1
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Lin Y, Chen CY, Ku YC, Wang LC, Hung CC, Lin ZQ, Chen BH, Hung JT, Sun YC, Hung KF. A modified SELEX approach to identify DNA aptamers with binding specificity to the major histocompatibility complex presenting ovalbumin model antigen. RSC Adv 2023; 13:32681-32693. [PMID: 37936644 PMCID: PMC10626974 DOI: 10.1039/d3ra04686a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023] Open
Abstract
Aptamers have sparked significant interest in cell recognition because of their superior binding specificity and biocompatibility. Cell recognition can be mediated by targeting the major histocompatibility complex (MHC) that presents short peptides derived from intracellular antigens. Although numerous antibodies have demonstrated a specific affinity for the peptide-MHC complex, the number of aptamers that exhibit comparable characteristics is limited. Aptamers are usually selected from large libraries via the Systemic Evolution of Ligands by Exponential Enrichment (SELEX), an iterative process of selection and PCR amplification to enrich a pool of aptamers with high affinity. However, the success rate of aptamer identification is low, possibly due to the presence of complementary sequences or sequences rich in guanine and cytosine that are less accessible for primers. Here, we modified SELEX by employing systemic consecutive selections with minimal PCR amplification. We also modified the analysis by selecting aptamers that were identified in multiple selection rounds rather than those that are highly enriched. Using this approach, we were able to identify two aptamers with binding specificity to cells expressing the ovalbumin alloantigen as a proof of concept. These two aptamers were also discovered among the top 150 abundant candidates, despite not being highly enriched, by performing conventional SELEX. Additionally, we found that highly enriched aptamers tend to contain fractions of the primer sequence and have minimal target affinity. Candidate aptamers are easily missed in the conventional SELEX process. Therefore, our modification for SELEX may facilitate the identification of aptamers for more application in diverse biomedical fields. Significance: we modify the conventional method to improve the efficiency in the identification of the aptamer, a single strand of nucleic acid with binding specificity to the target molecule, showing as a proof of concept that this approach is particularly useful to select aptamers that can selectively bind to cells presenting a particular peptide by the major histocompatibility complex (MHC) on the cell surface. Given that cancer cells may express mutant peptide-MHC complexes that are distinct from those expressed by normal cells, this study sheds light on the potential application of aptamers to cancer cell targeting.
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Affiliation(s)
- Yang Lin
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
| | - Cho-Yi Chen
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University Taipei Taiwan
| | - Yu-Chia Ku
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University Taipei Taiwan
| | - Li-Chin Wang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University Taipei Taiwan
| | - Chia-Chien Hung
- School of Computer Science, Georgia Institute of Technology Atlanta GA USA
| | - Zhi-Qian Lin
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
| | - Bing-Hong Chen
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
| | | | - Yi-Chen Sun
- School of Medicine, Tzu-Chi University Hualien Taiwan
- Department of Ophthalmology, Taipei Tzu Chi Hospital, The Buddhist Tzu Chi Medical Foundation New Taipei City Taiwan
| | - Kai-Feng Hung
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
- Department of Dentistry, School of Dentistry, National Yang Ming Chiao Tung University Taipei Taiwan
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2
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Narwade M, Shaikh A, Gajbhiye KR, Kesharwani P, Gajbhiye V. Advanced cancer targeting using aptamer functionalized nanocarriers for site-specific cargo delivery. Biomater Res 2023; 27:42. [PMID: 37149607 PMCID: PMC10164340 DOI: 10.1186/s40824-023-00365-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/20/2023] [Indexed: 05/08/2023] Open
Abstract
The non-specificity of standard anticancer therapies has profound detrimental consequences in clinical treatment. Therapeutic specificity can be precisely achieved using cutting-edge ligands. Small synthetic oligonucleotide-ligands chosen through Systematic evolution of ligands by exponential enrichment (SELEX) would be an unceasing innovation in using nucleic acids as aptamers, frequently referred to as "chemical antibodies." Aptamers act as externally controlled switching materials that can attach to various substrates, for example, membrane proteins or nucleic acid structures. Aptamers pose excellent specificity and affinity for target molecules and can be used as medicines to suppress tumor cell growth directly. The creation of aptamer-conjugated nanoconstructs has recently opened up innovative options in cancer therapy that are more effective and target tumor cells with minor toxicity to healthy tissues. This review focuses on a comprehensive description of the most capable classes of aptamer-tethered nanocarriers for precise recognition of cancer cells with significant development in proficiency, selectivity, and targetability for cancer therapy. Existing theranostic applications with the problems and future directions are also highlighted.
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Affiliation(s)
- Mahavir Narwade
- Department of Pharmaceutics, Poona College of Pharmacy, Bharati Vidyapeeth, Pune, India
| | - Aazam Shaikh
- Nanobioscience Group, Agharkar Research Institute, Pune, 411004, India
- Savitribai Phule Pune University, Ganeshkhind, Pune, 411 007, India
| | - Kavita R Gajbhiye
- Department of Pharmaceutics, Poona College of Pharmacy, Bharati Vidyapeeth, Pune, India
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India.
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Science, Chennai, India.
| | - Virendra Gajbhiye
- Nanobioscience Group, Agharkar Research Institute, Pune, 411004, India.
- Savitribai Phule Pune University, Ganeshkhind, Pune, 411 007, India.
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3
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Zhu Y, Hart GW. Dual-specificity RNA aptamers enable manipulation of target-specific O-GlcNAcylation and unveil functions of O-GlcNAc on β-catenin. Cell 2023; 186:428-445.e27. [PMID: 36626902 PMCID: PMC9868088 DOI: 10.1016/j.cell.2022.12.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 11/02/2022] [Accepted: 12/08/2022] [Indexed: 01/11/2023]
Abstract
O-GlcNAc is a dynamic post-translational modification (PTM) that regulates protein functions. In studying the regulatory roles of O-GlcNAc, a major roadblock is the inability to change O-GlcNAcylation on a single protein at a time. Herein, we developed a dual RNA-aptamer-based approach that simultaneously targeted O-GlcNAc transferase (OGT) and β-catenin, the key transcription factor of the Wnt signaling pathway, to selectively increase O-GlcNAcylation of the latter without affecting other OGT substrates. Using the OGT/β-catenin dual-specificity aptamers, we found that O-GlcNAcylation of β-catenin stabilizes the protein by inhibiting its interaction with β-TrCP. O-GlcNAc also increases β-catenin's interaction with EZH2, recruits EZH2 to promoters, and dramatically alters the transcriptome. Further, by coupling riboswitches or an inducible expression system to aptamers, we enabled inducible regulation of protein-specific O-GlcNAcylation. Together, our findings demonstrate the efficacy and versatility of dual-specificity aptamers for regulating O-GlcNAcylation on individual proteins.
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Affiliation(s)
- Yi Zhu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
| | - Gerald W Hart
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
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4
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Biomimetic functional material-based sensors for food safety analysis: a review. Food Chem 2022; 405:134974. [DOI: 10.1016/j.foodchem.2022.134974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/04/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022]
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5
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Kennedy A, Griffin G, Freemont PS, Polizzi KM, Moore SJ. A curcumin direct protein biosensor for cell‐free prototyping. ENGINEERING BIOLOGY 2022; 6:62-68. [PMID: 36969103 PMCID: PMC9996706 DOI: 10.1049/enb2.12024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
In synthetic biology, biosensors are routinely coupled with a gene expression system for detecting small molecules and physical signals. We reveal a fluorescent complex, based on the interaction of an Escherichia coli double bond reductase (EcCurA), as a detection unit with its substrate curcumin-we call this a direct protein (DiPro) biosensor. Using a cell-free synthetic biology approach, we use the EcCurA DiPro biosensor to fine tune 10 reaction parameters (cofactor, substrate, and enzyme levels) for cell-free curcumin biosynthesis, assisted through acoustic liquid handling robotics. Overall, we increase EcCurA-curcumin DiPro fluorescence within cell-free reactions by 78-fold. This finding adds to the growing family of protein-ligand complexes that are naturally fluorescent and potentially exploitable for a range of applications, including medical imaging to engineering high-value chemicals.
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Affiliation(s)
- Agata Kennedy
- School of Biosciences University of Kent Canterbury UK
| | - Guy Griffin
- School of Biosciences University of Kent Canterbury UK
| | - Paul S. Freemont
- Centre for Synthetic Biology and Innovation South Kensington Campus London UK
- Department of Medicine South Kensington Campus London UK
- Department of Infectious Disease Section of Structural and Synthetic Biology Imperial College London London UK
- Sir Alexander Fleming Building South Kensington Campus London UK
- UK Dementia Research Institute Care Research and Technology Centre Imperial College London Hammersmith Campus London UK
| | - Karen M. Polizzi
- Centre for Synthetic Biology and Innovation South Kensington Campus London UK
- Department of Life Sciences Imperial College London South Kensington Campus London UK
- Department of Chemical Engineering Imperial College London South Kensington Campus London UK
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6
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Tabb JS, Rapoport E, Han I, Lombardi J, Green O. An antigen-targeting assay for Lyme disease: Combining aptamers and SERS to detect the OspA protein. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2022; 41:102528. [PMID: 35104673 DOI: 10.1016/j.nano.2022.102528] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 12/25/2022]
Abstract
Lyme disease is the fastest growing vector-borne disease in the United States. However, current testing modalities are ill suited to detection of Lyme disease, leading to the diagnosis of many cases after treatment is effective. We present an improved, direct method Lyme disease diagnosis, where the Lyme specific biomarker Outer Surface Protein A (OspA) in clinical serum samples is identified using a diagnostic platform combining surface enhanced Raman scattering (SERS) and aptamers. Employing orthogonal projections to latent structures discriminant analysis, the system accurately identified 91% of serum samples from Lyme patients, and 96% of serum samples from symptomatic controls. In addition, the OspA limit-of-detection, determined to be 1 × 10-4 ng/mL, is greater than four orders of magnitude lower than that found in serum samples from early Lyme disease patients. The application of this platform to detect this difficult-to-diagnose disease suggests its potential for detecting other diseases that present similar difficulties.
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Affiliation(s)
| | | | - Il Han
- Ionica Sciences, Ithaca, NY, USA
| | - John Lombardi
- Department of Chemistry, The City College of New York, New York, NY, USA
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7
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Qian S, Chang D, He S, Li Y. Aptamers from random sequence space: Accomplishments, gaps and future considerations. Anal Chim Acta 2022; 1196:339511. [DOI: 10.1016/j.aca.2022.339511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 02/07/2023]
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8
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Serumula W, Fernandez G, Gonzalez VM, Parboosing R. Anti-HIV Aptamers: Challenges and Prospects. Curr HIV Res 2022; 20:7-19. [PMID: 34503417 DOI: 10.2174/1570162x19666210908114825] [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: 02/19/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
Human Immunodeficiency Virus (HIV) infection continues to be a significant health burden in many countries around the world. Current HIV treatment through a combination of different antiretroviral drugs (cART) effectively suppresses viral replication, but drug resistance and crossresistance are significant challenges. This has prompted the search for novel targets and agents, such as nucleic acid aptamers. Nucleic acid aptamers are oligonucleotides that attach to the target sites with high affinity and specificity. This review provides a target-by-target account of research into anti-HIV aptamers and summarises the challenges and prospects of this therapeutic strategy, specifically in the unique context of HIV infection.
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Affiliation(s)
- William Serumula
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, c/o Inkosi Albert Luthuli Central Hospital, 5th Floor Laboratory Building, 800 Bellair Road, Mayville, Durban 4091, South Africa
| | - Geronimo Fernandez
- Departamento de Bioquímica-Investigación, Aptus Biotech SL, Avda. Cardenal Herrera Oria, 298-28035 Madrid. Spain
| | - Victor M Gonzalez
- Departamento de Bioquímica-Investigación, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)-Hospital Ramón y Cajal, 28034 Madrid, Spain
| | - Raveen Parboosing
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, c/o Inkosi Albert Luthuli Central Hospital, 5th Floor Laboratory Building, 800 Bellair Road, Mayville, Durban 4091, South Africa
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9
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Ozturk M, Nilsen-Hamilton M, Ilgu M. Aptamer Applications in Neuroscience. Pharmaceuticals (Basel) 2021; 14:1260. [PMID: 34959661 PMCID: PMC8709198 DOI: 10.3390/ph14121260] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023] Open
Abstract
Being the predominant cause of disability, neurological diseases have received much attention from the global health community. Over a billion people suffer from one of the following neurological disorders: dementia, epilepsy, stroke, migraine, meningitis, Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, Huntington's disease, prion disease, or brain tumors. The diagnosis and treatment options are limited for many of these diseases. Aptamers, being small and non-immunogenic nucleic acid molecules that are easy to chemically modify, offer potential diagnostic and theragnostic applications to meet these needs. This review covers pioneering studies in applying aptamers, which shows promise for future diagnostics and treatments of neurological disorders that pose increasingly dire worldwide health challenges.
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Affiliation(s)
- Meric Ozturk
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | - Marit Nilsen-Hamilton
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Ames Laboratory, US DOE (United States Department of Energy), Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
| | - Muslum Ilgu
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
- Ames Laboratory, US DOE (United States Department of Energy), Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
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10
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Krissanaprasit A, Key CM, Pontula S, LaBean TH. Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers. Chem Rev 2021; 121:13797-13868. [PMID: 34157230 DOI: 10.1021/acs.chemrev.0c01332] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carson M Key
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Sahil Pontula
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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11
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Le ATH, Krylova SM, Beloborodov SS, Wang TY, Hili R, Johnson PE, Li F, Veedu RN, Belyanskaya S, Krylov SN. How to Develop and Prove High-Efficiency Selection of Ligands from Oligonucleotide Libraries: A Universal Framework for Aptamers and DNA-Encoded Small-Molecule Ligands. Anal Chem 2021; 93:5343-5354. [PMID: 33764056 DOI: 10.1021/acs.analchem.1c00601] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Screening molecular libraries for ligands capable of binding proteins is widely used for hit identification in the early drug discovery process. Oligonucleotide libraries provide a very high diversity of compounds, while the combination of the polymerase chain reaction and DNA sequencing allow the identification of ligands in low copy numbers selected from such libraries. Ligand selection from oligonucleotide libraries requires mixing the library with the target followed by the physical separation of the ligand-target complexes from the unbound library. Cumulatively, the low abundance of ligands in the library and the low efficiency of available separation methods necessitate multiple consecutive rounds of partitioning. Multiple rounds of inefficient partitioning make the selection process ineffective and prone to failures. There are continuing efforts to develop a separation method capable of reliably generating a pure pool of ligands in a single round of partitioning; however, none of the proposed methods for single-round selection have been universally adopted. Our analysis revealed that the developers' efforts are disconnected from each other and hindered by the lack of quantitative criteria of selection quality assessment. Here, we present a formalism that describes single-round selection mathematically and provides parameters for quantitative characterization of selection quality. We use this formalism to define a universal strategy for development and validation of single-round selection methods. Finally, we analyze the existing partitioning methods, the published single-round selection reports, and some pertinent practical considerations through the prism of this formalism. This formalism is not an experimental protocol but a framework for correct development of experimental protocols. While single-round selection is not a goal by itself and may not always suffice selection of good-quality ligands, our work will help developers of highly efficient selection approaches to consolidate their efforts under an umbrella of universal quantitative criteria of method development and assessment.
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Affiliation(s)
- An T H Le
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Stanislav S Beloborodov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Tong Y Wang
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Ryan Hili
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Philip E Johnson
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Feng Li
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University and Perron Institute for Neurological and Translational Science, Perth 6150, Australia
| | | | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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12
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Yang J, Tu R, Yuan H, Wang Q, Zhu L. Recent advances in droplet microfluidics for enzyme and cell factory engineering. Crit Rev Biotechnol 2021; 41:1023-1045. [PMID: 33730939 DOI: 10.1080/07388551.2021.1898326] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Enzymes and cell factories play essential roles in industrial biotechnology for the production of chemicals and fuels. The properties of natural enzymes and cells often cannot meet the requirements of different industrial processes in terms of cost-effectiveness and high durability. To rapidly improve their properties and performances, laboratory evolution equipped with high-throughput screening methods and facilities is commonly used to tailor the desired properties of enzymes and cell factories, addressing the challenges of achieving high titer and the yield of the target products at high/low temperatures or extreme pH, in unnatural environments or in the presence of unconventional media. Droplet microfluidic screening (DMFS) systems have demonstrated great potential for exploring vast genetic diversity in a high-throughput manner (>106/h) for laboratory evolution and have been increasingly used in recent years, contributing to the identification of extraordinary mutants. This review highlights the recent advances in concepts and methods of DMFS for library screening, including the key factors in droplet generation and manipulation, signal sources for sensitive detection and sorting, and a comprehensive summary of success stories of DMFS implementation for engineering enzymes and cell factories during the past decade.
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Affiliation(s)
- Jianhua Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ran Tu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Huiling Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Qinhong Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Leilei Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
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13
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Komarova N, Barkova D, Kuznetsov A. Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology. Int J Mol Sci 2020; 21:E8774. [PMID: 33233573 PMCID: PMC7699794 DOI: 10.3390/ijms21228774] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HTS) meets this demand of SELEX. Analysis of the data obtained from sequencing of the libraries produced during and after aptamer isolation provides an informative basis for precise aptamer identification and for examining the structure and function of nucleic acid ligands. This review discusses the technical aspects and the potential of the integration of HTS with SELEX.
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Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1–7 Shokin Square, Zelenograd, 124498 Moscow, Russia; (D.B.); (A.K.)
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14
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Hoang Trung Chau T, Hoang Anh Mai D, Ngoc Pham D, Thi Quynh Le H, Yeol Lee E. Developments of Riboswitches and Toehold Switches for Molecular Detection-Biosensing and Molecular Diagnostics. Int J Mol Sci 2020; 21:E3192. [PMID: 32366036 PMCID: PMC7247568 DOI: 10.3390/ijms21093192] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
Riboswitches and toehold switches are considered to have potential for implementation in various fields, i.e., biosensing, metabolic engineering, and molecular diagnostics. The specific binding, programmability, and manipulability of these RNA-based molecules enable their intensive deployments in molecular detection as biosensors for regulating gene expressions, tracking metabolites, or detecting RNA sequences of pathogenic microorganisms. In this review, we will focus on the development of riboswitches and toehold switches in biosensing and molecular diagnostics. This review introduces the operating principles and the notable design features of riboswitches as well as toehold switches. Moreover, we will describe the advances and future directions of riboswitches and toehold switches in biosensing and molecular diagnostics.
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Affiliation(s)
| | | | | | | | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Korea; (T.H.T.C.); (D.H.A.M.); (D.N.P.); (H.T.Q.L.)
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15
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Predicting Future Prospects of Aptamers in Field-Effect Transistor Biosensors. Molecules 2020; 25:molecules25030680. [PMID: 32033448 PMCID: PMC7036789 DOI: 10.3390/molecules25030680] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/26/2020] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
Aptamers, in sensing technology, are famous for their role as receptors in versatile applications due to their high specificity and selectivity to a wide range of targets including proteins, small molecules, oligonucleotides, metal ions, viruses, and cells. The outburst of field-effect transistors provides a label-free detection and ultra-sensitive technique with significantly improved results in terms of detection of substances. However, their combination in this field is challenged by several factors. Recent advances in the discovery of aptamers and studies of Field-Effect Transistor (FET) aptasensors overcome these limitations and potentially expand the dominance of aptamers in the biosensor market.
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Safarpour H, Dehghani S, Nosrati R, Zebardast N, Alibolandi M, Mokhtarzadeh A, Ramezani M. Optical and electrochemical-based nano-aptasensing approaches for the detection of circulating tumor cells (CTCs). Biosens Bioelectron 2019; 148:111833. [PMID: 31733465 DOI: 10.1016/j.bios.2019.111833] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023]
Abstract
More recently, detection of circulating tumor cells (CTCs) has been considered as an appealing prognostic and diagnostic approach for cancer patients. CTCs as a type of tumor-derived cells are secreted by the tumor and released into the blood circulation. Since the migration of CTCs is an early event in cancer progression, patients who still have tumor-free lymph nodes have to be well examined for the CTCs presence in their blood circulation. Nowadays, there is a broad range of detection methods available to identify CTCs. As artificial RNA oligonucleotides or single-stranded DNA with receptor and catalytic characteristics, aptamers have been standing out, owing to their target-induced conformational modifications, elevated stability, and target specificity to be implemented in biosensing techniques. To date, several sensitivity-enhancement methods alongside smart nanomaterials have been used for the creation of new aptasensors to address the limit of detection (LOD), and improve the sensitivity of numerous analyte identification methods. The present review article supports a focused overview of the recent studies in the identification and quantitative determination of CTCs by aptamer-based biosensors and nanobiosensors.
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Affiliation(s)
- Hossein Safarpour
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Sadegh Dehghani
- Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahim Nosrati
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nozhat Zebardast
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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Kaur SJ, Gilman V, Duong M, Asher DM, Gregori L. Rapid selection of single-stranded DNA aptamers binding Staphylococcus epidermidis in platelet concentrates. Biotechniques 2019; 65:331-338. [PMID: 30477331 DOI: 10.2144/btn-2018-0081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Staphylococcus epidermidis is the most common transfusion-associated pathogen contaminating platelet concentrates. Methods to reduce or eliminate contaminating bacteria from platelet units are critical for improving the safety of blood transfusions. We used rapid isolation of DNA aptamers (RIDA) to identify single-stranded (ss)DNA aptamers as ligands that specifically bind to S. epidermidis. Five target-specific ssDNA aptamers (76 mer) were obtained under stringent selection conditions. Aptamer SE43 demonstrated higher binding affinity compared with scrambled control. Furthermore, when binding assays were conducted in platelet concentrate, there was a twofold increase in binding affinity compared with the SE43 binding in buffer alone. Our data identified an aptamer that may be useful as a ligand to capture, detect or remove S. epidermidis contaminant from platelet concentrates.
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Affiliation(s)
- Simran J Kaur
- Division of Emerging & Transfusion-Transmitted Diseases, Laboratory of Bacterial & Transmissible Spongiform Encephalopathy Agents, Center for Biologics Evaluation & Research, Office of Blood Research & Review, US Food & Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.,Current Address: Department of Microbiology and Immunology, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201, USA
| | - Vladimir Gilman
- Engineering Center of Excellence, 267 Farley Road, Hollis, NH 03049, USA
| | - Minh Duong
- Engineering Center of Excellence, 267 Farley Road, Hollis, NH 03049, USA
| | - David M Asher
- Division of Emerging & Transfusion-Transmitted Diseases, Laboratory of Bacterial & Transmissible Spongiform Encephalopathy Agents, Center for Biologics Evaluation & Research, Office of Blood Research & Review, US Food & Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Luisa Gregori
- Division of Emerging & Transfusion-Transmitted Diseases, Laboratory of Bacterial & Transmissible Spongiform Encephalopathy Agents, Center for Biologics Evaluation & Research, Office of Blood Research & Review, US Food & Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
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Ali MH, Elsherbiny ME, Emara M. Updates on Aptamer Research. Int J Mol Sci 2019; 20:E2511. [PMID: 31117311 PMCID: PMC6566374 DOI: 10.3390/ijms20102511] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023] Open
Abstract
For many years, different probing techniques have mainly relied on antibodies for molecular recognition. However, with the discovery of aptamers, this has changed. The science community is currently considering using aptamers in molecular targeting studies because of the many potential advantages they have over traditional antibodies. Some of these possible advantages are their specificity, higher binding affinity, better target discrimination, minimized batch-to-batch variation, and reduced side effects. Overall, these characteristics of aptamers have attracted scholars to use them as molecular probes in place of antibodies, with some aptamer-based targeting products being now available in the market. The present review is aimed at discussing the potential of aptamers as probes in molecular biology and in super-resolution microscopy.
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Affiliation(s)
- Mohamed H Ali
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
- current address: Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
| | - Marwa E Elsherbiny
- Department of Pharmacology and Toxicology, Ahram Canadian University, 6th of October City, Giza 12566, Egypt.
| | - Marwan Emara
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
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Rossetti M, Del Grosso E, Ranallo S, Mariottini D, Idili A, Bertucci A, Porchetta A. Programmable RNA-based systems for sensing and diagnostic applications. Anal Bioanal Chem 2019; 411:4293-4302. [PMID: 30734852 DOI: 10.1007/s00216-019-01622-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/08/2019] [Accepted: 01/16/2019] [Indexed: 11/28/2022]
Abstract
The emerging field of RNA nanotechnology harnesses the versatility of RNA molecules to generate nature-inspired systems with programmable structure and functionality. Such methodology has therefore gained appeal in the fields of biosensing and diagnostics, where specific molecular recognition and advanced input/output processing are demanded. The use of RNA modules and components allows for achieving diversity in structure and function, for processing information with molecular precision, and for programming dynamic operations on the grounds of predictable non-covalent interactions. When RNA nanotechnology meets bioanalytical chemistry, sensing of target molecules can be performed by harnessing programmable interactions of RNA modules, advanced field-ready biosensors can be manufactured by interfacing RNA-based devices with supporting portable platforms, and RNA sensors can be engineered to be genetically encoded allowing for real-time imaging of biomolecules in living cells. In this article, we report recent advances in RNA-based sensing technologies and discuss current trends in RNA nanotechnology-enabled biomedical diagnostics. In particular, we describe programmable sensors that leverage modular designs comprising dynamic aptamer-based units, synthetic RNA nanodevices able to perform target-responsive regulation of gene expression, and paper-based sensors incorporating artificial RNA networks. Graphical Abstract ᅟ.
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Affiliation(s)
- Marianna Rossetti
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Erica Del Grosso
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Simona Ranallo
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Davide Mariottini
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Andrea Idili
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Alessandro Bertucci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy. .,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Alessandro Porchetta
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy.
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Wang T, Chen C, Larcher LM, Barrero RA, Veedu RN. Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development. Biotechnol Adv 2018; 37:28-50. [PMID: 30408510 DOI: 10.1016/j.biotechadv.2018.11.001] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/28/2018] [Accepted: 11/04/2018] [Indexed: 02/07/2023]
Abstract
Aptamers are short single-stranded nucleic acid sequences capable of binding to target molecules in a way similar to antibodies. Due to various advantages such as prolonged shelf life, low batch to batch variation, low/no immunogenicity, freedom to incorporate chemical modification for enhanced stability and targeting capacity, aptamers quickly found their potential in diverse applications ranging from therapy, drug delivery, diagnosis, and functional genomics to bio-sensing. Aptamers are generated by a process called SELEX. However, the current overall success rate of SELEX is far from being satisfactory, and still presents a major obstacle for aptamer-based research and application. The need for an efficient selection strategy consisting of defined procedures to deal with a wide variety of targets is significantly important. In this work, by analyzing key aspects of SELEX including initial library design, target preparation, PCR optimization, and single strand DNA separation, we provide a comprehensive analysis of individual steps to facilitate researchers intending to develop personalized protocols to address many of the obstacles in SELEX. In addition, this review provides suggestions and opinions for future aptamer development procedures to address the concerns on key SELEX steps, and post-SELEX modifications.
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Affiliation(s)
- Tao Wang
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia; Perron Institute for Neurological and Translational Science, Perth 6009, Australia; School of Nursing, Zhengzhou University & Nursing Department, The First Affiliated Hospital of Zheng Zhou University, Zhengzhou 450001, China
| | - Changying Chen
- School of Nursing, Zhengzhou University & Nursing Department, The First Affiliated Hospital of Zheng Zhou University, Zhengzhou 450001, China
| | - Leon M Larcher
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia
| | - Roberto A Barrero
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia
| | - Rakesh N Veedu
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia; Perron Institute for Neurological and Translational Science, Perth 6009, Australia.
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21
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Tapp MJN, Slocik JM, Dennis PB, Naik RR, Milam VT. Competition-Enhanced Ligand Selection to Identify DNA Aptamers. ACS COMBINATORIAL SCIENCE 2018; 20:585-593. [PMID: 30189130 DOI: 10.1021/acscombsci.8b00048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Competition-enhanced ligand screening (CompELS) was employed to rapidly screen through large DNA libraries to identify single-stranded, oligonucleotide-based ligands called aptamers that bind to a nonbiological target. This previously unreported aptamer screening approach involves the repeated introduction of unenriched random sequence populations during the biopanning process, but avoids iterative elution and polymerase chain reaction (PCR) amplification steps inherent to traditional SELEX (systematic evolution of ligands by exponential enrichment) screening. In this study, 25 aptamers were identified against a gold surface via CompELS and evaluated to identify patterns in primary structures and predicted secondary structures. Following a final one-round competition experiment with the 25 identified aptamers, one particular aptamer sequence (1N) emerged as the most competitive adsorbate species for the gold substrate. Binding analysis indicated at least an order of magnitude difference in the binding affinity of 1N ( Kd = 5.6 × 10-10 M) compared to five other high affinity aptamer candidates ( Kd = 10-8-10-9 M) from identical secondary structure families. Collectively, these studies introduce a rapid, reliable screening and ranking platform along with a classification scheme well-suited for identifying and characterizing aptamers for nonbiological as well as biological targets.
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Affiliation(s)
| | - Joseph M. Slocik
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Patrick B. Dennis
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Rajesh R. Naik
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
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Molefe PF, Masamba P, Oyinloye BE, Mbatha LS, Meyer M, Kappo AP. Molecular Application of Aptamers in the Diagnosis and Treatment of Cancer and Communicable Diseases. Pharmaceuticals (Basel) 2018; 11:ph11040093. [PMID: 30274155 PMCID: PMC6315466 DOI: 10.3390/ph11040093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/18/2022] Open
Abstract
Cancer and infectious diseases such as Ebola, HIV, tuberculosis, Zika, hepatitis, measles and human schistosomiasis are serious global health hazards. The increasing annual morbidities and mortalities of these diseases have been blamed on drug resistance and the inefficacy of available diagnostic tools, particularly those which are immunologically-based. Antibody-based tools rely solely on antibody production for diagnosis and for this reason they are the major cause of diagnostic delays. Unfortunately, the control of these diseases depends on early detection and administration of effective treatment therefore any diagnostic delay is a huge challenge to curbing these diseases. Hence, there is a need for alternative diagnostic tools, discovery and development of novel therapeutic agents. Studies have demonstrated that aptamers could potentially offer one of the best solutions to these problems. Aptamers are short sequences of either DNA or RNA molecules, which are identified in vitro through a SELEX process. They are sensitive and bind specifically to target molecules. Their promising features suggest they may serve as better diagnostic agents and can be used as drug carriers for therapeutic purposes. In this article, we review the applications of aptamers in the theranostics of cancer and some infectious diseases.
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Affiliation(s)
- Philisiwe Fortunate Molefe
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Priscilla Masamba
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Babatunji Emmanuel Oyinloye
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
- Department of Biochemistry, College of Sciences, Afe Babalola University, PMB 5454, Ado-Ekiti 360001, Nigeria.
| | - Londiwe Simphiwe Mbatha
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Mervin Meyer
- DST/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa.
| | - Abidemi Paul Kappo
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
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Kaur H. Recent developments in cell-SELEX technology for aptamer selection. Biochim Biophys Acta Gen Subj 2018; 1862:2323-2329. [PMID: 30059712 DOI: 10.1016/j.bbagen.2018.07.029] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/19/2018] [Accepted: 07/25/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND SELEX technique is employed to select aptamers against wide range of targets. The in vitro method of aptamer selection using live cells as the target is referred as cell-SELEX. SCOPE OF THE REVIEW The review provides a comprehensive description on the development of aptamers through various cell-SELEX methods and list of aptamers identified through this method. In addition, it pinpoints the advantages and limitations of the cell-SELEX process and its variants. MAJOR CONCLUSIONS The use of aptamers as therapeutic and diagnostic agents is rapidly evolving, selection techniques such as Cell-SELEX could be beneficial in identifying aptamers when the target is in its native conformation and without prior information of the cognate target, thereby bringing the aptamer development one step closer to the clinic. GENERAL SIGNIFICANCE The information in this review can serve as a database for the design and development of futuristic oligonucleotide based diagnostics and therapeutics work.
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Chen PC, Masiewicz P, Rybin V, Svergun D, Hennig J. A General Small-Angle X-ray Scattering-Based Screening Protocol Validated for Protein-RNA Interactions. ACS COMBINATORIAL SCIENCE 2018; 20:197-202. [PMID: 29553252 DOI: 10.1021/acscombsci.8b00007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a screening protocol utilizing small-angle X-ray scattering (SAXS) to obtain structural information on biomolecular interactions independent of prior knowledge, so as to complement affinity-based screening and provide leads for further exploration. This protocol categorizes ligand titrations by computing pairwise agreement between curves, and separately estimates affinities by quantifying complex formation as a departure from the linear sum properties of solution SAXS. The protocol is validated by sparse sequence search around the native poly uridine RNA motifs of the two-RRM domain Sex-lethal protein (Sxl). The screening of 35 RNA motifs between 4 to 10 nucleotides reveals a strong variation of resulting complexes, revealed to be preference-switching between 1:1 and 2:2 binding stoichiometries upon addition of structural modeling. Validation of select sequences in isothermal calorimetry and NMR titration retrieves domain-specific roles and function of a guanine anchor. These findings reinforce the suitability of SAXS as a complement in lead identification.
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Affiliation(s)
- Po-chia Chen
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69126 Heidelberg, Germany
| | - Pawel Masiewicz
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69126 Heidelberg, Germany
| | - Vladimir Rybin
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69126 Heidelberg, Germany
| | - Dmitri Svergun
- EMBL Hamburg, DESY, Building 25A, Notkestraße 85, 22607 Hamburg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69126 Heidelberg, Germany
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Bala J, Chinnapaiyan S, Dutta RK, Unwalla H. Aptamers in HIV research diagnosis and therapy. RNA Biol 2018; 15:327-337. [PMID: 29431588 PMCID: PMC5927724 DOI: 10.1080/15476286.2017.1414131] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/07/2017] [Accepted: 12/03/2017] [Indexed: 12/30/2022] Open
Abstract
Aptamers are high affinity single-stranded nucleic acid or protein ligands which exhibit specificity and avidity comparable to, or exceeding that of antibodies and can be generated against most targets. The functionality of aptamers is based on their unique tertiary structure, complexity and their ability to attain unique binding pockets by folding. Aptamers are selected in vitro by a process called Systematic Evolution of Ligands by Exponential enrichment (SELEX). The Kd values for the selected aptamer are often in the picomolar to low nanomolar range. Stable and nontoxic aptamers could be selected for a wide range of ligands including small molecules to large proteins. Aptamers have shown tremendous potential and have found multipurpose application in the field of therapeutic, diagnostic, biosensor and bio-imaging. While their mechanism of action can be similar to that of monoclonal antibodies, aptamers provide additional advantages in terms of production cost, simpler regulatory approval and lower immunogenicity as they are synthesized chemically. Human immunodeficiency virus (HIV) is the primary cause of acquired immune deficiency syndrome (AIDS), which causes significant morbidity and mortality with a significant consequent decrease in the quality of patient's lives. While cART has led to good viral control, people living with HIV now suffer from non-HIV comorbidities due to viral protein expression that cannot be controlled by cART. Hence pathophysiological mechanisms that govern these comorbidities with a focus on therapies that neutralize these HIV effects gained increased attention. Recent advances in HIV/AIDS research have identified several molecular targets and for the development of therapeutic and diagnostic using aptamers against HIV/AIDS. This review presents recent advances in aptamers technology for potential application in HIV diagnostics and therapeutics towards improving the quality of life of people living with HIV.
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Affiliation(s)
- Jyoti Bala
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Srinivasan Chinnapaiyan
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Rajib Kumar Dutta
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Hoshang Unwalla
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
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Damase TR, Miura TA, Parent CE, Allen PB. Application of the Open qPCR Instrument for the in Vitro Selection of DNA Aptamers against Epidermal Growth Factor Receptor and Drosophila C Virus. ACS COMBINATORIAL SCIENCE 2018; 20:45-54. [PMID: 29293309 DOI: 10.1021/acscombsci.7b00138] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The low-cost Open qPCR instrument can be used for different tasks in the aptamer selection process: quantification of DNA, cycle course optimization, screening, and final binding characterization. We have selected aptamers against whole Drosophila C virus (DCV) particles and recombinant epidermal growth factor receptor (EGFR). We performed systematic evolution of ligands by exponential enrichment (SELEX) using the Open qPCR to optimize each amplification step. The Open qPCR instrument identified the best aptamer candidate. The Open qPCR has the capacity to perform melt curves, and we used this function to perform thermofluorimetric analysis (TFA) to quantify target-aptamer binding. We confirmed target-aptamer binding using flow cytometry. A sandwich type luminescence bioassay based on our anti-DCV aptamer was sensitive to DCV and did not respond to a related virus, demonstrating that our selected anti-DCV aptamer can be used to specifically detect DCV.
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Affiliation(s)
- Tulsi Ram Damase
- University of Idaho, Department of Chemistry, 875 Perimeter Drive, Moscow, Idaho 83844-2343, United States
| | - Tanya A. Miura
- University of Idaho, Department of Biological Sciences, 875 Perimeter Drive, MS 3051, Moscow, Idaho 83844-3051, United States
| | - Christine E. Parent
- University of Idaho, Department of Biological Sciences, 875 Perimeter Drive, MS 3051, Moscow, Idaho 83844-3051, United States
| | - Peter B. Allen
- University of Idaho, Department of Chemistry, 875 Perimeter Drive, Moscow, Idaho 83844-2343, United States
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Selection and Identification of Skeletal-Muscle-Targeted RNA Aptamers. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 10:199-214. [PMID: 29499933 PMCID: PMC5862129 DOI: 10.1016/j.omtn.2017.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/06/2017] [Accepted: 12/06/2017] [Indexed: 01/16/2023]
Abstract
Oligonucleotide gene therapy has shown great promise for the treatment of muscular dystrophies. Nevertheless, the selective delivery to affected muscles has shown to be challenging because of their high representation in the body and the high complexity of their cell membranes. Current trials show loss of therapeutic molecules to non-target tissues leading to lower target efficacy. Therefore, strategies that increase uptake efficiency would be particularly compelling. To address this need, we applied a cell-internalization SELEX (Systematic Evolution of Ligands by Exponential Enrichment) approach and identified a skeletal muscle-specific RNA aptamer. A01B RNA aptamer preferentially internalizes in skeletal muscle cells and exhibits decreased affinity for off-target cells. Moreover, this in vitro selected aptamer retained its functionality in vivo, suggesting a potential new approach for targeting skeletal muscles. Ultimately, this will aid in the development of targeted oligonucleotide therapies against muscular dystrophies.
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28
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Takahashi M. Aptamers targeting cell surface proteins. Biochimie 2017; 145:63-72. [PMID: 29198584 DOI: 10.1016/j.biochi.2017.11.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/28/2017] [Indexed: 02/07/2023]
Abstract
High affinity binders targeting specific cell surface proteins are vital for development of basic and applied biosciences. However, despite sustained efforts to generate such binders by chemicals and antibodies, there are still many cell surface proteins that lack high affinity binders. Nucleic acid aptamers have potential as binding molecules for cell surface proteins, because they form distinct structures that have high affinity and specificity for a wide range of targets. Aptamers are isolated from large combinatorial libraries using a unique iterative selection-amplification process known as systematic evolution of ligands by exponential enrichment (SELEX). Among advantages of this method, purified and complex heterogeneous targets, such as bacteria, viruses, and whole-living cells, can be used for selection of aptamers. Moreover, SELEX allows generation of cell-surface-specific aptamers without prior knowledge of expression profiles in target cells. Therefore, the technology has been widely used as a valid and feasible method to generate aptamers binding to cell surface proteins with intact structure. Herein, this review summarizes and updates iconic SELEX technologies that target membrane proteins.
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Affiliation(s)
- Masaki Takahashi
- Division of RNA Medical Science, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, Japan.
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Jang S, Jang S, Xiu Y, Kang TJ, Lee SH, Koffas MAG, Jung GY. Development of Artificial Riboswitches for Monitoring of Naringenin In Vivo. ACS Synth Biol 2017; 6:2077-2085. [PMID: 28749656 DOI: 10.1021/acssynbio.7b00128] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Microbial strains are considered promising hosts for production of flavonoids because of their rapid growth rate and suitability for large-scale manufacturing. However, productivity and titer of current recombinant strains still do not meet the requirements of industrial processes. Genetically encoded biosensors have been applied for high-throughput screening or dynamic regulation of biosynthetic pathways for enhancing the performance of microbial strains that produce valuable chemicals. Currently, few protein sensor-regulators for flavonoids exist. Unlike the protein-based trans-regulating controllers, riboswitches can respond to their ligands faster and eliminate off-target effects. Here, we developed artificial riboswitches that activate gene expression in response to naringenin, an important flavonoid. RNA aptamers for naringenin were developed using SELEX and cloned upstream of a dual selectable marker gene to construct a riboswitch library. Two in vivo selection routes were applied separately to the library by supplementing naringenin at two different concentrations during enrichments to modulate the operational ranges of the riboswitches. The selected riboswitches were responsive to naringenin and activated gene expression up to 2.91-fold. Operational ranges of the riboswitches were distinguished on the basis of their selection route. Additionally, the specificity of the riboswitches was assessed, and their applicability as dynamic regulators was confirmed. Collectively, the naringenin riboswitches reported in this work will be valuable tools in metabolic engineering of microorganisms for the production of flavonoids.
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Affiliation(s)
- Sungho Jang
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
| | - Sungyeon Jang
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
| | - Yu Xiu
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Key Laboratory of Bioactive Substances and Functional Food, Beijing Union University, Beijing 100191, China
| | - Taek Jin Kang
- Department
of Chemical and Biochemical Engineering, Dongguk University, 30 Pildong-ro 1-gil, Jung-gu, Seoul, 04620, Korea
| | - Sang-Hyeup Lee
- Department
of Life Chemistry, Catholic University of Daegu, Hayang-ro 13-13,
Hayang-eup, Gyeongsan, Gyeongbuk 38430, Korea
| | - Mattheos A. G. Koffas
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Department
of Biological Sciences, Center for Biotechnology and Interdisciplinary
Studies, Rensselaer Polytechnic Institutee, Troy, New York 12180, United States
| | - Gyoo Yeol Jung
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
- School
of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
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Nik Kamarudin NAA, Mohammed NA, Mustaffa KMF. Aptamer Technology: Adjunct Therapy for Malaria. Biomedicines 2017; 5:biomedicines5010001. [PMID: 28536344 PMCID: PMC5423489 DOI: 10.3390/biomedicines5010001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/08/2016] [Accepted: 12/16/2016] [Indexed: 02/07/2023] Open
Abstract
Malaria is a life-threatening parasitic infection occurring in the endemic areas, primarily in children under the age of five, pregnant women, and patients with human immunodeficiency virus and acquired immunodeficiency syndrome (HIV)/(AIDS) as well as non-immune individuals. The cytoadherence of infected erythrocytes (IEs) to the host endothelial surface receptor is a known factor that contributes to the increased prevalence of severe malaria cases due to the accumulation of IEs, mainly in the brain and other vital organs. Therefore, further study is needed to discover a new potential anti-adhesive drug to treat severe malaria thus reducing its mortality rate. In this review, we discuss how the aptamer technology could be applied in the development of a new adjunct therapy for current malaria treatment.
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Affiliation(s)
- Nik Abdul Aziz Nik Kamarudin
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, Kubang Kerian, 16150 Kelantan, Malaysia.
| | - Nurul Adila Mohammed
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, Kubang Kerian, 16150 Kelantan, Malaysia.
| | - Khairul Mohd Fadzli Mustaffa
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, Kubang Kerian, 16150 Kelantan, Malaysia.
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de la Cruz S, López-Calleja I, Martín R, González I, Alcocer M, García T. Recent Advances in the Detection of Allergens in Foods. Methods Mol Biol 2017; 1592:263-295. [PMID: 28315226 DOI: 10.1007/978-1-4939-6925-8_20] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Food allergy is a public health issue that has significantly increased worldwide in the past decade affecting consumers' quality of life and making increasing demands on health service resources. Despite recent advances in many areas of diagnosis and treatment, our general knowledge of the basic mechanisms of the disease remained limited, i.e., not at pace with the exponential number of new cases and the explosion of the new technologies. For sensitized individuals, the only effective way to prevent allergic reactions is the strict avoidance of the offending food. For this reason, a number of regulatory bodies in several countries have recognized the importance of providing information about the presence of food allergens by enacting laws, regulations, or standards for food labeling of "priority allergens." This has resulted in the need for the development of analytical methods for protection of food-allergic consumers that should be among others highly specific, sensitive, and not influenced by the presence of the food matrix components. Several analytical approaches target either the allergen itself or a corresponding allergen marker such as peptide fragment or gene segment and have been used in the detection and quantification of allergens in food products. In this short review, some of the conventional and new methods for the detection of allergens in food are listed and briefly discussed.
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Affiliation(s)
- Silvia de la Cruz
- Facultad de Veterinaria, Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Universidad Complutense de Madrid, Av. Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Inés López-Calleja
- Facultad de Veterinaria, Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Universidad Complutense de Madrid, Av. Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Rosario Martín
- Facultad de Veterinaria, Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Universidad Complutense de Madrid, Av. Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Isabel González
- Facultad de Veterinaria, Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Universidad Complutense de Madrid, Av. Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Marcos Alcocer
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, Nottingham, UK
| | - Teresa García
- Facultad de Veterinaria, Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Universidad Complutense de Madrid, Av. Puerta de Hierro s/n, 28040, Madrid, Spain.
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Aptamer Selection Technology and Recent Advances. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 4:e223. [PMID: 28110747 PMCID: PMC4345306 DOI: 10.1038/mtna.2014.74] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/04/2014] [Indexed: 02/07/2023]
Abstract
Over the last decade, aptamers have begun to find their way from basic research to diverse commercial applications. The development of diagnostics is even more widespread than clinical applications because aptamers do not have to be extensively modified to enhance their in vivo stability and pharmacokinetics in diagnostic assays. The increasing attention has propelled the technical progress of the in vitro selection technology (SELEX) to enhance the efficiency of developing aptamers for commercially interesting targets. This review highlights recent progress in the technical steps of a SELEX experiment with a focus on high-throughput next-generation sequencing and bioinformatics. Achievements have been made in the optimization of aptamer libraries, separation schemes, amplification of the selected libraries and the identification of aptamer sequences from enriched libraries.
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Highly Multiplexed RNA Aptamer Selection using a Microplate-based Microcolumn Device. Sci Rep 2016; 6:29771. [PMID: 27432610 PMCID: PMC4949599 DOI: 10.1038/srep29771] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/17/2016] [Indexed: 02/07/2023] Open
Abstract
We describe a multiplexed RNA aptamer selection to 19 different targets simultaneously using a microcolumn-based device, MEDUSA (Microplate-based Enrichment Device Used for the Selection of Aptamers), as well as a modified selection process, that significantly reduce the time and reagents needed for selections. We exploited MEDUSA’s reconfigurable design between parallel and serially-connected microcolumns to enable the use of just 2 aliquots of starting library, and its 96-well microplate compatibility to enable the continued use of high-throughput techniques in downstream processes. Our modified selection protocol allowed us to perform the equivalent of a 10-cycle selection in the time it takes for 4 traditional selection cycles. Several aptamers were discovered with nanomolar dissociation constants. Furthermore, aptamers were identified that not only bound with high affinity, but also acted as inhibitors to significantly reduce the activity of their target protein, mouse decapping exoribonuclease (DXO). The aptamers resisted DXO’s exoribonuclease activity, and in studies monitoring DXO’s degradation of a 30-nucleotide substrate, less than 1 μM of aptamer demonstrated significant inhibition of DXO activity. This aptamer selection method using MEDUSA helps to overcome some of the major challenges with traditional aptamer selections, and provides a platform for high-throughput selections that lends itself to process automation.
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Chumakov AM, Yuhina ES, Frolova EI, Kravchenko JE, Chumakov SP. Expanding the application potential of DNA aptamers by their functionalization. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016010027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Das S, Nag A, Liang J, Bunck DN, Umeda A, Farrow B, Coppock MB, Sarkes DA, Finch AS, Agnew HD, Pitram S, Lai B, Yu MB, Museth AK, Deyle KM, Lepe B, Rodriguez‐Rivera FP, McCarthy A, Alvarez‐Villalonga B, Chen A, Heath J, Stratis‐Cullum DN, Heath JR. A General Synthetic Approach for Designing Epitope Targeted Macrocyclic Peptide Ligands. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Samir Das
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Arundhati Nag
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - JingXin Liang
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - David N. Bunck
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Aiko Umeda
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Blake Farrow
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Matthew B. Coppock
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Deborah A. Sarkes
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Amethist S. Finch
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Heather D. Agnew
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Suresh Pitram
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Bert Lai
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Mary Beth Yu
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - A. Katrine Museth
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Kaycie M. Deyle
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Bianca Lepe
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Frances P. Rodriguez‐Rivera
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Amy McCarthy
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Belen Alvarez‐Villalonga
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Ann Chen
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - John Heath
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Dimitra N. Stratis‐Cullum
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - James R. Heath
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
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Das S, Nag A, Liang J, Bunck DN, Umeda A, Farrow B, Coppock MB, Sarkes DA, Finch AS, Agnew HD, Pitram S, Lai B, Yu MB, Museth AK, Deyle KM, Lepe B, Rodriguez-Rivera FP, McCarthy A, Alvarez-Villalonga B, Chen A, Heath J, Stratis-Cullum DN, Heath JR. A General Synthetic Approach for Designing Epitope Targeted Macrocyclic Peptide Ligands. Angew Chem Int Ed Engl 2015; 54:13219-24. [PMID: 26377818 DOI: 10.1002/anie.201505243] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/12/2015] [Indexed: 12/20/2022]
Abstract
We describe a general synthetic strategy for developing high-affinity peptide binders against specific epitopes of challenging protein biomarkers. The epitope of interest is synthesized as a polypeptide, with a detection biotin tag and a strategically placed azide (or alkyne) presenting amino acid. This synthetic epitope (SynEp) is incubated with a library of complementary alkyne or azide presenting peptides. Library elements that bind the SynEp in the correct orientation undergo the Huisgen cycloaddition, and are covalently linked to the SynEp. Hit peptides are tested against the full-length protein to identify the best binder. We describe development of epitope-targeted linear or macrocycle peptide ligands against 12 different diagnostic or therapeutic analytes. The general epitope targeting capability for these low molecular weight synthetic ligands enables a range of therapeutic and diagnostic applications, similar to those of monoclonal antibodies.
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Affiliation(s)
- Samir Das
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Arundhati Nag
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - JingXin Liang
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - David N Bunck
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Aiko Umeda
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Blake Farrow
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Matthew B Coppock
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Deborah A Sarkes
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Amethist S Finch
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Heather D Agnew
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Suresh Pitram
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Bert Lai
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Mary Beth Yu
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - A Katrine Museth
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Kaycie M Deyle
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Bianca Lepe
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Frances P Rodriguez-Rivera
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Amy McCarthy
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Belen Alvarez-Villalonga
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Ann Chen
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - John Heath
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Dimitra N Stratis-Cullum
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - James R Heath
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA).
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Abstract
Long non-coding RNAs (lncRNAs) are associated to a plethora of cellular functions, most of which require the interaction with one or more RNA-binding proteins (RBPs); similarly, RBPs are often able to bind a large number of different RNAs. The currently available knowledge is already drawing an intricate network of interactions, whose deregulation is frequently associated to pathological states. Several different techniques were developed in the past years to obtain protein–RNA binding data in a high-throughput fashion. In parallel, in silico inference methods were developed for the accurate computational prediction of the interaction of RBP–lncRNA pairs. The field is growing rapidly, and it is foreseeable that in the near future, the protein–lncRNA interaction network will rise, offering essential clues for a better understanding of lncRNA cellular mechanisms and their disease-associated perturbations.
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Alam KK, Chang JL, Burke DH. FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections. MOLECULAR THERAPY-NUCLEIC ACIDS 2015; 4:e230. [PMID: 25734917 PMCID: PMC4354339 DOI: 10.1038/mtna.2015.4] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 01/08/2015] [Indexed: 12/22/2022]
Abstract
High-throughput sequence (HTS) analysis of combinatorial selection populations accelerates lead discovery and optimization and offers dynamic insight into selection processes. An underlying principle is that selection enriches high-fitness sequences as a fraction of the population, whereas low-fitness sequences are depleted. HTS analysis readily provides the requisite numerical information by tracking the evolutionary trajectory of individual sequences in response to selection pressures. Unlike genomic data, for which a number of software solutions exist, user-friendly tools are not readily available for the combinatorial selections field, leading many users to create custom software. FASTAptamer was designed to address the sequence-level analysis needs of the field. The open source FASTAptamer toolkit counts, normalizes and ranks read counts in a FASTQ file, compares populations for sequence distribution, generates clusters of sequence families, calculates fold-enrichment of sequences throughout the course of a selection and searches for degenerate sequence motifs. While originally designed for aptamer selections, FASTAptamer can be applied to any selection strategy that can utilize next-generation DNA sequencing, such as ribozyme or deoxyribozyme selections, in vivo mutagenesis and various surface display technologies (peptide, antibody fragment, mRNA, etc.). FASTAptamer software, sample data and a user's guide are available for download at http://burkelab.missouri.edu/fastaptamer.html.
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Affiliation(s)
- Khalid K Alam
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Jonathan L Chang
- 1] Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, USA [2] Current Address: School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Donald H Burke
- 1] Department of Biochemistry, University of Missouri, Columbia, Missouri, USA [2] Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, USA
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Darmostuk M, Rimpelova S, Gbelcova H, Ruml T. Current approaches in SELEX: An update to aptamer selection technology. Biotechnol Adv 2015; 33:1141-61. [PMID: 25708387 DOI: 10.1016/j.biotechadv.2015.02.008] [Citation(s) in RCA: 402] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 01/26/2015] [Accepted: 02/13/2015] [Indexed: 12/21/2022]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) is a well-established and efficient technology for the generation of oligonucleotides with a high target affinity. These SELEX-derived single stranded DNA and RNA molecules, called aptamers, were selected against various targets, such as proteins, cells, microorganisms, chemical compounds etc. They have a great potential in the use as novel antibodies, in cancer theragnostics and in biomedical research. Vast interest in aptamers stimulated continuous development of SELEX, which underwent numerous modifications since its first application in 1990. Novel modifications made the selection process more efficient, cost-effective and significantly less time-consuming. This article brings a comprehensive and up-to-date review of recent advances in SELEX methods and pinpoints advantages, main obstacles and limitations. The post-SELEX strategies and examples of application are also briefly outlined in this review.
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Affiliation(s)
- Mariia Darmostuk
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic.
| | - Silvie Rimpelova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic.
| | - Helena Gbelcova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic; Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, Bratislava 811 08, Slovak Republic.
| | - Tomas Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic.
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41
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Barman J. Targeting cancer cells using aptamers: cell-SELEX approach and recent advancements. RSC Adv 2015. [DOI: 10.1039/c4ra12407c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aptamers are short single stranded nucleic acid based therapeutic and diagnostic molecules which can be isolated from a random pool of oligonucleotides by Systematic Evolution of Ligands by EXponential Enrichment (SELEX).
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Affiliation(s)
- Jharna Barman
- Agricultural and Ecological Research Unit
- Biological Science Division
- Indian Statistical Institute
- Kolkata
- India
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42
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New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e183. [PMID: 25093707 PMCID: PMC4221594 DOI: 10.1038/mtna.2014.34] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/10/2014] [Indexed: 12/24/2022]
Abstract
Single-stranded oligonucleotide aptamers have attracted great attention in the past decade because of their diagnostic and therapeutic potential. These versatile, high affinity and specificity reagents are selected by an iterative in vitro process called SELEX, Systematic Evolution of Ligands by Exponential Enrichment. Numerous SELEX methods have been developed for aptamer selections; some that are simple and straightforward, and some that are specialized and complicated. The method of SELEX is crucial for selection of an aptamer with desired properties; however, success also depends on the starting aptamer library, the target molecule, aptamer enrichment monitoring assays, and finally, the analysis and characterization of selected aptamers. Here, we summarize key recent developments in aptamer selection methods, as well as other aspects of aptamer selection that have significant impact on the outcome. We discuss potential pitfalls and limitations in the selection process with an eye to aid researchers in the choice of a proper SELEX strategy, and we highlight areas where further developments and improvements are desired. We believe carefully designed multiplexed selection methods, when complemented with high-throughput downstream analysis and characterization assays, will yield numerous high-affinity aptamers to protein and small molecule targets, and thereby generate a vast array of reagents for probing basic biological mechanisms and implementing new diagnostic and therapeutic applications in the near future.
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Wilson R, Bourne C, Chaudhuri RR, Gregory R, Kenny J, Cossins A. Single-step selection of bivalent aptamers validated by comparison with SELEX using high-throughput sequencing. PLoS One 2014; 9:e100572. [PMID: 24963654 PMCID: PMC4070925 DOI: 10.1371/journal.pone.0100572] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/26/2014] [Indexed: 01/23/2023] Open
Abstract
The identification of nucleic acid aptamers would be advanced if they could be obtained after fewer rounds of selection and amplification. In this paper the identification of bivalent aptamers for thrombin by SELEX and single-step selection are compared using next generation sequencing and motif finding informatics. Results show that similar aptamers are identified by both methods. This is significant because it shows that next generation sequencing and motif finding informatics have the potential to simplify the selection of aptamers by avoiding multiple rounds of enzymatic transcription and amplification.
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Affiliation(s)
- Robert Wilson
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - Christian Bourne
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - Roy R. Chaudhuri
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - Richard Gregory
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - John Kenny
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - Andrew Cossins
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
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High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device. Anal Bioanal Chem 2014; 406:2727-32. [PMID: 24553662 PMCID: PMC3975076 DOI: 10.1007/s00216-014-7661-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/17/2014] [Accepted: 01/23/2014] [Indexed: 01/24/2023]
Abstract
We describe a versatile 96-well microplate-based device that utilizes affinity microcolumn chromatography to complement downstream plate-based processing in aptamer selections. This device is reconfigurable and is able to operate in serial and/or parallel mode with up to 96 microcolumns. We demonstrate the utility of this device by simultaneously performing characterizations of target binding using five RNA aptamers and a random library. This was accomplished through 96 total selection tests. Three sets of selections tested the effects of target concentration on aptamer binding compared to the random RNA library using aptamers to the proteins green fluorescent protein (GFP), human heat shock factor 1 (hHSF1), and negative elongation factor E (NELF-E). For all three targets, we found significant effects consistent with steric hindrance with optimum enrichments at predictable target concentrations. In a fourth selection set, we tested the partitioning efficiency and binding specificity of our three proteins’ aptamers, as well as two suspected background binding sequences, to eight targets running serially. The targets included an empty microcolumn, three affinity resins, three specific proteins, and a non-specific protein control. The aptamers showed significant enrichments only on their intended targets. Specifically, the hHSF1 and NELF-E aptamers enriched over 200-fold on their protein targets, and the GFP aptamer enriched 750-fold. By utilizing our device’s plate-based format with other complementary plate-based systems for all downstream biochemical processes and analysis, high-throughput selections, characterizations, and optimization were performed to significantly reduce the time and cost for completing large-scale aptamer selections. Schematic breakdown of a microplate-based enrichment device for the selection of aptamers (MEDUSA), which can be customized and assembled in both parallel and serial configurations. Up to 96 selections can be performed simultaneously. ![]()
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Pagano JM, Kwak H, Waters CT, Sprouse RO, White BS, Ozer A, Szeto K, Shalloway D, Craighead HG, Lis JT. Defining NELF-E RNA binding in HIV-1 and promoter-proximal pause regions. PLoS Genet 2014; 10:e1004090. [PMID: 24453987 PMCID: PMC3894171 DOI: 10.1371/journal.pgen.1004090] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 11/22/2013] [Indexed: 11/22/2022] Open
Abstract
The four-subunit Negative Elongation Factor (NELF) is a major regulator of RNA Polymerase II (Pol II) pausing. The subunit NELF-E contains a conserved RNA Recognition Motif (RRM) and is proposed to facilitate Poll II pausing through its association with nascent transcribed RNA. However, conflicting ideas have emerged for the function of its RNA binding activity. Here, we use in vitro selection strategies and quantitative biochemistry to identify and characterize the consensus NELF-E binding element (NBE) that is required for sequence specific RNA recognition (NBE: CUGAGGA(U) for Drosophila). An NBE-like element is present within the loop region of the transactivation-response element (TAR) of HIV-1 RNA, a known regulatory target of human NELF-E. The NBE is required for high affinity binding, as opposed to the lower stem of TAR, as previously claimed. We also identify a non-conserved region within the RRM that contributes to the RNA recognition of Drosophila NELF-E. To understand the broader functional relevance of NBEs, we analyzed promoter-proximal regions genome-wide in Drosophila and show that the NBE is enriched +20 to +30 nucleotides downstream of the transcription start site. Consistent with the role of NELF in pausing, we observe a significant increase in NBEs among paused genes compared to non-paused genes. In addition to these observations, SELEX with nuclear run-on RNA enrich for NBE-like sequences. Together, these results describe the RNA binding behavior of NELF-E and supports a biological role for NELF-E in promoter-proximal pausing of both HIV-1 and cellular genes. RNA polymerase II (Pol II) is a molecular machine that is responsible for transcribing all protein coding genes in the eukaryotic genome. Transcription by Pol II is a highly regulated process consisting of several rate-limiting steps. During transcription elongation, a number of transcription factors are essential to modulate Pol II activity. One of these factors is the Negative Elongation Factor (NELF), and it plays a major role in promoter-proximal pausing, a widespread phenomenon during early transcription elongation. NELF-E, a protein subunit of the NELF complex contains a conserved RNA binding domain that is thought to regulate transcription through its interaction with newly transcribed RNA made by Pol II. However, the function of the RNA binding activity of NELF-E remains unresolved due to prior conflicting studies. Here, we clarify the RNA binding properties of NELF-E and provide insight into how this protein might facilitate promoter-proximal pausing of Pol II in transcription. Moreover, we identify the precise region of NELF-E binding in one of its known regulatory targets, HIV-1. Taken together, the results presented indicate a dynamic interplay between NELF and specific RNA sequences around the promoter pause region to modulate early transcription elongation.
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Affiliation(s)
- John M Pagano
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Colin T Waters
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Rebekka O Sprouse
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Brian S White
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Abdullah Ozer
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Kylan Szeto
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| | - David Shalloway
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Harold G Craighead
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
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