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Shafiei N, Mahmoodzadeh Hosseini H, Amani J, Mirhosseini SA, Jafary H. Screening and identification of DNA nucleic acid aptamers against F1 protein of Yersinia pestis using SELEX method. Mol Biol Rep 2024; 51:722. [PMID: 38829419 DOI: 10.1007/s11033-024-09561-y] [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: 11/19/2023] [Accepted: 04/16/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Yersinia pestis is a bacterium that causes the disease plague. It has caused the deaths of many people throughout history. The bacterium possesses several virulence factors (pPla, pFra, and PYV). PFra plasmid encodes fraction 1 (F1) capsular antigen. F1 protein protects the bacterium against host immune cells through phagocytosis process. This protein is specific for Y. pestis. Many diagnostic techniques are based on molecular and serological detection and quantification of F1 protein in different food and clinical samples. Aptamers are small nucleic acid sequences that can act as specific ligands for many targets.This study, aimed to isolate the high-affinity ssDNA aptamers against F1 protein. METHODS AND RESULTS In this study, SELEX was used as the main strategy in screening aptamers. Moreover, enzyme-linked aptamer sorbent assay (ELASA) and surface plasmon resonance (SPR) were used to determine the affinity and specificity of obtained aptamers to F1 protein. The analysis showed that among the obtained aptamers, the three aptamers of Yer 21, Yer 24, and Yer 25 were selected with a KD value of 1.344E - 7, 2.004E - 8, and 1.68E - 8 M, respectively. The limit of detection (LoD) was found to be 0.05, 0.076, and 0.033 μg/ml for Yer 21, Yer 24, and Yer 25, respectively. CONCLUSION This study demonstrated that the synthesized aptamers could serve as effective tools for detecting and analyzing the F1 protein, indicating their potential value in future diagnostic applications.
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Affiliation(s)
- Nafiseh Shafiei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamideh Mahmoodzadeh Hosseini
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Jafar Amani
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Seyed Ali Mirhosseini
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hanieh Jafary
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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2
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Mili M, Bachu V, Kuri PR, Singh NK, Goswami P. Improving synthesis and binding affinities of nucleic acid aptamers and their therapeutics and diagnostic applications. Biophys Chem 2024; 309:107218. [PMID: 38547671 DOI: 10.1016/j.bpc.2024.107218] [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: 11/21/2023] [Revised: 02/21/2024] [Accepted: 03/17/2024] [Indexed: 04/22/2024]
Abstract
Nucleic acid aptamers have captivated the attention of analytical and medicinal scientists globally due to their several advantages as recognition molecules over conventional antibodies because of their small size, simple and inexpensive synthesis, broad target range, and high stability in varied environmental conditions. These recognition molecules can be chemically modified to make them resistant to nuclease action in blood serum, reduce rapid renel clearance, improve the target affinity and selectivity, and make them amenable to chemically conjugate with a support system that facilitates their selective applications. This review focuses on the development of efficient aptamer candidates and their application in clinical diagnosis and therapeutic applications. Significant advances have been made in aptamer-based diagnosis of infectious and non-infectious diseases. Collaterally, the progress made in therapeutic applications of aptamers is encouraging, as evident from their use in diagnosing cancer, neurodegenerative diseases, microbial infection, and in imaging. This review also updates the progress on clinical trials of many aptamer-based products of commercial interests. The key development and critical issues on the subject have been summarized in the concluding remarks.
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Affiliation(s)
- Malaya Mili
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | - Vinay Bachu
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | - Pooja Rani Kuri
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | | | - Pranab Goswami
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India.
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3
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Kissmann AK, Bolotnikov G, Li R, Müller F, Xing H, Krämer M, Gottschalk KE, Andersson J, Weil T, Rosenau F. IMPATIENT-qPCR: monitoring SELEX success during in vitro aptamer evolution. Appl Microbiol Biotechnol 2024; 108:284. [PMID: 38573322 PMCID: PMC10995058 DOI: 10.1007/s00253-024-13085-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 04/05/2024]
Abstract
SELEX (Systematic Evolution of Ligands by Exponential enrichment) processes aim on the evolution of high-affinity aptamers as binding entities in diagnostics and biosensing. Aptamers can represent game-changers as constituents of diagnostic assays for the management of instantly occurring infectious diseases or other health threats. Without in-process quality control measures SELEX suffers from low overall success rates. We present a quantitative PCR method for fast and easy quantification of aptamers bound to their targets. Simultaneous determination of melting temperatures (Tm) of each SELEX round delivers information on the evolutionary success via the correlation of increasing GC content and Tm alone with a round-wise increase of aptamer affinity to the respective target. Based on nine successful and published previous SELEX processes, in which the evolution/selection of aptamer affinity/specificity was demonstrated, we here show the functionality of the IMPATIENT-qPCR for polyclonal aptamer libraries and resulting individual aptamers. Based on the ease of this new evolution quality control, we hope to introduce it as a valuable tool to accelerate SELEX processes in general. IMPATIENT-qPCR SELEX success monitoring. Selection and evolution of high-affinity aptamers using SELEX technology with direct aptamer evolution monitoring using melting curve shifting analyses to higher Tm by quantitative PCR with fluorescence dye SYBR Green I. KEY POINTS: • Fast and easy analysis. • Universal applicability shown for a series of real successful projects.
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Affiliation(s)
- Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128, Mainz, Germany
| | - Grigory Bolotnikov
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Runliu Li
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Franziska Müller
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Hu Xing
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Kay-E Gottschalk
- Institute of Experimental Physics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Jakob Andersson
- AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210, Vienna, Austria
| | - Tanja Weil
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128, Mainz, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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4
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Wang B, Kobeissy F, Golpich M, Cai G, Li X, Abedi R, Haskins W, Tan W, Benner SA, Wang KKW. Aptamer Technologies in Neuroscience, Neuro-Diagnostics and Neuro-Medicine Development. Molecules 2024; 29:1124. [PMID: 38474636 DOI: 10.3390/molecules29051124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Aptamers developed using in vitro Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology are single-stranded nucleic acids 10-100 nucleotides in length. Their targets, often with specificity and high affinity, range from ions and small molecules to proteins and other biological molecules as well as larger systems, including cells, tissues, and animals. Aptamers often rival conventional antibodies with improved performance, due to aptamers' unique biophysical and biochemical properties, including small size, synthetic accessibility, facile modification, low production cost, and low immunogenicity. Therefore, there is sustained interest in engineering and adapting aptamers for many applications, including diagnostics and therapeutics. Recently, aptamers have shown promise as early diagnostic biomarkers and in precision medicine for neurodegenerative and neurological diseases. Here, we critically review neuro-targeting aptamers and their potential applications in neuroscience research, neuro-diagnostics, and neuro-medicine. We also discuss challenges that must be overcome, including delivery across the blood-brain barrier, increased affinity, and improved in vivo stability and in vivo pharmacokinetic properties.
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Affiliation(s)
- Bang Wang
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
- The Foundation for Applied Molecular Evolution, 1501 NW 68th Terrace, Gainesville, FL 32605, USA
| | - Firas Kobeissy
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
- Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, 1601 SW Archer Road, Gainesville, FL 32608, USA
- Center for Visual and Neurocognitive Rehabilitation (CVNR), Atlanta VA Health Care System, 1670 Clairmont Rd, Decatur, GA 30033, USA
| | - Mojtaba Golpich
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Guangzheng Cai
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Xiaowei Li
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Reem Abedi
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107-2020, Lebanon
| | - William Haskins
- Gryphon Bio, Inc., 611 Gateway Blvd. Suite 120 #253, South San Francisco, CA 94080, USA
| | - Weihong Tan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou 310022, China
| | - Steven A Benner
- The Foundation for Applied Molecular Evolution, 1501 NW 68th Terrace, Gainesville, FL 32605, USA
| | - Kevin K W Wang
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
- Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, 1601 SW Archer Road, Gainesville, FL 32608, USA
- Center for Visual and Neurocognitive Rehabilitation (CVNR), Atlanta VA Health Care System, 1670 Clairmont Rd, Decatur, GA 30033, USA
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5
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Ferreira L, Flanagan SP, Fogel R, Limson JL. Generation of epitope-specific hCG aptamers through a novel targeted selection approach. PLoS One 2024; 19:e0295673. [PMID: 38394285 PMCID: PMC10890750 DOI: 10.1371/journal.pone.0295673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/28/2023] [Indexed: 02/25/2024] Open
Abstract
Human chorionic gonadotropin (hCG) is a glycoprotein hormone used as a biomarker for several medical conditions, including pregnancy, trophoblastic and nontrophoblastic cancers. Most commercial hCG tests rely on a combination of antibodies, one of which is usually specific to the C-terminal peptide of the β-subunit. However, cleavage of this region in many hCG degradation variants prevents rapid diagnostic tests from quantifying all hCG variants in serum and urine samples. An epitope contained within the core fragment, β1, represents an under-researched opportunity for developing immunoassays specific to most variants of hCG. In the study described here, we report on a SELEX procedure tailored towards the identification of two pools of aptamers, one specific to the β-subunit of hCG and another to the β1 epitope within it. The described SELEX procedure utilized antibody-blocked targets, which is an underutilized strategy to exert negative selection pressure and in turn direct aptamer enrichment to a specific epitope. We report on the first aptamers, designated as R4_64 and R6_5, each capable of recognising two distinct sites of the hCG molecule-the β-subunit and the (presumably) β1-epitope, respectively. This study therefore presents a new SELEX approach and the generation of novel aptamer sequences that display potential hCG-specific biorecognition.
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Affiliation(s)
- Lauren Ferreira
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, Eastern Cape, South Africa
| | - Shane Patrick Flanagan
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, Eastern Cape, South Africa
| | - Ronen Fogel
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, Eastern Cape, South Africa
| | - Janice Leigh Limson
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, Eastern Cape, South Africa
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6
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Yu H, Zhu J, Shen G, Deng Y, Geng X, Wang L. Improving aptamer performance: key factors and strategies. Mikrochim Acta 2023; 190:255. [PMID: 37300603 DOI: 10.1007/s00604-023-05836-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Aptamers are functional single-stranded oligonucleotide fragments isolated from randomized libraries by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), exhibiting excellent affinity and specificity toward targets. Compared with traditional antibody reagents, aptamers display many desirable properties, such as low variation and high flexibility, and they are suitable for artificial and large-scale synthesis. These advantages make aptamers have a broad application potential ranging from biosensors, bioimaging to therapeutics and other areas of application. However, the overall performance of aptamer pre-selected by SELEX screening is far from being satisfactory. To improve aptamer performance and applicability, various post-SELEX optimization methods have been developed in the last decade. In this review, we first discuss the key factors that influence the performance or properties of aptamers, and then we summarize the key strategies of post-SELEX optimization which have been successfully used to improve aptamer performance, such as truncation, extension, mutagenesis and modification, splitting, and multivalent integration. This review shall provide a comprehensive summary and discussion of post-SELEX optimization methods developed in recent years. Moreover, by discussing the mechanism of each approach, we highlight the importance of choosing the proper method to perform post-SELEX optimization.
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Affiliation(s)
- Hong Yu
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Jiangxiong Zhu
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Guoqing Shen
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Yun Deng
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Xueqing Geng
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Lumei Wang
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China.
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China.
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China.
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7
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Poolsup S, Zaripov E, Hüttmann N, Minic Z, Artyushenko PV, Shchugoreva IA, Tomilin FN, Kichkailo AS, Berezovski MV. Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:731-743. [PMID: 36816615 PMCID: PMC9927813 DOI: 10.1016/j.omtn.2023.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
The spread of COVID-19 has affected billions of people across the globe, and the diagnosis of viral infection still needs improvement. Because of high immunogenicity and abundant expression during viral infection, SARS-CoV-2 nucleocapsid (N) protein could be an important diagnostic marker. This study aimed to develop a label-free optical aptasensor fabricated with a novel single-stranded DNA aptamer to detect the N protein. The N-binding aptamers selected using asymmetric-emulsion PCR-SELEX and their binding affinity and cross-reactivity were characterized by biolayer interferometry. The tNSP3 aptamer (44 nt) was identified to bind the N protein of wild type and Delta and Omicron variants with high affinity (KD in the range of 0.6-3.5 nM). Utilizing tNSP3 to detect the N protein spiked in human saliva evinced the potential of this aptamer with a limit of detection of 4.5 nM. Mass spectrometry analysis was performed along with molecular dynamics simulation to obtain an insight into how tNSP3 binds to the N protein. The identified epitope peptides are localized within the RNA-binding domain and C terminus of the N protein. Hence, we confirmed the performance of this aptamer as an analytical tool for COVID-19 diagnosis.
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Affiliation(s)
- Suttinee Poolsup
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Emil Zaripov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Nico Hüttmann
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Polina V Artyushenko
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk 660036, Russia.,Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia.,Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Irina A Shchugoreva
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk 660036, Russia.,Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia.,Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Felix N Tomilin
- Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia.,Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk 660036, Russia
| | - Anna S Kichkailo
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk 660036, Russia.,Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.,John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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8
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Kohlberger M, Gadermaier G. SELEX: Critical factors and optimization strategies for successful aptamer selection. Biotechnol Appl Biochem 2022; 69:1771-1792. [PMID: 34427974 PMCID: PMC9788027 DOI: 10.1002/bab.2244] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/22/2021] [Indexed: 12/30/2022]
Abstract
Within the last decade, the application range of aptamers in biochemistry and medicine has expanded rapidly. More than just a replacement for antibodies, these intrinsically structured RNA- or DNA-oligonucleotides show great potential for utilization in diagnostics, specific drug delivery, and treatment of certain medical conditions. However, what is analyzed less frequently is the process of aptamer identification known as systematic evolution of ligands by exponential enrichment (SELEX) and the functional mechanisms that lie at its core. SELEX involves numerous singular processes, each of which contributes to the success or failure of aptamer generation. In this review, critical steps during aptamer selection are discussed in-depth, and specific problems are presented along with potential solutions. The discussed aspects include the size and molecule type of the selected target, the nature and stringency of the selection process, the amplification step with its possible PCR bias, the efficient regeneration of RNA or single-stranded DNA, and the different sequencing procedures and screening assays currently available. Finally, useful quality control steps and their role within SELEX are presented. By understanding the mechanisms through which aptamer selection is influenced, the design of more efficient SELEX procedures leading to a higher success rate in aptamer identification is enabled.
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Affiliation(s)
- Michael Kohlberger
- Department of BiosciencesParis Lodron University SalzburgSalzburgAustria,Christian Doppler Laboratory for Biosimilar CharacterizationParis Lodron University SalzburgSalzburgAustria
| | - Gabriele Gadermaier
- Department of BiosciencesParis Lodron University SalzburgSalzburgAustria,Christian Doppler Laboratory for Biosimilar CharacterizationParis Lodron University SalzburgSalzburgAustria
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9
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Spirov AV, Myasnikova EM. Heuristic algorithms in evolutionary computation and modular organization of biological macromolecules: Applications to in vitro evolution. PLoS One 2022; 17:e0260497. [PMID: 35085255 PMCID: PMC8794168 DOI: 10.1371/journal.pone.0260497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
Evolutionary computing (EC) is an area of computer sciences and applied mathematics covering heuristic optimization algorithms inspired by evolution in Nature. EC extensively study all the variety of methods which were originally based on the principles of selectionism. As a result, many new algorithms and approaches, significantly more efficient than classical selectionist schemes, were found. This is especially true for some families of special problems. There are strong arguments to believe that EC approaches are quite suitable for modeling and numerical analysis of those methods of synthetic biology and biotechnology that are known as in vitro evolution. Therefore, it is natural to expect that the new algorithms and approaches developed in EC can be effectively applied in experiments on the directed evolution of biological macromolecules. According to the John Holland's Schema theorem, the effective evolutionary search in genetic algorithms (GA) is provided by identifying short schemata of high fitness which in the further search recombine into the larger building blocks (BBs) with higher and higher fitness. The multimodularity of functional biological macromolecules and the preservation of already found modules in the evolutionary search have a clear analogy with the BBs in EC. It seems reasonable to try to transfer and introduce the methods of EC, preserving BBs and essentially accelerating the search, into experiments on in vitro evolution. We extend the key instrument of the Holland's theory, the Royal Roads fitness function, to problems of the in vitro evolution (Biological Royal Staircase, BioRS, functions). The specific version of BioRS developed in this publication arises from the realities of experimental evolutionary search for (DNA-) RNA-devices (aptazymes). Our numerical tests showed that for problems with the BioRS functions, simple heuristic algorithms, which turned out to be very effective for preserving BBs in GA, can be very effective in in vitro evolution approaches. We are convinced that such algorithms can be implemented in modern methods of in vitro evolution to achieve significant savings in time and resources and a significant increase in the efficiency of evolutionary search.
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Affiliation(s)
- Alexander V. Spirov
- I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Sciences, St. Petersburg, Russia
- The Institute of Scientific Information for Social Sciences RAS, Moscow, Russia
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10
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Srivastava S, Abraham PR, Mukhopadhyay S. Aptamers: An Emerging Tool for Diagnosis and Therapeutics in Tuberculosis. Front Cell Infect Microbiol 2021; 11:656421. [PMID: 34277465 PMCID: PMC8280756 DOI: 10.3389/fcimb.2021.656421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/09/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) has been plaguing human civilization for centuries, and currently around one-third of the global population is affected with TB. Development of novel intervention tools for early diagnosis and therapeutics against Mycobacterium tuberculosis (M.tb) is the main thrust area in today's scenario. In this direction global efforts were made to use aptamers, the chemical antibodies as tool for TB diagnostics and therapeutics. This review describes the various aptamers introduced for targeting M.tb and highlights the need for development of novel aptamers to selectively target virulent proteins of M.tb for vaccine and anti-TB drugs. The objective of this review is to highlight the diagnostic and therapeutic application of aptamers used for tuberculosis. The discovery of aptamers, SELEX technology, different types of SELEX development processes, DNA and RNA aptamers reported for diseases and pathogenic agents as well have also been described in detail. But the emphasis of this review is on the development of aptamers which can block the function of virulent mycobacterial components for developing newer TB vaccine candidates and/or drug targets. Aptamers designed to target M.tb cell wall proteins, virulent factors, secretory proteins, or combination could orchestrate advanced diagnosis and therapeutic measures for tuberculosis.
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Affiliation(s)
- Shruti Srivastava
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Philip Raj Abraham
- Unit of OMICS, ICMR-Vector Control Research Centre (VCRC), Puducherry, India
| | - Sangita Mukhopadhyay
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
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11
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Roy D, Pascher A, Juratli MA, Sporn JC. The Potential of Aptamer-Mediated Liquid Biopsy for Early Detection of Cancer. Int J Mol Sci 2021; 22:ijms22115601. [PMID: 34070509 PMCID: PMC8199038 DOI: 10.3390/ijms22115601] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/08/2021] [Accepted: 05/18/2021] [Indexed: 01/08/2023] Open
Abstract
The early detection of cancer favors a greater chance of curative treatment and long-term survival. Exciting new technologies have been developed that can help to catch the disease early. Liquid biopsy is a promising non-invasive tool to detect cancer, even at an early stage, as well as to continuously monitor disease progression and treatment efficacy. Various methods have been implemented to isolate and purify bio-analytes in liquid biopsy specimens. Aptamers are short oligonucleotides consisting of either DNA or RNA that are capable of binding to target molecules with high specificity. Due to their unique properties, they are considered promising recognition ligands for the early detection of cancer by liquid biopsy. A variety of circulating targets have been isolated with high affinity and specificity by facile modification and affinity regulation of the aptamers. In this review, we discuss recent progress in aptamer-mediated liquid biopsy for cancer detection, its associated challenges, and its future potential for clinical applications.
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Affiliation(s)
- Dhruvajyoti Roy
- Helio Health, Irvine, CA 92618, USA
- Correspondence: ; Tel.: +1-949-8722383
| | - Andreas Pascher
- Department of General, Visceral and Transplant Surgery, University Hospital Münster, 48149 Münster, Germany; (A.P.); (M.A.J.); (J.C.S.)
| | - Mazen A. Juratli
- Department of General, Visceral and Transplant Surgery, University Hospital Münster, 48149 Münster, Germany; (A.P.); (M.A.J.); (J.C.S.)
| | - Judith C. Sporn
- Department of General, Visceral and Transplant Surgery, University Hospital Münster, 48149 Münster, Germany; (A.P.); (M.A.J.); (J.C.S.)
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12
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Chen J, Wang J, Luo Z, Fang X, He L, Zhu J, Qurat Ul Ain Z, He J, Ma H, Zhang H, Liu M, He L. Productive screening of single aptamers with ddPCR. Analyst 2021; 145:4130-4137. [PMID: 32421137 DOI: 10.1039/d0an00460j] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Antibodies have now been widely used for clinical treatment of a number of tumors. However, there are serious problems associated with antibody therapy, such as potential interactions of antibodies with the immune system as well as long production cycles. Recently, aptamers have been found to function similar to antibodies in terms of affinity and specificity to certain proteins and are attracting much attention for their low immunogenicity, easy chemical synthesis, and efficient penetration into tissues due to their small size. However, how to access high affinity and selectivity aptamers efficiently for further analysis is still open to be resolved. Herein, an aptamer discovery method that combines the continuous flow ddPCR technology with cytometer sorting of beads is reported, such that we have obtained DNA aptamers binding specifically to PD-1 with an affinity of over 60-fold higher than that for the best-reported method.
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Affiliation(s)
- Jinyu Chen
- Department of Thermal Science and Energy Engineering, University of Science and Technology of China, Hefei, 230027, China.
| | - Jinjun Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Zhaofeng Luo
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Xiaona Fang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Lei He
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Jianwei Zhu
- Department of Thermal Science and Energy Engineering, University of Science and Technology of China, Hefei, 230027, China.
| | - Zahra Qurat Ul Ain
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Jinlong He
- Department of Thermal Science and Energy Engineering, University of Science and Technology of China, Hefei, 230027, China.
| | - Huan Ma
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Haiyan Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Minghou Liu
- Department of Thermal Science and Energy Engineering, University of Science and Technology of China, Hefei, 230027, China.
| | - Liqun He
- Department of Thermal Science and Energy Engineering, University of Science and Technology of China, Hefei, 230027, China.
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Ayodele OO, Adesina AO, Pourianejad S, Averitt J, Ignatova T. Recent Advances in Nanomaterial-Based Aptasensors in Medical Diagnosis and Therapy. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:932. [PMID: 33917467 PMCID: PMC8067492 DOI: 10.3390/nano11040932] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
Rapid and accurate diagnosis of various biomarkers associated with medical conditions including early detection of viruses and bacteria with highly sensitive biosensors is currently a research priority. Aptamer is a chemically derived recognition molecule capable of detecting and binding small molecules with high specificity and its fast preparation time, cost effectiveness, ease of modification, stability at high temperature and pH are some of the advantages it has over traditional detection methods such as High Performance Liquid Chromatography (HPLC), Enzyme-linked Immunosorbent Assay (ELISA), Polymerase Chain Reaction (PCR). Higher sensitivity and selectivity can further be achieved via coupling of aptamers with nanomaterials and these conjugates called "aptasensors" are receiving greater attention in early diagnosis and therapy. This review will highlight the selection protocol of aptamers based on Traditional Systematic Evolution of Ligands by EXponential enrichment (SELEX) and the various types of modified SELEX. We further identify both the advantages and drawbacks associated with the modified version of SELEX. Furthermore, we describe the current advances in aptasensor development and the quality of signal types, which are dependent on surface area and other specific properties of the selected nanomaterials, are also reviewed.
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Affiliation(s)
| | | | | | | | - Tetyana Ignatova
- Nanoscience Department, The Joint School of Nanoscience & Nanoengineering, University of North Carolina, Greensboro, NC 27401, USA; (O.O.A.); (A.O.A.); (S.P.); (J.A.)
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14
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Modeling SELEX for regulatory regions using Royal Road and Royal Staircase fitness functions. Biosystems 2020; 200:104312. [PMID: 33278501 DOI: 10.1016/j.biosystems.2020.104312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/11/2020] [Accepted: 11/23/2020] [Indexed: 01/24/2023]
Abstract
The field of evolutionary algorithms (EAs) emerged in the area of computer science due to transfer of ideas from biology and developed independently for several decades, enriched with techniques from probability theory, complexity theory and optimization methods. In this paper, we consider some recent results form the EAs theory transferred back into biology. The well-known biotechnological procedure SELEX (Systematic Evolution of Ligands by EXponential enrichment) is viewed as an experimental implementation of an evolutionary algorithm. Theoretical bounds on EAs runtime are applied to model SELEX search for a regulatory region consisting of promoter and enhancer sequences. A comparison of theoretical bounds to the results of computational simulation indicates some cases where the theoretical bounds give favorable prediction, while simulation requires prohibitive computational resource.
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15
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Allemailem KS, Almatroudi A, Alsahli MA, Basfar GT, Alrumaihi F, Rahmani AH, Khan AA. Recent advances in understanding oligonucleotide aptamers and their applications as therapeutic agents. 3 Biotech 2020; 10:551. [PMID: 33269185 PMCID: PMC7686427 DOI: 10.1007/s13205-020-02546-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
The innovative discovery of aptamers was based on target-specific treatment in clinical diagnostics and therapeutics. Aptamers are synthetic, single-stranded oligonucleotides, simply described as chemical antibodies, which can bind to diverse targets with high specificity and affinity. Aptamers are synthesized by the SELEX technique, and possess distinctive properties as small size (10-50 kDa), higher stability, easy manufacture and less immunogenicity. These oligonucleotides are easily degraded by nucleases, so require some important modifications like capping and incorporation of modified nucleotides. RNA aptamers can be modified chemically on 2' positions using -NH3, -F, -deoxy, or -OMe groups to enhance their nuclease resistance. Aptamers have been employed for multiple purposes, as direct drugs or aptamer-drug conjugates targeted against different diseased cells. Different aptamer-conjugated nanovehicles (e.g., micelles, liposomes, silica nano-shells) have been designed to transport diverse anticancer-drugs like doxorubicin and cisplatin in bulk to minimize systemic cytotoxicity. Some drug-loaded nanovehicles (up to 97% loading capacity) and conjugated with specific aptamer resulted in more than 60% tumor inhibition as compared to unconjugated drug-loaded nanovehicles which showed only 31% cancer inhibition. In addition, aptamers have been widely used in basic research, food safety, environmental monitoring, clinical diagnostics and therapeutics. Different FDA-approved RNA and DNA aptamers are now available in the market, used for the treatment of diverse diseases, especially cancer. These aptamers include Macugen, Pegaptanib, etc. Despite a good progress in aptamer use, the present-day chemotherapeutics and drug targeting systems still face great challenges. Here in this review article, we are discussing nucleic acid aptamers, preparation, role in the transportation of different nanoparticle vehicles and their applications as therapeutic agents.
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Affiliation(s)
- Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, P.O. Box 6699, Buraydah, 51452 Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Mohammed A. Alsahli
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ghaiyda Talal Basfar
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Amjad Ali Khan
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, P.O. Box 6699, Buraydah, 51452 Saudi Arabia
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16
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Jain S, Kaur J, Prasad S, Roy I. Nucleic acid therapeutics: a focus on the development of aptamers. Expert Opin Drug Discov 2020; 16:255-274. [PMID: 32990095 DOI: 10.1080/17460441.2021.1829587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Aptamers provide exciting opportunities for the development of specific and targeted therapeutic approaches. AREAS COVERED In this review, the authors discuss different therapeutic options available with nucleic acids, including aptamers, focussing on similarities and differences between them. The authors concentrate on case studies with specific aptamers, which exemplify their distinct advantages. The reasons for failure, wherever available, are deliberated upon. Attempts to accelerate the in vitro selection process have been discussed. Challenges with aptamers in terms of their specificity and targeted delivery and strategies to overcome these are described. Examples of precise regulation of systemic half-life of aptamers using antidotes are discussed. EXPERT OPINION Despite their nontoxic nature, a variety of reasons limit the therapeutic potential of aptamers in the clinic. The analysis of adverse effects observed with the pegnivacogin/anivamersen pair has highlighted the need to screen for preexisting PEG antibodies in any clinical trial involving pegylated molecules. Surprisingly, and promisingly, the ability of nucleic acid therapeutics to breach the blood brain barrier seems achievable. The recognition of specific motifs, e.g. G-quadruplex in thrombin-binding aptamers, or a 'nucleation' zone while designing aptamer-antidote pairs, is likely to accelerate the discovery of therapeutically efficacious molecules.
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Affiliation(s)
- Swati Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Jaskirat Kaur
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Shivcharan Prasad
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
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17
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Amero P, Khatua S, Rodriguez-Aguayo C, Lopez-Berestein G. Aptamers: Novel Therapeutics and Potential Role in Neuro-Oncology. Cancers (Basel) 2020; 12:cancers12102889. [PMID: 33050158 PMCID: PMC7600320 DOI: 10.3390/cancers12102889] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022] Open
Abstract
A relatively new paradigm in cancer therapeutics is the use of cancer cell-specific aptamers, both as therapeutic agents and for targeted delivery of anticancer drugs. After the first therapeutic aptamer was described nearly 25 years ago, and the subsequent first aptamer drug approved, many efforts have been made to translate preclinical research into clinical oncology settings. Studies of aptamer-based technology have unveiled the vast potential of aptamers in therapeutic and diagnostic applications. Among pediatric solid cancers, brain tumors are the leading cause of death. Although a few aptamer-related translational studies have been performed in adult glioblastoma, the use of aptamers in pediatric neuro-oncology remains unexplored. This review will discuss the biology of aptamers, including mechanisms of targeting cell surface proteins, various modifications of aptamer structure to enhance therapeutic efficacy, the current state and challenges of aptamer use in neuro-oncology, and the potential therapeutic role of aptamers in pediatric brain tumors.
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Affiliation(s)
- Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA;
| | - Soumen Khatua
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA;
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Correspondence: (C.R.-A.); (G.L.-B.); Tel.: +1-713-563-6150 (C.R.-A.); +1-713-792-8140 (G.L.-B.)
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA;
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: (C.R.-A.); (G.L.-B.); Tel.: +1-713-563-6150 (C.R.-A.); +1-713-792-8140 (G.L.-B.)
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18
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Bakhtiari H, Palizban AA, Khanahmad H, Mofid MR. Aptamer-based approaches for in vitro molecular detection of cancer. Res Pharm Sci 2020; 15:107-122. [PMID: 32582351 PMCID: PMC7306249 DOI: 10.4103/1735-5362.283811] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/06/2020] [Accepted: 02/26/2020] [Indexed: 01/08/2023] Open
Abstract
Cancer is typically associated with abnormal production of various tumor-specific molecules known as tumor markers. Probing these markers by utilizing efficient approaches could be beneficial for cancer diagnosis. The current widely-used biorecognition probes, antibodies, suffer from some undeniable shortcomings. Fortunately, novel oligonucleotide-based molecular probes named aptamers are being emerged as alternative detection tools with distinctive advantages compared to antibodies. All of the existing strategies in cancer diagnostics, including those of in vitro detection, can potentially implement aptamers as the detecting moiety. Several studies have been performed in the field of in vitro cancer detection over the last decade. In order to direct future studies, it is necessary to comprehensively summarize and review the current status of the field. Most previous studies involve only a few cancer diagnostic strategies. Here, we thoroughly review recent significant advances on the applications of aptamer in various in vitro detection strategies. Furthermore, we will discuss the status of diagnostic aptamers in clinical trials.
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Affiliation(s)
- Hadi Bakhtiari
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Abbas Ali Palizban
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Mohammad Reza Mofid
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
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19
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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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20
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Komarova N, Kuznetsov A. Inside the Black Box: What Makes SELEX Better? Molecules 2019; 24:E3598. [PMID: 31591283 PMCID: PMC6804172 DOI: 10.3390/molecules24193598] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023] Open
Abstract
Aptamers are small oligonucleotides that are capable of binding specifically to a target, with impressive potential for analysis, diagnostics, and therapeutics applications. Aptamers are isolated from large nucleic acid combinatorial libraries using an iterative selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Since being implemented 30 years ago, the SELEX protocol has undergone many modifications and improvements, but it remains a laborious, time-consuming, and costly method, and the results are not always successful. Each step in the aptamer selection protocol can influence its results. This review discusses key technical points of the SELEX procedure and their influence on the outcome of aptamer selection.
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Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
| | - Alexander Kuznetsov
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
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21
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Kumar P, Kumar A. Nucleobase sequence based building up of reliable QSAR models with the index of ideality correlation using Monte Carlo method. J Biomol Struct Dyn 2019; 38:3296-3306. [PMID: 31411551 DOI: 10.1080/07391102.2019.1656109] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This study describes in silico designing of aptamers against the influenza virus using Monte Carlo method. Aptamers are short, single-stranded oligonucleotides and these bind to an ample range of biologically important proteins which are related to many disease conditions. The affinities and specificities of aptamers are comparable to antibodies. In the medicinal chemistry, quantitative structure-activity relationship (QSAR) is an important skill which is used for drug design and development. To study the inhibitory activity of aptamers, we have developed QSAR models based on Monte Carlo method. The nucleobase sequence descriptors Bk, BBk and BBBk are used to generate the QSAR models. A number of statistical benchmarks together with index of ideality of correlation (IIC) is considered to validate the build QSAR models. Data set of 98 aptamers is divided into four random splits. The statistical criteria R2 = 0.8711 and CCC = 0.9207 of the validation set of split 3 are best, so the build QSAR model of split 3 is the paramount model. The aptamer fragment responsible for the promotors of endpoint increase and decrease are also determined. These fragments are applied to design new nine aptamers from the lead aptamer APT01.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Parvin Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra, Haryana, India
| | - Ashwani Kumar
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India
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22
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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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23
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Highly Efficient and Reliable DNA Aptamer Selection Using the Partitioning Capabilities of ddPCR: The Hi-Fi SELEX Method. Methods Mol Biol 2019; 1768:531-554. [PMID: 29717463 DOI: 10.1007/978-1-4939-7778-9_30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In addition to its growing use in detecting and quantifying genes and larger genomic events, the partitioning used in digital PCR can serve as a powerful tool for high-fidelity amplification of synthetic combinatorial libraries of single-stranded DNA. Sequence-diverse libraries of this type are used as a basis for selecting tight-binding aptamers against a specific target. Here we provide a detailed description of the Hi-Fi SELEX protocol for rapid and efficient DNA aptamer selection. As part of that methodology, we describe how Hi-Fi SELEX gains advantages over other aptamer selection methods in part through the use of the massive partitioning capability of digital PCR.
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24
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Abstract
This chapter provides a brief introduction to followed by discussion of recent preclinical studies on potential aptamer drugs grouped into two broad categories, namely, “aptamer structures” and “non-ocular diseases.” Examples of aptamer-based targeting of drugs are then described. Next is an overview of the status of nearly 30 clinical trials of aptamer drugs currently listed in ClinicalTrials.gov, which is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world, and is a service of the US National Institutes of Health. This overview includes brief descriptions of each study sponsor, aptamer drug, disease(s), and type of study, as well as separate tables for completed studies, withdrawn or terminated studies, and active studies. The final section discusses Conclusions and Prospects.
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Affiliation(s)
- G. Zon
- TriLink BioTechnologies 9955 Mesa Rim Road San Diego 92121 USA
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25
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Li K, Qi L, Gao L, Shi M, Li J, Liu Z, Zhao L. Selection and preliminary application of a single stranded DNA aptamer targeting colorectal cancer serum. RSC Adv 2019; 9:38867-38876. [PMID: 35540214 PMCID: PMC9075956 DOI: 10.1039/c9ra04777h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/16/2019] [Indexed: 12/26/2022] Open
Abstract
Colorectal cancer is one of the common causes of malignant tumors in recent years, thus the discovery of potential compounds that detect the occurrence of colorectal cancer by efficient approaches is necessary. In this study, the method of systematic evolution of ligands by exponential enrichment (SELEX) was used for recognizing serum from colorectal cancer patients by a single-stranded DNA library of aptamers assisted by single-walled carbon nanotubes (SWCNTs) to remove single-stranded DNA with low affinity. Ten rounds of selection were applied using colorectal cancer serum as a target with the serum of healthy individuals as a control. As the result, we have successfully identified four candidate aptamers after high-throughput genome sequencing analysis, comparison analysis and secondary structure prediction. Among them, aptamer Seq-2 exhibited the highest affinity and the strongest selectivity with an equilibrium dissociation constant (Kd) of 11.31 ± 3.25 nM and a Ct difference value of 4.25 ± 0.38 between the colorectal cancer group and the healthy group. Moreover, with fifty negative control serum samples, the positive detection rate of fifty positive serum samples tested by aptamer Seq-2 was over 90%. In particular, aptamer Seq-2 can strongly bind the colorectal cancer serum, less strongly bind the non-colon cancer serum and hardly bind the healthy serum. Therefore, aptamer Seq-2 presents enormous potential for exploring as a tumor diagnostic kit and detecting unknown tumor markers in serum to reflect colorectal cancer. Aptamer Seq-2 with high affinity and selectivity was screened against colorectal cancer serum directly for clinical application.![]()
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Affiliation(s)
- Kun Li
- College of Environmental & Chemical Engineering
- Yanshan University
- Qinhuangdao
- China
- Applied Chemistry Key Laboratory of Hebei Province
| | - Liqing Qi
- College of Environmental & Chemical Engineering
- Yanshan University
- Qinhuangdao
- China
- Applied Chemistry Key Laboratory of Hebei Province
| | - LiMing Gao
- The First Hospital of Qinhuangdao City
- Qinhuangdao
- China
| | - Ming Shi
- College of Environmental & Chemical Engineering
- Yanshan University
- Qinhuangdao
- China
- Applied Chemistry Key Laboratory of Hebei Province
| | - Jian Li
- College of Environmental & Chemical Engineering
- Yanshan University
- Qinhuangdao
- China
- Applied Chemistry Key Laboratory of Hebei Province
| | - ZhiWei Liu
- College of Environmental & Chemical Engineering
- Yanshan University
- Qinhuangdao
- China
- Applied Chemistry Key Laboratory of Hebei Province
| | - Lu Zhao
- College of Environmental & Chemical Engineering
- Yanshan University
- Qinhuangdao
- China
- Applied Chemistry Key Laboratory of Hebei Province
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Gu L, Yan W, Liu S, Ren W, Lyu M, Wang S. Trypsin enhances aptamer screening: A novel method for targeting proteins. Anal Biochem 2018; 561-562:89-95. [PMID: 30196049 DOI: 10.1016/j.ab.2018.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 12/25/2022]
Abstract
A novel screening method for protein aptamer selection was developed in this study. Aptamers with high affinity and specificity to the surface recombinant antigen of Helicobacter pylori (HP-Ag) and to tumor markers carcinoembryonic antigen (CEA), cancer antigen 125 (CA125) and cancer antigen 19-9(CA19-9) were screened using trypsin enhanced screening method. Briefly, the target proteins above were immobilized onto 96-well polystyrene plates and incubated with a single-stranded DNA (ssDNA) library for aptamer selection. Then, trypsin was introduced to digest the proteins and obtain ssDNA that bound to the target proteins with high specificity. The concentration of ssDNA that shed from protein-ssDNA complexes was detected. After sequencing, the enrichment of target-specific aptamers was monitored and the affinity of each aptamer was analyzed. Urea, which has been reported in other article, was used to compare with trypsin. The results revealed that trypsin was more effective than urea for protein aptamer selection. The protocol used in this study provided a novel method for generating aptamers.
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Affiliation(s)
- Lide Gu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Huaihai Institute of Technology, Lianyungang, 222005, PR China; Jiangsu Marine Resources Development Research Institute, Lianyungang, 222005, PR China; College of Marine Life and Fisheries, Huaihai Institute of Technology, Lianyungang, 222005, PR China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, PR China
| | - Wanli Yan
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Huaihai Institute of Technology, Lianyungang, 222005, PR China; Jiangsu Marine Resources Development Research Institute, Lianyungang, 222005, PR China; College of Marine Life and Fisheries, Huaihai Institute of Technology, Lianyungang, 222005, PR China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, PR China.
| | - Shu Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Huaihai Institute of Technology, Lianyungang, 222005, PR China; Jiangsu Marine Resources Development Research Institute, Lianyungang, 222005, PR China; College of Marine Life and Fisheries, Huaihai Institute of Technology, Lianyungang, 222005, PR China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, PR China
| | - Wei Ren
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Huaihai Institute of Technology, Lianyungang, 222005, PR China; Key Laboratory of Marine Biology, Nanjing Agricultural University, Nanjing, Jiangsu, 210000, PR China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, PR China
| | - Mingsheng Lyu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Huaihai Institute of Technology, Lianyungang, 222005, PR China; Jiangsu Marine Resources Development Research Institute, Lianyungang, 222005, PR China; College of Marine Life and Fisheries, Huaihai Institute of Technology, Lianyungang, 222005, PR China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, PR China.
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Huaihai Institute of Technology, Lianyungang, 222005, PR China; Jiangsu Marine Resources Development Research Institute, Lianyungang, 222005, PR China; College of Marine Life and Fisheries, Huaihai Institute of Technology, Lianyungang, 222005, PR China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, PR China.
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Bayat P, Nosrati R, Alibolandi M, Rafatpanah H, Abnous K, Khedri M, Ramezani M. SELEX methods on the road to protein targeting with nucleic acid aptamers. Biochimie 2018; 154:132-155. [PMID: 30193856 DOI: 10.1016/j.biochi.2018.09.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/02/2018] [Indexed: 12/14/2022]
Abstract
Systematic evolution of ligand by exponential enrichment (SELEX) is an efficient method used to isolate high-affinity single stranded oligonucleotides from a large random sequence pool. These SELEX-derived oligonucleotides named aptamer, can be selected against a broad spectrum of target molecules including proteins, cells, microorganisms and chemical compounds. Like antibodies, aptamers have a great potential in interacting with and binding to their targets through structural recognition and are therefore called "chemical antibodies". However, aptamers offer advantages over antibodies including smaller size, better tissue penetration, higher thermal stability, lower immunogenicity, easier production, lower cost of synthesis and facilitated conjugation or modification with different functional moieties. Thus, aptamers represent an attractive substitution for protein antibodies in the fields of biomarker discovery, diagnosis, imaging and targeted therapy. Enormous interest in aptamer technology triggered the development of SELEX that has underwent numerous modifications since its introduction in 1990. This review will discuss the recent advances in SELEX methods and their advantages and limitations. Aptamer applications are also briefly outlined in this review.
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Affiliation(s)
- Payam Bayat
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahim Nosrati
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Houshang Rafatpanah
- Inflammation and Inflammatory Diseases Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mostafa Khedri
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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In vivo biosensors: mechanisms, development, and applications. ACTA ACUST UNITED AC 2018; 45:491-516. [DOI: 10.1007/s10295-018-2004-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/30/2017] [Indexed: 01/09/2023]
Abstract
Abstract
In vivo biosensors can recognize and respond to specific cellular stimuli. In recent years, biosensors have been increasingly used in metabolic engineering and synthetic biology, because they can be implemented in synthetic circuits to control the expression of reporter genes in response to specific cellular stimuli, such as a certain metabolite or a change in pH. There are many types of natural sensing devices, which can be generally divided into two main categories: protein-based and nucleic acid-based. Both can be obtained either by directly mining from natural genetic components or by engineering the existing genetic components for novel specificity or improved characteristics. A wide range of new technologies have enabled rapid engineering and discovery of new biosensors, which are paving the way for a new era of biotechnological progress. Here, we review recent advances in the design, optimization, and applications of in vivo biosensors in the field of metabolic engineering and synthetic biology.
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Mei H, Liao JY, Jimenez RM, Wang Y, Bala S, McCloskey C, Switzer C, Chaput JC. Synthesis and Evolution of a Threose Nucleic Acid Aptamer Bearing 7-Deaza-7-Substituted Guanosine Residues. J Am Chem Soc 2018; 140:5706-5713. [PMID: 29667819 DOI: 10.1021/jacs.7b13031] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In vitro selection experiments carried out on artificial genetic polymers require robust and faithful methods for copying genetic information back and forth between DNA and xeno-nucleic acids (XNA). Previously, we have shown that Kod-RI, an engineered polymerase developed to transcribe DNA templates into threose nucleic acid (TNA), can function with high fidelity in the absence of manganese ions. However, the transcriptional efficiency of this enzyme diminishes greatly when individual templates are replaced with libraries of DNA sequences, indicating that manganese ions are still required for in vitro selection. Unfortunately, the presence of manganese ions in the transcription mixture leads to the misincorporation of tGTP nucleotides opposite dG residues in the templating strand, which are detected as G-to-C transversions when the TNA is reverse transcribed back into DNA. Here we report the synthesis and fidelity of TNA replication using 7-deaza-7-modified guanosine base analogues in the DNA template and incoming TNA nucleoside triphosphate. Our findings reveal that tGTP misincorporation occurs via a Hoogsteen base pair in which the incoming tGTP residue adopts a syn conformation with respect to the sugar. Substitution of tGTP for 7-deaza-7-phenyl tGTP enabled the synthesis of TNA polymers with >99% overall fidelity. A TNA library containing the 7-deaza-7-phenyl guanine analogue was used to evolve a biologically stable TNA aptamer that binds to HIV reverse transcriptase with low nanomolar affinity.
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Affiliation(s)
| | | | | | | | | | | | - Christopher Switzer
- Department of Chemistry , University of California , Riverside , California 92521 , United States
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Park KS. Nucleic acid aptamer-based methods for diagnosis of infections. Biosens Bioelectron 2018; 102:179-188. [PMID: 29136589 PMCID: PMC7125563 DOI: 10.1016/j.bios.2017.11.028] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 02/07/2023]
Abstract
Infectious diseases are a serious global problem, which not only take an enormous human toll but also incur tremendous economic losses. In combating infectious diseases, rapid and accurate diagnostic tests are required for pathogen identification at the point of care (POC). In this review, investigations of diagnostic strategies for infectious diseases that are based on aptamers, especially nucleic acid aptamers, oligonucleotides that have high affinities and specificities toward their targets, are described. Owing to their unique features including low cost of production, easy chemical modification, high chemical stability, reproducibility, and low levels of immunogenicity and toxicity, aptamers have been widely utilized as bio-recognition elements (bio-receptors) for the development of infection diagnostic systems. We discuss nucleic acid aptamer-based methods that have been developed for diagnosis of infections using a format that organizes discussion according to the target pathogenic analytes including toxins or proteins, whole cells and nucleic acids. Also included is, a summary of recent advances made in the sensitive detection of pathogenic bacteria utilizing the isothermal nucleic acid amplification method. Lastly, a nucleic acid aptamer-based POC system is described and future directions of studies in this area are discussed.
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Affiliation(s)
- Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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Practical Application of Aptamer-Based Biosensors in Detection of Low Molecular Weight Pollutants in Water Sources. Molecules 2018; 23:molecules23020344. [PMID: 29414854 PMCID: PMC6017897 DOI: 10.3390/molecules23020344] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 01/30/2018] [Accepted: 01/30/2018] [Indexed: 01/08/2023] Open
Abstract
Water pollution has become one of the leading causes of human health problems. Low molecular weight pollutants, even at trace concentrations in water sources, have aroused global attention due to their toxicity after long-time exposure. There is an increased demand for appropriate methods to detect these pollutants in aquatic systems. Aptamers, single-stranded DNA or RNA, have high affinity and specificity to each of their target molecule, similar to antigen-antibody interaction. Aptamers can be selected using a method called Systematic Evolution of Ligands by EXponential enrichment (SELEX). Recent years we have witnessed great progress in developing aptamer selection and aptamer-based sensors for low molecular weight pollutants in water sources, such as tap water, seawater, lake water, river water, as well as wastewater and its effluents. This review provides an overview of aptamer-based methods as a novel approach for detecting low molecular weight pollutants in water sources.
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Vorobyeva MA, Davydova AS, Vorobjev PE, Pyshnyi DV, Venyaminova AG. Key Aspects of Nucleic Acid Library Design for in Vitro Selection. Int J Mol Sci 2018; 19:E470. [PMID: 29401748 PMCID: PMC5855692 DOI: 10.3390/ijms19020470] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid aptamers capable of selectively recognizing their target molecules have nowadays been established as powerful and tunable tools for biospecific applications, be it therapeutics, drug delivery systems or biosensors. It is now generally acknowledged that in vitro selection enables one to generate aptamers to almost any target of interest. However, the success of selection and the affinity of the resulting aptamers depend to a large extent on the nature and design of an initial random nucleic acid library. In this review, we summarize and discuss the most important features of the design of nucleic acid libraries for in vitro selection such as the nature of the library (DNA, RNA or modified nucleotides), the length of a randomized region and the presence of fixed sequences. We also compare and contrast different randomization strategies and consider computer methods of library design and some other aspects.
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Affiliation(s)
- Maria A. Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
| | - Anna S. Davydova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
| | - Pavel E. Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova St., 2, 630090 Novosibirsk, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova St., 2, 630090 Novosibirsk, Russia
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
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Hori SI, Herrera A, Rossi JJ, Zhou J. Current Advances in Aptamers for Cancer Diagnosis and Therapy. Cancers (Basel) 2018; 10:cancers10010009. [PMID: 29301363 PMCID: PMC5789359 DOI: 10.3390/cancers10010009] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 12/22/2017] [Accepted: 12/26/2017] [Indexed: 12/24/2022] Open
Abstract
Nucleic acid aptamers are single-stranded oligonucleotides that interact with target molecules with high affinity and specificity in unique three-dimensional structures. Aptamers are generally isolated by a simple selection process called systematic evolution of ligands by exponential enrichment (SELEX) and then can be chemically synthesized and modified. Because of their high affinity and specificity, aptamers are promising agents for biomarker discovery, as well as cancer diagnosis and therapy. In this review, we present recent progress and challenges in aptamer and SELEX technology and highlight some representative applications of aptamers in cancer therapy.
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Affiliation(s)
- Shin-Ichiro Hori
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA.
- Drug Discovery & Disease Research Laboratory, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka 561-0825, Japan.
| | - Alberto Herrera
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA.
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA.
| | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA.
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA.
| | - Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA.
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Ruscito A, McConnell EM, Koudrina A, Velu R, Mattice C, Hunt V, McKeague M, DeRosa MC. In Vitro Selection and Characterization of DNA Aptamers to a Small Molecule Target. ACTA ACUST UNITED AC 2017; 9:233-268. [PMID: 29241295 DOI: 10.1002/cpch.28] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aptamers, synthetic oligonucleotide-based molecular recognition probes, have found use in a wide array of biosensing technologies based on their tight and highly selective binding to a variety of molecular targets. However, the inherent challenges associated with the selection and characterization of aptamers for small molecule targets have resulted in their underrepresentation, despite the need for small molecule detection in fields such as medicine, the environment, and agriculture. This protocol describes the steps in the selection, sequencing, affinity characterization, and truncation of DNA aptamers that are specific for small molecule targets. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Erin M McConnell
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | - Anna Koudrina
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | - Ranganathan Velu
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | | | - Vernon Hunt
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | - Maureen McKeague
- Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Maria C DeRosa
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
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35
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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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36
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Liu M, Yu X, Chen Z, Yang T, Yang D, Liu Q, Du K, Li B, Wang Z, Li S, Deng Y, He N. Aptamer selection and applications for breast cancer diagnostics and therapy. J Nanobiotechnology 2017; 15:81. [PMID: 29132385 PMCID: PMC5683342 DOI: 10.1186/s12951-017-0311-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 10/24/2017] [Indexed: 12/17/2022] Open
Abstract
Aptamers are short non-coding, single-stranded oligonucleotides (RNA or DNA) developed through Systematic Evolution of Ligands by Exponential enrichment (SELEX) in vitro. Similar to antibodies, aptamers can bind to specific targets with high affinity, and are considered promising therapeutic agents as they have several advantages over antibodies, including high specificity, stability, and non-immunogenicity. Furthermore, aptamers can be produced at a low cost and easily modified, and are, therefore, called "chemical antibodies". In the past years, a variety of aptamers specifically bound to both breast cancer biomarkers and cells had been selected. Besides, taking advantage of nanomaterials, there were a number of aptamer-nanomaterial conjugates been developed and widely investigated for diagnostics and targeted therapy of breast cancer. In this short review, we first present a systematical review of various aptamer selection methods. Then, various aptamer-based diagnostic and therapeutic strategies of breast cancer were provided. Finally, the current problems, challenges, and future perspectives in the field were thoroughly discussed.
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MESH Headings
- Antibiotics, Antineoplastic/chemistry
- Antibiotics, Antineoplastic/therapeutic use
- Aptamers, Nucleotide/chemical synthesis
- Aptamers, Nucleotide/pharmacokinetics
- Aptamers, Nucleotide/therapeutic use
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/diagnosis
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Breast Neoplasms/therapy
- Cell Line, Tumor
- Doxorubicin/chemistry
- Doxorubicin/therapeutic use
- Epithelial Cell Adhesion Molecule/genetics
- Epithelial Cell Adhesion Molecule/metabolism
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Female
- Gene Expression
- Humans
- Ligands
- Molecular Targeted Therapy/methods
- Nanotubes
- Protein Binding
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- SELEX Aptamer Technique
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Affiliation(s)
- Mei Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189 People’s Republic of China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Xiaocheng Yu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Zhu Chen
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou, 412007 People’s Republic of China
| | - Tong Yang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Dandan Yang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189 People’s Republic of China
| | - Qianqian Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189 People’s Republic of China
| | - Keke Du
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189 People’s Republic of China
| | - Bo Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Zhifei Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189 People’s Republic of China
| | - Song Li
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou, 412007 People’s Republic of China
| | - Yan Deng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 People’s Republic of China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou, 412007 People’s Republic of China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 People’s Republic of China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou, 412007 People’s Republic of China
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Agyei D, Acquah C, Tan KX, Hii HK, Rajendran SRCK, Udenigwe CC, Danquah MK. Prospects in the use of aptamers for characterizing the structure and stability of bioactive proteins and peptides in food. Anal Bioanal Chem 2017; 410:297-306. [PMID: 28884330 DOI: 10.1007/s00216-017-0599-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/01/2017] [Accepted: 08/22/2017] [Indexed: 12/28/2022]
Abstract
Food-derived bioactive proteins and peptides have gained acceptance among researchers, food manufacturers and consumers as health-enhancing functional food components that also serve as natural alternatives for disease prevention and/or management. Bioactivity in food proteins and peptides is determined by their conformations and binding characteristics, which in turn depend on their primary and secondary structures. To maintain their bioactivities, the molecular integrity of bioactive peptides must remain intact, and this warrants the study of peptide form and structure, ideally with robust, highly specific and sensitive techniques. Short single-stranded nucleic acids (i.e. aptamers) are known to have high affinity for cognate targets such as proteins and peptides. Aptamers can be produced cost-effectively and chemically derivatized to increase their stability and shelf life. Their improved binding characteristics and minimal modification of the target molecular signature suggests their suitability for real-time detection of conformational changes in both proteins and peptides. This review discusses the developmental progress of systematic evolution of ligands by exponential enrichment (SELEX), an iterative technology for generating cost-effective aptamers with low dissociation constants (K d) for monitoring the form and structure of bioactive proteins and peptides. The review also presents case studies of this technique in monitoring the structural stability of bioactive peptide formulations to encourage applications in functional foods. The challenges and potential of aptamers in this research field are also discussed. Graphical abstract Advancing bioactive proteins and peptide functionality via aptameric ligands.
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Affiliation(s)
- Dominic Agyei
- Department of Food Science, University of Otago, Dunedin, 9054, New Zealand
| | - Caleb Acquah
- Curtin Sarawak Research Institute, Curtin University, 98009, Sarawak, Malaysia.,Department of Chemical Engineering, Curtin University, 98009, Sarawak, Malaysia
| | - Kei Xian Tan
- Curtin Sarawak Research Institute, Curtin University, 98009, Sarawak, Malaysia.,Department of Chemical Engineering, Curtin University, 98009, Sarawak, Malaysia
| | - Hieng Kok Hii
- Department of Chemical Engineering, Curtin University, 98009, Sarawak, Malaysia
| | - Subin R C K Rajendran
- Verschuren Centre for Sustainability in Energy and the Environment, Cape Breton University, Sydney, NS, B1P 6L2, Canada
| | - Chibuike C Udenigwe
- School of Nutrition Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Michael K Danquah
- Curtin Sarawak Research Institute, Curtin University, 98009, Sarawak, Malaysia. .,Department of Chemical Engineering, Curtin University, 98009, Sarawak, Malaysia.
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Donkor DA, Bhakta V, Eltringham-Smith LJ, Stafford AR, Weitz JI, Sheffield WP. Selection and characterization of a DNA aptamer inhibiting coagulation factor XIa. Sci Rep 2017; 7:2102. [PMID: 28522812 PMCID: PMC5437010 DOI: 10.1038/s41598-017-02055-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 04/05/2017] [Indexed: 12/26/2022] Open
Abstract
Factor XIa (FXIa) is a serine protease that catalyzes the activation of Factor IX (FIX) in the blood coagulation cascade. FXIa and its precursor FXI are emergent therapeutic targets for the development of safer anticoagulant agents. Here, we sought a novel DNA-based agent to inhibit FXIa. Towards this goal, an 80 base, single-stranded DNA aptamer library (containing a 40 base randomized core) was screened for FXIa-binding candidates, using ten rounds of positive and negative selection. After selection, 6 of 89 different sequences inhibited FXIa-mediated chromogenic substrate S2366 cleavage. The most active anti-FXIa aptamer had a hypervariable central sequence 5′-AACCTATCGGACTATTGTTAGTGATTTTTATAGTGT-3′ and was designated Factor ELeven Inhibitory APtamer (FELIAP). FELIAP, but not a scrambled aptamer control (SCRAPT), competitively inhibited FXIa-catalyzed S2366 cleavage, FIX activation, and complex formation with antithrombin. No effect of FELIAP on FXI activation was observed. FELIAP inhibited plasma clotting and thrombin generation assays to a significantly greater extent than SCRAPT. Immobilized FELIAP bound FXIa with strong affinity and an equilibrium binding constant (KD) in the low nanomolar range determined using surface plasmon resonance. FELIAP is the first FXIa-inhibitory aptamer to be described and constitutes a lead compound to develop related aptamers for in vivo use.
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Affiliation(s)
- David A Donkor
- Centre for Innovation, Canadian Blood Services, Hamilton, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Varsha Bhakta
- Centre for Innovation, Canadian Blood Services, Hamilton, Ontario, Canada
| | | | - Alan R Stafford
- Departments of Medicine and Biochemistry and Biomedical Sciences, McMaster University and the Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | - Jeffrey I Weitz
- Departments of Medicine and Biochemistry and Biomedical Sciences, McMaster University and the Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | - William P Sheffield
- Centre for Innovation, Canadian Blood Services, Hamilton, Ontario, Canada. .,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.
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Abstract
Nucleic acid aptamers, often termed 'chemical antibodies', are functionally comparable to traditional antibodies, but offer several advantages, including their relatively small physical size, flexible structure, quick chemical production, versatile chemical modification, high stability and lack of immunogenicity. In addition, many aptamers are internalized upon binding to cellular receptors, making them useful targeted delivery agents for small interfering RNAs (siRNAs), microRNAs and conventional drugs. However, several crucial factors have delayed the clinical translation of therapeutic aptamers, such as their inherent physicochemical characteristics and lack of safety data. This Review discusses these challenges, highlighting recent clinical developments and technological advances that have revived the impetus for this promising class of therapeutics.
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Affiliation(s)
- Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - John Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
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Sharma TK, Bruno JG, Dhiman A. ABCs of DNA aptamer and related assay development. Biotechnol Adv 2017; 35:275-301. [PMID: 28108354 DOI: 10.1016/j.biotechadv.2017.01.003] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/19/2016] [Accepted: 01/17/2017] [Indexed: 12/14/2022]
Abstract
This review is intended to guide the novice in aptamer research and development to understand virtually all of the aptamer development options and currently available assay modalities. Aptamer development topics range from discussions of basic and advanced versions of Systematic Evolution of Ligands by EXponential Enrichment (SELEX) and SELEX variations involving incorporation of exotic unnatural nucleotides to expand library diversity for even greater aptamer affinity and specificity to improved next generation methods of DNA sequencing, screening and tracking aptamer development throughout the SELEX process and characterization of lead aptamer candidates. Aptamer assay development topics include descriptions of various colorimetric and fluorescent assays in microplates or on membranes including homogeneous beacon and multiplexed Fluorescence Resonance Energy Transfer (FRET) assays. Finally, a discussion of the potential for marketing successful aptamer-based assays or test kits is included.
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Affiliation(s)
- Tarun Kumar Sharma
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India; AptaBharat Innovation Private Limited, Translational Health Science and Technology Institute Incubator, Haryana 121001, India.
| | - John G Bruno
- Operational Technologies Corporation, 4100 NW Loop 410, Suite, 230, San Antonio, TX 78229, USA..
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India.; Faculty of Pharmacy, Uttarakhand Technical University, Dehradun 248007, Uttarakhand, India
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High throughput sequencing analysis of RNA libraries reveals the influences of initial library and PCR methods on SELEX efficiency. Sci Rep 2016; 6:33697. [PMID: 27652575 PMCID: PMC5031971 DOI: 10.1038/srep33697] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/31/2016] [Indexed: 12/25/2022] Open
Abstract
The systemic evolution of ligands by exponential enrichment (SELEX) technique is a powerful and effective aptamer-selection procedure. However, modifications to the process can dramatically improve selection efficiency and aptamer performance. For example, droplet digital PCR (ddPCR) has been recently incorporated into SELEX selection protocols to putatively reduce the propagation of byproducts and avoid selection bias that result from differences in PCR efficiency of sequences within the random library. However, a detailed, parallel comparison of the efficacy of conventional solution PCR versus the ddPCR modification in the RNA aptamer-selection process is needed to understand effects on overall SELEX performance. In the present study, we took advantage of powerful high throughput sequencing technology and bioinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects of initial library and PCR methods in the RNA aptamer identification. Our analysis revealed that distinct “biased sequences” and nucleotide composition existed in the initial, unselected libraries purchased from two different manufacturers and that the fate of the “biased sequences” was target-dependent during selection. Our comparison of solution PCR- and ddPCR-driven HT-SELEX demonstrated that PCR method affected not only the nucleotide composition of the enriched sequences, but also the overall SELEX efficiency and aptamer efficacy.
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Rosch JC, Hollmann EK, Lippmann ES. In vitro selection technologies to enhance biomaterial functionality. Exp Biol Med (Maywood) 2016; 241:962-71. [PMID: 27188514 DOI: 10.1177/1535370216647182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Cells make decisions and fate choices based in part on cues they receive from their external environment. Factors that affect the interpretation of these cues include the soluble proteins that are present at any given time, the cell surface receptors that are available to bind these proteins, and the relative affinities of the soluble proteins for their cognate receptors. Researchers have identified many of the biological motifs responsible for the high-affinity interactions between proteins and their receptors, and subsequently incorporated these motifs into biomaterials to elicit control over cell behavior. Common modes of control include localized sequestration of proteins to improve bioavailability and direct inhibition or activation of a receptor by an immobilized peptide or protein. However, naturally occurring biological motifs often possess promiscuous affinity for multiple proteins and receptors or lack programmable actuation in response to dynamic stimuli, thereby limiting the amount of control they can exert over cellular decisions. These natural motifs only represent a small fraction of the biological diversity that can be assayed by in vitro selection strategies, and the discovery of "artificial" motifs with varying affinity, specificity, and functionality could greatly expand the repertoire of engineered biomaterial properties. This minireview provides a brief summary of classical and emerging techniques in peptide phage display and nucleic acid aptamer selections and discusses prospective applications in the areas of cell adhesion, angiogenesis, neural regeneration, and immune modulation.
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Affiliation(s)
- Jonah C Rosch
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Emma K Hollmann
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Ethan S Lippmann
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
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Miranda-Castro R, de-los-Santos-Álvarez N, Miranda-Ordieres AJ, Lobo-Castañón MJ. Harnessing Aptamers to Overcome Challenges in Gluten Detection. BIOSENSORS-BASEL 2016; 6:16. [PMID: 27104578 PMCID: PMC4931476 DOI: 10.3390/bios6020016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 12/13/2022]
Abstract
Celiac disease is a lifelong autoimmune disorder triggered by foods containing gluten, the storage protein in wheat, rye, and barley. The rapidly escalating number of patients diagnosed with this disease poses a great challenge to both food industry and authorities to guarantee food safety for all. Therefore, intensive efforts are being made to establish minimal disease-eliciting doses of gluten and consequently to improve gluten-free labeling. These efforts depend to a high degree on the availability of methods capable of detecting the protein in food samples at levels as low as possible. Current analytical approaches rely on the use of antibodies as selective recognition elements. With limited sensitivity, these methods exhibit some deficiencies that compromise the accuracy of the obtained results. Aptamers provide an ideal alternative for designing biosensors for fast and selective measurement of gluten in foods. This article highlights the challenges in gluten detection, the current status of the use of aptamers for solving this problem, and what remains to be done to move these systems into commercial applications.
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Affiliation(s)
- Rebeca Miranda-Castro
- Departamento de Química-Física y Analítica, Universidad de Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain.
| | | | - Arturo J Miranda-Ordieres
- Departamento de Química-Física y Analítica, Universidad de Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain.
| | - María Jesús Lobo-Castañón
- Departamento de Química-Física y Analítica, Universidad de Oviedo, Julián Clavería, 8, 33006 Oviedo, Spain.
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Yüce M, Ullah N, Budak H. Trends in aptamer selection methods and applications. Analyst 2016; 140:5379-99. [PMID: 26114391 DOI: 10.1039/c5an00954e] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aptamers are target specific ssDNA, RNA or peptide sequences generated by an in vitro selection and amplification method called SELEX (Systematic Evolution of Ligands by EXponential Enrichment), which involves repetitive cycles of binding, recovery and amplification steps. Aptamers have the ability to bind with a variety of targets such as drugs, proteins, heavy metals, and pathogens with high specificity and selectivity. Aptamers are similar to monoclonal antibodies regarding their binding affinities, but they offer a number of advantages over the existing antibody-based detection methods, which make the aptamers promising diagnostic and therapeutic tools for future biomedical and analytical applications. The aim of this review article is to provide an overview of the recent advancements in aptamer screening methods along with a concise description of the major application areas of aptamers including biomarker discovery, diagnostics, imaging and nanotechnology.
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Affiliation(s)
- Meral Yüce
- Sabanci University, Nanotechnology Research and Application Centre, 34956, Istanbul, Turkey.
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46
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Trends in the Design and Development of Specific Aptamers Against Peptides and Proteins. Protein J 2016; 35:81-99. [DOI: 10.1007/s10930-016-9653-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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47
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McKeague M, Wong RS, Smolke CD. Opportunities in the design and application of RNA for gene expression control. Nucleic Acids Res 2016; 44:2987-99. [PMID: 26969733 PMCID: PMC4838379 DOI: 10.1093/nar/gkw151] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 02/29/2016] [Indexed: 12/15/2022] Open
Abstract
The past decade of synthetic biology research has witnessed numerous advances in the development of tools and frameworks for the design and characterization of biological systems. Researchers have focused on the use of RNA for gene expression control due to its versatility in sensing molecular ligands and the relative ease by which RNA can be modeled and designed compared to proteins. We review the recent progress in the field with respect to RNA-based genetic devices that are controlled through small molecule and protein interactions. We discuss new approaches for generating and characterizing these devices and their underlying components. We also highlight immediate challenges, future directions and recent applications of synthetic RNA devices in engineered biological systems.
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Affiliation(s)
- Maureen McKeague
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Remus S Wong
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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Aptamers as Synthetic Receptors for Food Quality and Safety Control. BIOSENSORS FOR SUSTAINABLE FOOD - NEW OPPORTUNITIES AND TECHNICAL CHALLENGES 2016. [DOI: 10.1016/bs.coac.2016.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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49
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A Highlight of Recent Advances in Aptamer Technology and Its Application. Molecules 2015; 20:11959-80. [PMID: 26133761 PMCID: PMC6331864 DOI: 10.3390/molecules200711959] [Citation(s) in RCA: 204] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 01/10/2023] Open
Abstract
Aptamers and SELEX (systematic evolution of ligands by exponential enrichment) technology have gained increasing attention over the past 25 years. Despite their functional similarity to protein antibodies, oligonucleotide aptamers have many unique properties that are suitable for clinical applications and industrialization. Aptamers may be superior to antibodies in fields such as biomarker discovery, in vitro and in vivo diagnosis, precisely controlled drug release, and targeted therapy. However, aptamer commercialization has not occurred as quickly as expected, and few aptamer-based products have yet successfully entered clinical and industrial use. Thus, it is important to critically review some technical barriers of aptamer and SELEX technology per se that may impede aptamer development and application. To date, how to rapidly obtain aptamers with superior bioavailability over antibodies remains the key issue. In this review, we discuss different chemical and structural modification strategies aimed to enhance aptamer bioavailability. We also discuss improvements to SELEX process steps to shorten the selection period and improve the SELEX process success rate. Applications in which aptamers are particularly suited and perform differently or superior to antibodies are briefly introduced.
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