected using the SELEX process, considering its homology rate and the stability of its secondary structures. This aptamer exhibited a satisfactory affinity towards OPN, showing dissociation constants lower than 2.5 nM. It was further used to develop a simple, label-free electrochemical aptasensor against OPN. The aptasensor showed good sensitivity towards OPN in standard solutions, being the square wave voltammetry (SWV), compared to the cyclic voltammetry, the most sensitive technique with detection and quantification limits of 1.4 ± 0.4 nM and 4.2 ± 1.1 nM, respectively. It showed good reproducibility and acceptable selectivity, exhibiting low signal interferences from other proteins, as thrombin, with 2.6-10 times lower current signals-off than for OPN. The aptasensor also successfully detected OPN in spiked synthetic human plasma. Using SWV, detection and quantification limits (1.3 ± 0.1 and 3.9 ± 0.4 nM) within the OPN plasma levels reported for patients with breast cancer (0.4-4.5 nM) or with metastatic or recurrent breast cancer (0.9-8.4 nM) were found. Moreover, preliminary assays, using a sample of human plasma, showed that the aptasensor and the standard ELISA method quantified similar OPN levels (2.2 ± 0.7 and 1.7 ± 0.1 nM, respectively). Thus, our aptasensor coupled with SWV represents a promising alternative for the detection of relevant breast cancer biomarkers.
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Affiliation(s)
- Sofia G Meirinho
- Laboratory of Separation and Reaction Engineering, Laboratory of Catalysis and Materials (LSRE-LCM), ESA, Instituto Politécnico de Bragança, Campus Santa Apolónia, 5300-253 Bragança, Portugal; CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Luís G Dias
- ESA - Instituto Politécnico de Bragança, Campus Santa Apolónia, 5300-253 Bragança, Portugal; CQ-VR - Centro de Química - Vila Real, University of Trás-os-Montes, Apartado 1013, 5001-801 Vila Real, Portugal
| | - António M Peres
- Laboratory of Separation and Reaction Engineering, Laboratory of Catalysis and Materials (LSRE-LCM), ESA, Instituto Politécnico de Bragança, Campus Santa Apolónia, 5300-253 Bragança, Portugal
| | - Lígia R Rodrigues
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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41
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Lee KH, Zeng H. A general double library SELEX strategy for aptamer selection using unmodified nonimmobilized targets. Anal Bioanal Chem 2017. [DOI: 10.1007/s00216-017-0454-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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42
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Sett A, Borthakur BB, Sharma JD, Kataki AC, Bora U. DNA aptamer probes for detection of estrogen receptor α positive carcinomas. Transl Res 2017; 183:104-120.e2. [PMID: 28087261 DOI: 10.1016/j.trsl.2016.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 12/07/2016] [Accepted: 12/17/2016] [Indexed: 01/05/2023]
Abstract
Estrogen receptor alpha (ERα) also known as NR3A1 (nuclear receptor subfamily 3, group A, member 1) is a ligand-activated transcription factor. It is an important biomarker for breast cancer metastasis. In the present study, we report a novel DNA aptamer candidate against estrogen receptor (ER) alpha structure. The enriched aptamer candidate was obtained after 14 iterative cycles of in vitro protein-SELEX process. Isothermal calorimetry study suggests the nanomolar sensitivity of the candidate ER_Apt1 to its target protein. Fluorescence- and chemiluminescence-binding assays confirm the specificity of the candidate aptamer to ER alpha positive breast cancer cell line. Comparative analysis of ER_Apt1 to ER alpha monoclonal antibody was also performed to analyze the expression of ER alpha in various malignant cancer cell line. Cytochemical and immunohistochemistry assay indicates its potential use as a diagnostic agent against ERα positive carcinomas. The nucleotide aptamer sequences described in the present study can be used for the detection, treatment, prophylaxis and diagnosis of ERα-related disorder.
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Affiliation(s)
- Arghya Sett
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Bibhuti Bhusan Borthakur
- Department of Surgical Oncology, Dr. Bhubaneswar Borooah Cancer Institute, Guwahati, Assam, India; Mugagen Laboratories Pvt. Ltd, Technology Incubation Centre, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Jagannath Dev Sharma
- Department of Surgical Oncology, Dr. Bhubaneswar Borooah Cancer Institute, Guwahati, Assam, India
| | - Amal Chandra Kataki
- Department of Surgical Oncology, Dr. Bhubaneswar Borooah Cancer Institute, Guwahati, Assam, India
| | - Utpal Bora
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India; Mugagen Laboratories Pvt. Ltd, Technology Incubation Centre, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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43
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Lee J, Lee BJ, Lee YM, Park H, Kim JH, Kim WJ. Self-Assembled Nanoconstructs Modified with Amplified Aptamers Inhibited Tumor Growth and Retinal Vascular Hyperpermeability via Vascular Endothelial Growth Factor Capturing. Mol Pharm 2017; 14:1460-1468. [PMID: 28191845 DOI: 10.1021/acs.molpharmaceut.6b00949] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Here, nanoconstructs consisting of a DNA-amplified aptamer with a biocompatible polymer backbone for capturing target biomolecules are presented. First, the polymer-DNA nanoconstructs were prepared by hybridization of two complementary single-stranded DNAs that were each conjugated to a dextran polymer backbone. The designed polymer-DNA amplified aptamer nanoconstructs (PA-aNCs) were then prepared by utilizing polymer-DNA nanoconstructs conjugated with an aptamer (PA-NCs) using a rolling circle amplification reaction to amplify the aptamer. These PA-aNCs were successfully applied to alleviate tumor growth and vascular endothelial growth factor (VEGF)-induced retinal vascular hyperpermeability in vivo through the highly effective capture of human VEGF as a target molecule. These PA-aNCs could be used as therapeutic agent for anti-VEGF therapy by efficiently capturing human VEGF.
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Affiliation(s)
- Jihyun Lee
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS) , Pohang 37673, Republic of Korea.,Department of Chemistry, Pohang University of Science and Technology (POSTECH) , Pohang 37673, Republic of Korea
| | - Byung Joo Lee
- Fight Against Angiogenesis-Related Blindness Laboratory, Clinical Research Institute, Seoul National University Hospital , Seoul 03080, Republic of Korea.,Department of Biomedical Sciences, College of Medicine, Seoul National University , Seoul 03080, Republic of Korea
| | - Yeong Mi Lee
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS) , Pohang 37673, Republic of Korea.,Department of Chemistry, Pohang University of Science and Technology (POSTECH) , Pohang 37673, Republic of Korea
| | - Hansoo Park
- School of Integrative Engineering, Chung-Ang University , Seoul 156-751, Republic of Korea
| | - Jeong Hun Kim
- Fight Against Angiogenesis-Related Blindness Laboratory, Clinical Research Institute, Seoul National University Hospital , Seoul 03080, Republic of Korea.,Department of Biomedical Sciences, College of Medicine, Seoul National University , Seoul 03080, Republic of Korea.,Department of Ophthalmology, College of Medicine, Seoul National University , Seoul 03080, Republic of Korea
| | - Won Jong Kim
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS) , Pohang 37673, Republic of Korea.,Department of Chemistry, Pohang University of Science and Technology (POSTECH) , Pohang 37673, Republic of Korea
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Amano R, Takada K, Tanaka Y, Nakamura Y, Kawai G, Kozu T, Sakamoto T. Kinetic and Thermodynamic Analyses of Interaction between a High-Affinity RNA Aptamer and Its Target Protein. Biochemistry 2016; 55:6221-6229. [PMID: 27766833 DOI: 10.1021/acs.biochem.6b00748] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AML1 (RUNX1) protein is an essential transcription factor involved in the development of hematopoietic cells. Several genetic aberrations that disrupt the function of AML1 have been frequently observed in human leukemia. AML1 contains a DNA-binding domain known as the Runt domain (RD), which recognizes the RD-binding double-stranded DNA element of target genes. In this study, we identified high-affinity RNA aptamers that bind to RD by systematic evolution of ligands by exponential enrichment. The binding assay using surface plasmon resonance indicated that a shortened aptamer retained the ability to bind to RD when 1 M potassium acetate was used. A thermodynamic study using isothermal titration calorimetry (ITC) showed that the aptamer-RD interaction is driven by a large enthalpy change, and its unfavorable entropy change is compensated by a favorable enthalpy change. Furthermore, the binding heat capacity change was identified from the ITC data at various temperatures. The aptamer binding showed a large negative heat capacity change, which suggests that a large apolar surface is buried upon such binding. Thus, we proposed that the aptamer binds to RD with long-range electrostatic force in the early stage of the association and then changes its conformation and recognizes a large surface area of RD. These findings about the biophysics of aptamer binding should be useful for understanding the mechanism of RNA-protein interaction and optimizing and modifying RNA aptamers.
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Affiliation(s)
- Ryo Amano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Kenta Takada
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Yoichiro Tanaka
- Facility for RI Research and Education, Instrumental Analysis Center, Yokohama National University , 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Yoshikazu Nakamura
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo , Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Ribomic Inc. , 3-16-13 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology , Saitama Cancer Center, Ina, Saitama 362-0806, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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45
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Bayraç C, Öktem HA. Evaluation of Staphylococcus aureus DNA aptamer by enzyme-linked aptamer assay and isothermal titration calorimetry. J Mol Recognit 2016; 30. [PMID: 27696554 DOI: 10.1002/jmr.2583] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/06/2016] [Accepted: 09/02/2016] [Indexed: 01/08/2023]
Abstract
To monitor the specificity of Staphylococcus aureus aptamer (SA-31) against its target cell, we used enzyme-linked aptamer assay. In the presence of target cell, horseradish peroxidase-conjugated streptavidin bound to biotin-labeled SA-31 showed specific binding to S aureus among 3 different bacteria with limit of detection of 103 colony-forming unit per milliliter. The apparent Ka was 1.39 μM-1 ± 0.3 μM-1 . The binding of SA-31 to membrane proteins extracted from cell surface was characterized using isothermal titration calorimetry, and the effect of changes in binding temperature and salt concentrations of binding buffer was evaluated based on thermodynamic parameters (Ka , ΔH, and ΔG). Since binding of aptamer to its targets solely depends on its 3-dimensional structure under experimental conditions used in selection process, the change in temperature and ion concentration changed the affinity of SA-31 to its target on surface of bacteria. At 4°C, SA-31 did not show an affinity to its target with poor heat change upon injection of membrane fraction to aptamer solution. However, the apparent association constants of SA-31 slightly varied from Ka = 1.56 μM-1 ± 0.69 μM-1 at 25°C to Ka = 1.03 μM-1 ± 0.9 μM-1 at 37°C. At spontaneously occurring exothermic binding reactions, affinities of S aureus aptamer to its target were also 9.44 μM-1 ± 0.38 μM-1 at 50mM, 1.60 μM-1 ± 0.11 μM-1 at 137mM, and 3.28 μM-1 ± 0.46 μM-1 at 200 mM of salt concentration. In this study, it was demonstrated that enzyme-linked aptamer assay and isothermal titration calorimetry were useful tools for studying the fundamental binding mechanism between a DNA aptamer and its target on the outer surface of S aureus.
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Affiliation(s)
- Ceren Bayraç
- Bioengineering Department, Karamanoğlu Mehmetbey University, Yunus Emre Campus, Karaman, Turkey.,Nanobiotechnology Research and Development Group, Department of Biotechnology, Middle East Technical University, Ankara, Turkey
| | - Hüseyin Avni Öktem
- Konya Food & Agriculture University, Dedekorkut Mah. Beyşehir Cad. No. 9, Konya, Turkey.,Nanobiotechnology Research and Development Group, Department of Biotechnology, Middle East Technical University, Ankara, Turkey
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46
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Feng L, Lyu Z, Offenhäusser A, Mayer D. Electrochemically triggered aptamer immobilization via click reaction for vascular endothelial growth factor detection. Eng Life Sci 2016. [DOI: 10.1002/elsc.201600068] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Lingyan Feng
- Peter Grünberg Institute, PGI-8, Bioelectronics, Research Center Jülich; JARA-Fundamentals of Future Information Technology; Jülich Germany
- Materials Genome Institute; Shanghai University; Shanghai China
| | - Zhaozi Lyu
- Peter Grünberg Institute, PGI-8, Bioelectronics, Research Center Jülich; JARA-Fundamentals of Future Information Technology; Jülich Germany
| | - Andreas Offenhäusser
- Peter Grünberg Institute, PGI-8, Bioelectronics, Research Center Jülich; JARA-Fundamentals of Future Information Technology; Jülich Germany
| | - Dirk Mayer
- Peter Grünberg Institute, PGI-8, Bioelectronics, Research Center Jülich; JARA-Fundamentals of Future Information Technology; Jülich Germany
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47
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Chattaraj R, Mohan P, Livingston CM, Besmer JD, Kumar K, Goodwin AP. Mutually-Reactive, Fluorogenic Hydrocyanine/Quinone Reporter Pairs for In-Solution Biosensing via Nanodroplet Association. ACS APPLIED MATERIALS & INTERFACES 2016; 8:802-8. [PMID: 26710239 PMCID: PMC5051691 DOI: 10.1021/acsami.5b10036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Mutually reactive, fluorogenic molecules are presented as a simple and novel technique for in-solution biosensing. The hypothesis behind this work was that aggregating droplets into close proximity would cause rapid mixing of their contents. To take advantage of this effect, a novel pair of fluorogenic redox molecules were designed to remain in lipid-stabilized oil droplets but mix once aggregated. First, the hydrophobic cyanine dye 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate (DiI) was reduced with sodium borohydride to form a nonfluorescent analog (HDiI). Hydrophobic quinone derivatives were then screened as oxidizing agents, and it was found that p-fluoranil oxidized nonfluorescent HDiI back to fluorescent DiI. Next, HDiI and p-fluoranil were loaded into NEOBEE oil nanodroplets of average diameter 600 nm that were stabilized by a monolayer of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-distearoyl-sn-glycero-3-phosphoethanolamine (DSPE)-polyethylene glycol (PEG), and DSPE-PEG-biotin. Addition of streptavidin caused aggregation of droplets and the appearance of red fluorescent aggregates within 30 min. Next, Nanoparticle Tracking Analysis was used to record the fluorescence of the droplets and their aggregates. By integrating the fluorescence emission of the tracked droplets, streptavidin could be detected down to 100 fM. Finally, the droplets were reformulated to sense for vascular endothelial growth factor (VEGF), a biomarker for tumor metastasis. Using anti-VEGF aptamers attached to DSPE-PEG incorporated into the nanodroplet monolayer, VEGF could also be detected down to 100 fM.
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Affiliation(s)
- Rajarshi Chattaraj
- Department of Mechanical Engineering, University of Colorado Boulder. Boulder, CO 80309
| | - Praveena Mohan
- Department of Chemical and Biological Engineering. University of Colorado Boulder. Boulder, CO 80303
| | - Clare M. Livingston
- Department of Chemical and Biological Engineering. University of Colorado Boulder. Boulder, CO 80303
| | - Jeremy D. Besmer
- Department of Chemical and Biological Engineering. University of Colorado Boulder. Boulder, CO 80303
| | - Kaushlendra Kumar
- Department of Chemical and Biological Engineering. University of Colorado Boulder. Boulder, CO 80303
| | - Andrew P. Goodwin
- Department of Chemical and Biological Engineering. University of Colorado Boulder. Boulder, CO 80303
- Corresponding Author: To whom correspondence should be addressed:
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48
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Dong L, Tan Q, Ye W, Liu D, Chen H, Hu H, Wen D, Liu Y, Cao Y, Kang J, Fan J, Guo W, Wu W. Screening and Identifying a Novel ssDNA Aptamer against Alpha-fetoprotein Using CE-SELEX. Sci Rep 2015; 5:15552. [PMID: 26497223 PMCID: PMC4620443 DOI: 10.1038/srep15552] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 09/28/2015] [Indexed: 01/01/2023] Open
Abstract
Alpha-fetoprotein (AFP) is a liver cancer associated protein and has long been utilized as a serum tumor biomarker of disease progression. AFP is usually detected in HCC patients by an antibody based system. Recently, however, aptamers generated from systematic evolution of ligands by exponential enrichment (SELEX) were reported to have an alternative potential in targeted imaging, diagnosis and therapy. In this study, AFP-bound ssDNA aptamers were screened and identified using capillary electrophoresis (CE) SELEX technology. After cloning, sequencing and motif analysis, we successfully confirmed an aptamer, named AP273, specifically targeting AFP. The aptamer could be used as a probe in AFP immunofluorescence imaging in HepG2, one AFP positive cancer cell line, but not in A549, an AFP negative cancer cell line. More interesting, the aptamer efficiently inhibited the migration and invasion of HCC cells after in vivo transfection. Motif analysis revealed that AP273 had several stable secondary motifs in its structure. Our results indicate that CE-SELEX technology is an efficient method to screen specific protein-bound ssDNA, and AP273 could be used as an agent in AFP-based staining, diagnosis and therapy, although more works are still needed.
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Affiliation(s)
- Lili Dong
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Qiwen Tan
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Wei Ye
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongli Liu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Haifeng Chen
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hongwei Hu
- Shanghai Aijin Biochemical Science &Technology Co. Ltd., Shanghai 200336, China
| | - Duo Wen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Yang Liu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Ya Cao
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Key Laboratory of Chinese Ministry of Education, Changsha 410078, China
| | - Jingwu Kang
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Weizhong Wu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
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49
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Gaddes ER, Lee D, Gydush G, Wang Y, Dong C. Regulation of fibrin-mediated tumor cell adhesion to the endothelium using anti-thrombin aptamer. Exp Cell Res 2015; 339:417-26. [PMID: 26481421 DOI: 10.1016/j.yexcr.2015.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 09/29/2015] [Accepted: 10/09/2015] [Indexed: 12/27/2022]
Abstract
Molecular intervention during transient stages of various metastatic pathways may lead to development of promising therapeutic technologies. One of such involves soluble fibrin (sFn) that has been implicated as a cross-linker between circulating blood or tumor cells and endothelial cell receptors, promoting cell arrest on the endothelium during circulation. sFn generation is a result of thrombin-mediated fibrinogen (Fg) cleavage due to either vascular injuries or a tumor microenvironment. For cancer therapy, thrombin-mediated conversions of Fg to sFn thus serve as potential intervention points to decrease circulating tumor cell adhesion to the endothelium and subsequent metastatic events. The purpose of this work was to investigate the function of an anti-thrombin oligonucleotide aptamer in reducing tumor cell arrest. Both molecular and cellular interactions were examined to demonstrate the binding and inhibitory effects of anti-thrombin aptamer. The results show that the aptamer is capable of inhibiting thrombin-mediated Fg conversion, thereby reducing sFn-mediated tumor cell adhesion in a concentration-dependent manner. Notably, the aptamer is able to bind thrombin under dynamic flow conditions and reduce tumor cell adhesive events at various physiological shear rates. This study further indicates that oligonucleotide aptamers hold great promise as therapeutic regulators of tumor cell adhesion, and consequently, metastatic activity.
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Affiliation(s)
- Erin R Gaddes
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Deborah Lee
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Gregory Gydush
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Cheng Dong
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
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50
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Kang WJ, Lee J, Lee YS, Cho S, Ali BA, Al-Khedhairy AA, Heo H, Kim S. Multimodal imaging probe for targeting cancer cells using uMUC-1 aptamer. Colloids Surf B Biointerfaces 2015; 136:134-40. [PMID: 26387066 DOI: 10.1016/j.colsurfb.2015.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 07/16/2015] [Accepted: 09/01/2015] [Indexed: 01/10/2023]
Abstract
For adequate cancer therapy, newer imaging modalities with more specific ligands for unique targets are crucial. Underglycosylated mucin-1 (uMUC-1) antigen is an early marker of tumor development and is widely overexpressed on most tumors. A combination of nanotechnology with optical, radionuclide, and magnetic resonance (MR) imaging has great potential to improve cancer diagnosis and therapy. In this study, a multimodal nanoparticle imaging system was developed that can be used for optical, MR and positron emission tomography (PET) imaging. Cobalt ferrite magnetic nanoparticles surrounded by fluorescent rhodamine (designated MF) within a silica shell matrix were conjugated with an aptamer targeting uMUC-1 (designated MF-uMUC-1) and further labeled by (68)Ga (designated MFR-uMUC-1) with the help of a p-SCN-bn-NOTA chelating agent, resulting in single multimodal nanoparticles. The resultant nanoparticles are spherical and monodispersed, as revealed by transmission electron microscopy. The MFR-uMUC-1 nanoparticle showed specific and dose-dependent fluorescent, radioisotope and MR signals targeting BT-20 cells expressing uMUC-1. In vivo targeting and multimodal imaging in tumor-bearing nude mice also showed great specificity for targeting cancers with MFR-uMUC-1. The MFR-uMUC-1 probe could be used as a single multimodal probe to visualize cancer cells by means of optical, radionuclide and MR imaging.
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Affiliation(s)
- Won Jun Kang
- Division of Nuclear Medicine, Department of Radiology, Yonsei University College of Medicine, Republic of Korea
| | - Jonghwan Lee
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do 270-701, Republic of Korea; Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City 404-834, Republic of Korea
| | - Yong Seung Lee
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do 270-701, Republic of Korea; Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City 404-834, Republic of Korea
| | - Sujeong Cho
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do 270-701, Republic of Korea; Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City 404-834, Republic of Korea
| | - Bahy A Ali
- Al-Jeraisy DNA Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; Department of Nucleic Acids Research, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technological Applications, Alexandria, Egypt
| | | | - Hyejung Heo
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do 270-701, Republic of Korea; Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City 404-834, Republic of Korea
| | - Soonhag Kim
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do 270-701, Republic of Korea; Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City 404-834, Republic of Korea.
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