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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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Aptamer-based enzyme-linked oligonucleotide assay for specific detection of clinical bacterial strains isolated from cerebrospinal fluid samples. J Biosci Bioeng 2022; 134:441-449. [PMID: 36109302 DOI: 10.1016/j.jbiosc.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/07/2022] [Accepted: 07/13/2022] [Indexed: 11/23/2022]
Abstract
Meningitis, acute infection of the meninges, is the 10th leading cause of mortality among infectious diseases. Although many different causes for meningitis (viruses and bacteria) have been diagnosed, the most common ones are Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae. The effort to find a new method for detection of bacterial meningitis is an urgent need for clinical treatment. DNA aptamers generated by cell-systematic evolution of ligands by exponential enrichment (SELEX) against bacterial cells provide a novel cell labeling and biosensing technique. Here, we isolated single-stranded DNA aptamers during the SELEX method with a high affinity for different bacterial genera. This approach was demonstrated on H. influenzae type B, N. meningitidis serogroups A, B, C, and Y, and Streptococcus pneumoniae serotypes 18, 14, 19A, 6A, and 6B which served as targets in 20 rounds of cell-SELEX. After 20 rounds of SELEX, a total of 93 aptamers were identified. Among these, aptamers C65 and C50 showed the highest affinity toward targets with a dissociation constant of 6.98 and 15.79, respectively. Selected aptamers were able to successfully detect clinical bacterial strains isolated from cerebrospinal fluid samples of meningitis patients by double-aptamer sandwich enzyme-linked oligonucleotide assay (ELONA). Our findings demonstrated that aptamers with broad affinity to bacterial taxa in different genera can be isolated for the development of diagnostic tools for multiple targets. We further showed that sandwich ELONA based on single-stranded DNA aptamer is sensitive and specific enough for detection of the superior cause of bacterial meningitis.
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Song MY, Nguyen D, Hong SW, Kim BC. Broadly reactive aptamers targeting bacteria belonging to different genera using a sequential toggle cell-SELEX. Sci Rep 2017; 7:43641. [PMID: 28272554 PMCID: PMC5341558 DOI: 10.1038/srep43641] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/25/2017] [Indexed: 12/23/2022] Open
Abstract
Conventional cell-SELEX aims to isolate aptamers to a single unique target bacteria species. We propose a method to isolate single-stranded DNA aptamers that have broad reactivity to multiple bacterial targets belonging to different genera. The key of the proposed method is that targets of interest are changed sequentially at each SELEX round. The general scheme was examined using six bacteria from different genera, Escherichia coli, Enterobacter aerogenes, Klebsiella pneumoniae, Citrobacter freundii, Bacillus subtilis, and Staphylococcus epidermidis (four gram-negative and two gram-positive bacteria). In the first round of SELEX, the DNA library was incubated with E. coli and amplicons bound to E. coli were separated. The amplicons were sequentially separated by incubation with E. aerogenes, K. pneumoniae, C. freundii, B. subtilis, and S. epidermidis at each SELEX. The amplicons obtained using the last bacterial species were incubated again with the first bacterial species and this loop was repeated two more times. We refer to this method as sequential toggle cell-SELEX (STC-SELEX). The isolated aptamers had dissociation constants of 9.22–38.5 nM and had no affinity to other bacteria that were not included in STC-SELEX. These results demonstrate the potential to isolate aptamers with broad affinity to bacterial taxa in different genera.
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Affiliation(s)
- Min Young Song
- Center for Environment, Health and Welfare Research, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Dung Nguyen
- Department of Energy and Environmental Engineering, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Seok Won Hong
- Department of Energy and Environmental Engineering, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.,Center for Water Resources Cycle Research, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Byoung Chan Kim
- Center for Environment, Health and Welfare Research, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Department of Energy and Environmental Engineering, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
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Harris RC, Boschitsch AH, Fenley MO. Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation. J Chem Phys 2014; 140:075102. [PMID: 24559370 DOI: 10.1063/1.4864460] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Experimental results have demonstrated that the numbers of counterions surrounding nucleic acids differ from those predicted by the nonlinear Poisson-Boltzmann equation, NLPBE. Some studies have fit these data against the ion size in the size-modified Poisson-Boltzmann equation, SMPBE, but the present study demonstrates that other parameters, such as the Stern layer thickness and the molecular surface definition, can change the number of bound ions by amounts comparable to varying the ion size. These parameters will therefore have to be fit simultaneously against experimental data. In addition, the data presented here demonstrate that the derivative, SK, of the electrostatic binding free energy, ΔGel, with respect to the logarithm of the salt concentration is sensitive to these parameters, and experimental measurements of SK could be used to parameterize the model. However, although better values for the Stern layer thickness and ion size and better molecular surface definitions could improve the model's predictions of the numbers of ions around biomolecules and SK, ΔGel itself is more sensitive to parameters, such as the interior dielectric constant, which in turn do not significantly affect the distributions of ions around biomolecules. Therefore, improved estimates of the ion size and Stern layer thickness to use in the SMPBE will not necessarily improve the model's predictions of ΔGel.
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Affiliation(s)
- Robert C Harris
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306-3408, USA
| | | | - Marcia O Fenley
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306-3408, USA
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Abstract
Aptamers are single-stranded structured oligonucleotides (DNA or RNA) that can bind to a wide range of targets ("apatopes") with high affinity and specificity. These nucleic acid ligands, generated from pools of random-sequence by an in vitro selection process referred to as systematic evolution of ligands by exponential enrichment (SELEX), have now been identified as excellent tools for chemical biology, therapeutic delivery, diagnosis, research, and monitoring therapy in real-time imaging. Today, aptamers represent an interesting class of modern Pharmaceuticals which with their low immunogenic potential mimic extend many of the properties of monoclonal antibodies in diagnostics, research, and therapeutics. More recently, chimeric aptamer approach employing many different possible types of chimerization strategies has generated more stable and efficient chimeric aptamers with aptamer-aptamer, aptamer-nonaptamer biomacromolecules (siRNAs, proteins) and aptamer-nanoparticle chimeras. These chimeric aptamers when conjugated with various biomacromolecules like locked nucleic acid (LNA) to potentiate their stability, biodistribution, and targeting efficiency, have facilitated the accurate targeting in preclinical trials. We developed LNA-aptamer (anti-nucleolin and EpCAM) complexes which were loaded in iron-saturated bovine lactofeerin (Fe-blf)-coated dopamine modified surface of superparamagnetic iron oxide (Fe3O4) nanoparticles (SPIONs). This complex was used to deliver the specific aptamers in tumor cells in a co-culture model of normal and cancer cells. This review focuses on the chimeric aptamers, currently in development that are likely to find future practical applications in concert with other therapeutic molecules and modalities.
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Affiliation(s)
- Jagat R Kanwar
- Nanomedicine Laboratory of Immunology and Molecular Biomedical Research (LIMBR), Centre for Biotechnology and Interdisciplinary Biosciences (BioDeakin), Institute for Technology and Research Innovation (ITRI), Geelong Technology Precinct (GTP), Deakin University, Victoria, Australia.
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Stewart S, Syrett A, Pothukuchy A, Bhadra S, Ellington A, Anslyn E. Identifying protein variants with cross-reactive aptamer arrays. Chembiochem 2011; 12:2021-4. [PMID: 21796750 PMCID: PMC3454492 DOI: 10.1002/cbic.201100046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Indexed: 11/11/2022]
Affiliation(s)
- Sara Stewart
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, 78712, U.S.A, Fax: (+1) 512-471-7014
| | - Angel Syrett
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, 78712, U.S.A, Fax: (+1) 512-471-7014
| | - Arti Pothukuchy
- Accacia International, 2114 Wells Brach Pkwy Suite 6900, Austin, TX, 78728, Fax: (+1) 512-252-1056
| | - Sancheeta Bhadra
- Accacia International, 2114 Wells Brach Pkwy Suite 6900, Austin, TX, 78728, Fax: (+1) 512-252-1056
| | - Andrew Ellington
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, 78712, U.S.A, Fax: (+1) 512-471-7014
| | - Eric Anslyn
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, 78712, U.S.A, Fax: (+1) 512-471-7014
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Harris RC, Bredenberg JH, Silalahi ARJ, Boschitsch AH, Fenley MO. Understanding the physical basis of the salt dependence of the electrostatic binding free energy of mutated charged ligand-nucleic acid complexes. Biophys Chem 2011; 156:79-87. [PMID: 21458909 DOI: 10.1016/j.bpc.2011.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 02/08/2011] [Accepted: 02/21/2011] [Indexed: 12/01/2022]
Abstract
The predictions of the derivative of the electrostatic binding free energy of a biomolecular complex, ΔG(el), with respect to the logarithm of the 1:1 salt concentration, d(ΔG(el))/d(ln[NaCl]), SK, by the Poisson-Boltzmann equation, PBE, are very similar to those of the simpler Debye-Hückel equation, DHE, because the terms in the PBE's predictions of SK that depend on the details of the dielectric interface are small compared to the contributions from long-range electrostatic interactions. These facts allow one to obtain predictions of SK using a simplified charge model along with the DHE that are highly correlated with both the PBE and experimental binding data. The DHE-based model developed here, which was derived from the generalized Born model, explains the lack of correlation between SK and ΔG(el) in the presence of a dielectric discontinuity, which conflicts with the popular use of this supposed correlation to parse experimental binding free energies into electrostatic and nonelectrostatic components. Moreover, the DHE model also provides a clear justification for the correlations between SK and various empirical quantities, like the number of ion pairs, the ligand charge on the interface, the Coulomb binding free energy, and the product of the charges on the complex's components, but these correlations are weak, questioning their usefulness.
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Affiliation(s)
- Robert C Harris
- Department of Physics, Institute of Molecular Biophysics, Florida State University, Tallahasse, 32306, USA.
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