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Fang Z, Feng X, Tang F, Jiang H, Han S, Tao R, Lu C. Aptamer Screening: Current Methods and Future Trend towards Non-SELEX Approach. BIOSENSORS 2024; 14:350. [PMID: 39056626 PMCID: PMC11274700 DOI: 10.3390/bios14070350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
Aptamers are nucleic acid sequences that specifically bind with target molecules and are vital to applications such as biosensing, drug development, disease diagnostics, etc. The traditional selection procedure of aptamers is based on the Systematic Evolution of Ligands by an Exponential Enrichment (SELEX) process, which relies on repeating cycles of screening and amplification. With the rapid development of aptamer applications, RNA and XNA aptamers draw more attention than before. But their selection is troublesome due to the necessary reverse transcription and transcription process (RNA) or low efficiency and accuracy of enzymes for amplification (XNA). In light of this, we review the recent advances in aptamer selection methods and give an outlook on future development in a non-SELEX approach, which simplifies the procedure and reduces the experimental costs. We first provide an overview of the traditional SELEX methods mostly designed for screening DNA aptamers to introduce the common tools and methods. Then a section on the current screening methods for RNA and XNA is prepared to demonstrate the efforts put into screening these aptamers and the current difficulties. We further predict that the future trend of aptamer selection lies in non-SELEX methods that do not require nucleic acid amplification. We divide non-SELEX methods into an immobilized format and non-immobilized format and discuss how high-resolution partitioning methods could facilitate the further improvement of selection efficiency and accuracy.
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Affiliation(s)
- Zhihui Fang
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Xiaorui Feng
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Fan Tang
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Han Jiang
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Shuyuan Han
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Ran Tao
- Shenzhen Key Laboratory of Advanced Thin Films and Applications, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Chenze Lu
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
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Hsu SH, Yang HY, Chang CC, Tsai SK, Li C, Chang MY, Ko YC, Chou LF, Tsai CY, Tian YC, Yang CW. Blocking pathogenic Leptospira invasion with aptamer molecules targeting outer membrane LipL32 protein. Microbes Infect 2024; 26:105299. [PMID: 38224944 DOI: 10.1016/j.micinf.2024.105299] [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: 07/25/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
This study aimed to develop aptamers targeting LipL32, a most abundant lipoprotein in pathogenic Leptospira, to hinder bacterial invasion. The objectives were to identify high-affinity aptamers through SELEX and evaluate their specificity and inhibitory effects. SELEX was employed to generate LipL32 aptamers (L32APs) over 15 rounds of selection. L32APs' binding affinity and specificity for pathogenic Leptospira were assessed. Their ability to inhibit LipL32-ECM interaction and Leptospira invasion was investigated. Animal studies were conducted to evaluate the impact of L32AP treatment on survival rates, Leptospira colonization, and kidney damage. Three L32APs with strong binding affinity were identified. They selectively detected pathogenic Leptospira, sparing non-pathogenic strains. L32APs inhibited LipL32-ECM interaction and Leptospira invasion. In animal studies, L32AP administration significantly improved survival rates, reduced Leptospira colonies, and mitigated kidney damage compared to infection alone. This pioneering research developed functional aptamers targeting pathogenic Leptospira. The identified L32APs exhibited high affinity, pathogen selectivity, and inhibition of invasion and ECM interaction. L32AP treatment showed promising results, enhancing survival rates and reducing Leptospira colonization and kidney damage. These findings demonstrate the potential of aptamers to impede pathogenic Leptospira invasion and aid in recovery from Leptospira-induced kidney injury (190 words).
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Affiliation(s)
- Shen-Hsing Hsu
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan.
| | - Huang-Yu Yang
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chia-Chen Chang
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | | | - Chien Li
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ming-Yang Chang
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yi-Ching Ko
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Li-Fang Chou
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chung-Ying Tsai
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ya-Chung Tian
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chih-Wei Yang
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Nephrology, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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Lim H, Chang J, Kim KI, Moon Y, Lee S, Lee B, Lee JH, Lee J. On-chip selection of adenosine aptamer using graphene oxide-coated magnetic nanoparticles. BIOMICROFLUIDICS 2022; 16:044102. [PMID: 35909647 PMCID: PMC9337878 DOI: 10.1063/5.0095419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) is a method that is generally used for developing aptamers, which have arisen the promising alternatives for antibodies. However, conventional SELEX methods have limitations, such as a limited selection of target molecules, time-consuming and complex fabrication processes, and labor-intensive processes, which result in low selection yields. Here, we used (i) graphene oxide (GO)-coated magnetic nanoparticles in the selection process for separation and label-free detection and (ii) a multilayered microfluidic device manufactured using a three-dimensionally printed mold that is equipped with automated control valves to achieve precise fluid flows. The developed on-chip aptamer selection device and GO-coated magnetic nanoparticles were used to screen aptamer candidates for adenosine in eight cycles of the selection process within approximately 2 h for each cycle. Based on results from isothermal titration calorimetry, an aptamer with a dissociation constant of 18.6 ± 1.5 μM was selected. Therefore, the on-chip platform based on GO-coated magnetic nanoparticles provides a novel label-free screening technology for biosensors and micro/nanobiotechnology for achieving high-quality aptamers.
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Affiliation(s)
| | - Junhyuck Chang
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Kyung-il Kim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Youngkwang Moon
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Saebom Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Byoungsang Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jung Heon Lee
- Authors to whom correspondence should be addressed:, Tel.: +82-31-290-7404 and , Tel.: +82-31-299-4845
| | - Jinkee Lee
- Authors to whom correspondence should be addressed:, Tel.: +82-31-290-7404 and , Tel.: +82-31-299-4845
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Zhou R, Gao Y, Yang C, Zhang X, Hu B, Zhao L, Guo H, Sun M, Wang L, Jiao B. A Novel SELEX Based on Immobilizing Libraries Enables Screening of Saxitoxin Aptamers for BLI Aptasensor Applications. Toxins (Basel) 2022; 14:228. [PMID: 35324725 PMCID: PMC8955768 DOI: 10.3390/toxins14030228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/18/2022] [Indexed: 12/20/2022] Open
Abstract
Saxitoxin (STX) is one of the potent marine biotoxins that has high rate of lethality. However, there are no effective treatments at present, and the existing detection methods need to be further explored because of ethical problems or technical limitations. In this work, oligonucleotide aptamers toward STX were screened based on immobilizing libraries on Immobilized Metal-Chelate (IMC), such as Ni-NTA Sepharose, and the IMC-SELEX was conducted by the G-quadruplex library and the random library, respectively. Aptamer 45e (from the G-quadruplex library) and aptamer 75a were obtained after optimization, and aptamer 45e turned out to have a higher affinity toward STX. Furthermore, it was found that the hydrogen bonding and the van der Waals forces (VDW) played major roles in the high efficiency and specificity between STX and 45e by means of molecular docking and dynamics simulation. Based on this, aptamer 45e-1 with the Kd value of 19 nM was obtained by further optimization, which was then used to construct a simple, label-free and real-time optical BLI aptasensor for the detection of STX. This aptasensor showed good reproducibility and stability. In summary, with the advantages of screening aptamers of high efficiency and specificity toward the targets, the proposed IMC-SELEX provides a promising screening strategy for discovering aptamers, which could be used as the potential molecular recognition elements in the fields of biomedicine, food safety and environmental monitoring.
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Affiliation(s)
- Rong Zhou
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
| | - Yun Gao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
| | - Chengfang Yang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
| | - Xiaojuan Zhang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
- College of Medicine, Shaoxing University, 900th Chengnan Avenue, Shaoxing 312000, China
| | - Bo Hu
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center of PLA, Navy Medical University, Shanghai 200433, China;
| | - Luming Zhao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
| | - Han Guo
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
| | - Mingjuan Sun
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
| | - Lianghua Wang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
| | - Binghua Jiao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Navy Medical University, Shanghai 200433, China; (R.Z.); (Y.G.); (C.Y.); (X.Z.); (L.Z.); (H.G.); (M.S.)
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Woolfork AG, Iftekhar S, Ovbude S, Suh K, Sharmeen S, Kyei I, Jones J, Hage DS. Recent Advances in Supramolecular Affinity Separations: Affinity Chromatography and Related Methods. ADVANCES IN CHROMATOGRAPHY 2021; 58:1-74. [PMID: 36186535 PMCID: PMC9520669 DOI: 10.1201/9781003223405-1] [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] [Indexed: 09/06/2024]
Abstract
Affinity chromatography is a technique that uses a stationary phase based on the supramolecular interactions that occur in biological systems or mimics of these systems. This method has long been a popular tool for the isolation, measurement, and characterization of specific targets in complex samples. This review discusses the basic concepts of this method and examines recent developments in affinity chromatography and related supramolecular separation methods. Topics that are examined include advances that have occurred in the types of supports, approaches to immobilization, and binding agents that are employed in this method. New developments in the applications of affinity chromatography are also summarized, including an overview on the use of this method for biochemical purification, sample preparation or analysis, chiral separations, and biointeraction studies.
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Affiliation(s)
- Ashley G. Woolfork
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 (USA)
| | - Sazia Iftekhar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 (USA)
| | - Susan Ovbude
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 (USA)
| | - Kyungah Suh
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 (USA)
| | - Sadia Sharmeen
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 (USA)
| | - Isaac Kyei
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 (USA)
| | - Jacob Jones
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 (USA)
| | - David S. Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 (USA)
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Rodriguez EL, Poddar S, Iftekhar S, Suh K, Woolfork AG, Ovbude S, Pekarek A, Walters M, Lott S, Hage DS. Affinity chromatography: A review of trends and developments over the past 50 years. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1157:122332. [PMID: 32871378 PMCID: PMC7584770 DOI: 10.1016/j.jchromb.2020.122332] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022]
Abstract
The field of affinity chromatography, which employs a biologically-related agent as the stationary phase, has seen significant growth since the modern era of this method began in 1968. This review examines the major developments and trends that have occurred in this technique over the past five decades. The basic principles and history of this area are first discussed. This is followed by an overview of the various supports, immobilization strategies, and types of binding agents that have been used in this field. The general types of applications and fields of use that have appeared for affinity chromatography are also considered. A survey of the literature is used to identify major trends in these topics and important areas of use for affinity chromatography in the separation, analysis, or characterization of chemicals and biochemicals.
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Affiliation(s)
| | - Saumen Poddar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Sazia Iftekhar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Kyungah Suh
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Ashley G Woolfork
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Susan Ovbude
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Allegra Pekarek
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Morgan Walters
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Shae Lott
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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7
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Ma Y, Li W, Xing R, Li P, Liu Z. Epitope-Imprinted Magnetic Nanoparticles as a General Platform for Efficient In Vitro Evolution of Protein-Binding Aptamers. ACS Sens 2020; 5:2537-2544. [PMID: 32631049 DOI: 10.1021/acssensors.0c00846] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aptamers are usually created by in vitro selection using a strategy termed systematic evolution of ligands by exponential enrichment (SELEX). Although numerous SELEX alternatives with improved selection efficiency have been developed, the overall success rate of SELEX at present is still not very ideal, which remains a great obstacle to aptamer-based research and application. In this study, an efficient and facile SELEX method was developed for in vitro screening of protein-binding aptamers, applying epitope-imprinted magnetic nanoparticles (MNPs) that exhibit highly favorable binding properties as a general affinity platform. As a proof of the principle, myoglobin (Mb) and β2-microglobulin were employed as two target proteins. Two satisfied aptamers toward each target protein, with the dissociation constant at the 10-8 M level and cross-reactivity less than 16.5%, were selected within three rounds, taking only 1 day. A dual aptamer-based fluorescence sandwich assay was constructed using a pair of the selected aptamers. The resulting assay allowed for quantitatively detecting Mb in human serum and distinguishing acute myocardial infarction patients from healthy individuals. The epitope-imprinted MNP-based SELEX is straightforward and generally applicable for a wide range of target proteins, providing a promising aptamer selection tool for aptamer-based research and real-world applications.
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Affiliation(s)
- Yanyan Ma
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wei Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Rongrong Xing
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Pengfei Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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Wu W, Yu C, Wang Q, Zhao F, He H, Liu C, Yang Q. Research advances of DNA aptasensors for foodborne pathogen detection. Crit Rev Food Sci Nutr 2019; 60:2353-2368. [PMID: 31298036 DOI: 10.1080/10408398.2019.1636763] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aptamers, referring to single-stranded DNA or RNA molecules can specifically recognize and bind to their targets. Based on their excellent specificity, sensitivity, high affinity, and simplicity of modification, aptamers offer great potential for pathogen detection and biomolecular screening. This article reviews aptamer screening technologies and aptamer application technologies, including gold-nanoparticle lateral flow assays, fluorescence assays, electrochemical assays, colorimetric assays, and surface-enhanced Raman assays, in the detection of foodborne pathogens. Although notable progress (more rapid, sensitive, and accurate) has been achieved in the field, challenges and drawbacks in their applications still remain to be overcome.
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Affiliation(s)
- Wei Wu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China.,State Key Laboratory of Bio-fibers and Eco-textiles, Institute of Biochemical Engineering, School of Materials Science and Engineering, Qingdao University, Qingdao, China
| | - Chundi Yu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Qi Wang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Fangyuan Zhao
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Hong He
- Clinical Laboratory, Affiliated Hospital to Qingdao University, Qingdao, China
| | - Chunzhao Liu
- State Key Laboratory of Bio-fibers and Eco-textiles, Institute of Biochemical Engineering, School of Materials Science and Engineering, Qingdao University, Qingdao, China.,State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Qingli Yang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
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Kowalska E, Bartnicki F, Fujisawa R, Bonarek P, Hermanowicz P, Tsurimoto T, Muszynska K, Strzalka W. Inhibition of DNA replication by an anti-PCNA aptamer/PCNA complex. Nucleic Acids Res 2019; 46:25-41. [PMID: 29186524 PMCID: PMC5758903 DOI: 10.1093/nar/gkx1184] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 11/13/2017] [Indexed: 12/29/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a multifunctional protein present in the nuclei of eukaryotic cells that plays an important role as a component of the DNA replication machinery, as well as DNA repair systems. PCNA was recently proposed as a potential non-oncogenic target for anti-cancer therapy. In this study, using the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method, we developed a short DNA aptamer that binds human PCNA. In the presence of PCNA, the anti-PCNA aptamer inhibited the activity of human DNA polymerase δ and ϵ at nM concentrations. Moreover, PCNA protected the anti-PCNA aptamer against the exonucleolytic activity of these DNA polymerases. Investigation of the mechanism of anti-PCNA aptamer-dependent inhibition of DNA replication revealed that the aptamer did not block formation, but was a component of PCNA/DNA polymerase δ or ϵ complexes. Additionally, the anti-PCNA aptamer competed with the primer-template DNA for binding to the PCNA/DNA polymerase δ or ϵ complex. Based on the observations, a model of anti-PCNA aptamer/PCNA complex-dependent inhibition of DNA replication was proposed.
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Affiliation(s)
- Ewa Kowalska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
| | - Filip Bartnicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
| | - Ryo Fujisawa
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Piotr Bonarek
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
| | - Pawel Hermanowicz
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland.,Laboratory of Photobiology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Krakow 30-387, Poland
| | - Toshiki Tsurimoto
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Klaudia Muszynska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
| | - Wojciech Strzalka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
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10
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Wang T, Chen C, Larcher LM, Barrero RA, Veedu RN. Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development. Biotechnol Adv 2018; 37:28-50. [PMID: 30408510 DOI: 10.1016/j.biotechadv.2018.11.001] [Citation(s) in RCA: 282] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/28/2018] [Accepted: 11/04/2018] [Indexed: 02/07/2023]
Abstract
Aptamers are short single-stranded nucleic acid sequences capable of binding to target molecules in a way similar to antibodies. Due to various advantages such as prolonged shelf life, low batch to batch variation, low/no immunogenicity, freedom to incorporate chemical modification for enhanced stability and targeting capacity, aptamers quickly found their potential in diverse applications ranging from therapy, drug delivery, diagnosis, and functional genomics to bio-sensing. Aptamers are generated by a process called SELEX. However, the current overall success rate of SELEX is far from being satisfactory, and still presents a major obstacle for aptamer-based research and application. The need for an efficient selection strategy consisting of defined procedures to deal with a wide variety of targets is significantly important. In this work, by analyzing key aspects of SELEX including initial library design, target preparation, PCR optimization, and single strand DNA separation, we provide a comprehensive analysis of individual steps to facilitate researchers intending to develop personalized protocols to address many of the obstacles in SELEX. In addition, this review provides suggestions and opinions for future aptamer development procedures to address the concerns on key SELEX steps, and post-SELEX modifications.
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Affiliation(s)
- Tao Wang
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia; Perron Institute for Neurological and Translational Science, Perth 6009, Australia; School of Nursing, Zhengzhou University & Nursing Department, The First Affiliated Hospital of Zheng Zhou University, Zhengzhou 450001, China
| | - Changying Chen
- School of Nursing, Zhengzhou University & Nursing Department, The First Affiliated Hospital of Zheng Zhou University, Zhengzhou 450001, China
| | - Leon M Larcher
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia
| | - Roberto A Barrero
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia
| | - Rakesh N Veedu
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia; Perron Institute for Neurological and Translational Science, Perth 6009, Australia.
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11
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Xuan W, Peng Y, Deng Z, Peng T, Kuai H, Li Y, He J, Jin C, Liu Y, Wang R, Tan W. A basic insight into aptamer-drug conjugates (ApDCs). Biomaterials 2018; 182:216-226. [PMID: 30138784 DOI: 10.1016/j.biomaterials.2018.08.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 12/19/2022]
Abstract
Aptamers are often compared with antibodies since both types of molecules function as targeting ligands for specific cancer cell recognition. However, aptamers offer several advantages, including small size, facile chemical modification, high chemical stability, low immunogenicity, rapid tissue penetration, and engineering simplicity. Despite these advantages, several crucial factors have delayed their clinical translation, such as concerns over inherent physicochemical stability and safety. Meanwhile, steps have been taken to make aptamer-drug conjugates, or ApDCs, a clinically practical tool. In this review, we highlight the development of ApDCs and discuss how researchers are solving some problems associated with their clinical application for targeted therapy.
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Affiliation(s)
- Wenjing Xuan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yongbo Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Zhengyu Deng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Tianhuan Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Hailan Kuai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yingying Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Jiaxuan He
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Cheng Jin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yanlan Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Ruowen Wang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, College of Chemistry and Chemical Engineering, Shanghai 200240, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China; Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, College of Chemistry and Chemical Engineering, Shanghai 200240, China; Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States.
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12
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Abstract
Nucleic acid aptamers have tremendous potential as molecular recognition elements in biomedical targeting, analytical arrays, and self-signaling sensors. However, practical limitations and inefficiencies in the process of selecting novel aptamers (SELEX) have hampered widespread adoption of aptamer technologies. Many factors have recently contributed to more effective aptamer screening, but no influence has done more to increase the efficiency, scale, and automation of aptamer selection than that of new microfluidic SELEX techniques. This review introduces aptamers as a powerful chemical and biological tool, briefly highlights traditional SELEX techniques and their limitations, covers in detail the recent advancements in microfluidic methods of aptamer selection and characterization, and suggests possible future directions of the field.
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Affiliation(s)
- Sean K Dembowski
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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13
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Bartnicki F, Bonarek P, Kowalska E, Strzalka W. The Argi system: one-step purification of proteins tagged with arginine-rich cell-penetrating peptides. Sci Rep 2017; 7:2619. [PMID: 28572575 PMCID: PMC5453957 DOI: 10.1038/s41598-017-02432-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/11/2017] [Indexed: 12/04/2022] Open
Abstract
The discovery of cell penetrating peptides (CPPs) opened new perspectives for the delivery of proteins into human cells. It is considered that in the future CPP-mediated transport of therapeutic proteins may find applications in the treatment of human diseases. Despite this fact a fast and simple method for the purification of CPP-tagged proteins, free of additional tags, was not available to date. To fill this gap we developed the Argi system for one-step purification of proteins tagged with arginine rich CPPs.
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Affiliation(s)
- Filip Bartnicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Piotr Bonarek
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ewa Kowalska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Wojciech Strzalka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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14
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Chen K, Liu B, Yu B, Zhong W, Lu Y, Zhang J, Liao J, Liu J, Pu Y, Qiu L, Zhang L, Liu H, Tan W. Advances in the development of aptamer drug conjugates for targeted drug delivery. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2017; 9:10.1002/wnan.1438. [PMID: 27800663 PMCID: PMC5507701 DOI: 10.1002/wnan.1438] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 08/29/2016] [Accepted: 09/06/2016] [Indexed: 12/20/2022]
Abstract
A key goal of modern medicine is target-specific therapeutic intervention. However, most drugs lack selectivity, resulting in 'off-target' side effects. To address the requirements of 'targeted therapy,' aptamers, which are artificial oligonucleotides, have been used as novel targeting ligands to construct aptamer drug conjugates (ApDC) that can specifically bind to a broad spectrum of targets, including diseased cells. Accordingly, the application of aptamers in targeted drug delivery has attracted broad interest due to their impressive selectivity and affinity, low immunogenicity, easy synthesis with high reproducibility, facile modification, and relatively rapid tissue penetration with no toxicity. Functionally, aptamers themselves can be used as macromolecular drugs, and they are also commonly used in biomarker discovery and targeted drug delivery. In this review, we will highlight the most recent advances in the development of aptamers and aptamer conjugates, and discuss their potential in targeted therapy. WIREs Nanomed Nanobiotechnol 2017, 9:e1438. doi: 10.1002/wnan.1438 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ke Chen
- Xiangya Hospital, Central South University, Changsha, China
| | - Bo Liu
- Xiangya Hospital, Central South University, Changsha, China
| | - Bo Yu
- Xiangya Hospital, Central South University, Changsha, China
| | - Wen Zhong
- Xiangya Hospital, Central South University, Changsha, China
| | - Yi Lu
- Xiangya Hospital, Central South University, Changsha, China
| | - Jiani Zhang
- Xiangya Hospital, Central South University, Changsha, China
| | - Jie Liao
- Xiangya Hospital, Central South University, Changsha, China
| | - Jun Liu
- Xiangya Hospital, Central South University, Changsha, China
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha, China
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, Hunan University, Changsha, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Ying Pu
- Xiangya Hospital, Central South University, Changsha, China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha, China
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, Hunan University, Changsha, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Liqin Zhang
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha, China
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, Hunan University, Changsha, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Huixia Liu
- Xiangya Hospital, Central South University, Changsha, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha, China
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, Hunan University, Changsha, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, University of Florida, Gainesville, FL, USA
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15
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Single-stranded DNA aptamer targeting and neutralization of anti-D alloantibody: a potential therapeutic strategy for haemolytic diseases caused by Rhesus alloantibody. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2016; 16:184-192. [PMID: 27893356 DOI: 10.2450/2016.0123-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/26/2016] [Indexed: 01/09/2023]
Abstract
BACKGROUND Rhesus (Rh) D antigen is the most important antigen in the Rh blood group system because of its strong immunogenicity. When RhD-negative individuals are exposed to RhD-positive blood, they may produce anti-D alloantibody, potentially resulting in delayed haemolytic transfusion reactions and Rh haemolytic disease of the foetus and newborn, which are difficult to treat. Inhibition of the binding of anti-D antibody with RhD antigens on the surface of red blood cells may effectively prevent immune haemolytic diseases. MATERIALS AND METHODS In this study, single-stranded (ss) DNA aptamers, specifically binding to anti-D antibodies, were selected via systematic evolution of ligands by exponential enrichment (SELEX) technology. After 14 rounds of selection, the purified ssDNA was sequenced using a Personal Genome Machine system. Haemagglutination inhibition assays were performed to screen aptamers for biological activity in terms of blocking antigen-antibody reactions: the affinity and specificity of the aptamers were also determined. RESULTS In addition to high specificity, the aptamers which were selected showed high affinity for anti-D antibodies with dissociation constant (Kd) values ranging from 51.46±14.90 to 543.30±92.59 nM. By the combined use of specific ssDNA aptamer 7 and auxiliary ssDNA aptamer 2, anti-D could be effectively neutralised at low concentrations of the aptamers. DISCUSSION Our results demonstrate that ssDNA aptamers may be a novel, promising strategy for the treatment of delayed haemolytic transfusion reactions and Rh haemolytic disease of the foetus and newborn.
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16
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Bo C, Wang C, Wei Y. Novel bis(5-methyltetrazolium)amine ligand-bonded stationary phase with reduced leakage of metal ions in immobilized metal affinity chromatography of proteins. Anal Bioanal Chem 2016; 408:7595-7605. [DOI: 10.1007/s00216-016-9826-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/14/2016] [Accepted: 07/22/2016] [Indexed: 11/29/2022]
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17
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Bartnicki F, Kowalska E, Pels K, Strzalka W. Imidazole-free purification of His3-tagged recombinant proteins using ssDNA aptamer-based affinity chromatography. J Chromatogr A 2015; 1418:130-139. [PMID: 26427325 DOI: 10.1016/j.chroma.2015.09.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 09/11/2015] [Accepted: 09/16/2015] [Indexed: 02/07/2023]
Abstract
Immobilized metal ion affinity chromatography (IMAC) is widely used for the purification of many different His6-tagged recombinant proteins. On the one hand, it is a powerful technique but on the other hand it has its disadvantages. In this report, we present the development of a unique ssDNA aptamer for the purification of His3-tagged recombinant proteins. Our study shows that stability of the His3-tag/H3T aptamer complex can be controlled by the sodium ion concentration. Based on this feature, we demonstrate that H3T aptamer resin was successfully employed for the purification of three out of four tested His3-tagged recombinant proteins from an E. coli total protein extract using imidazole-free buffers. Finally, we show that the purity of His3-tagged proteins is superior when purified with the help of the H3T aptamer in comparison with Ni-NTA resin.
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Affiliation(s)
- Filip Bartnicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Ewa Kowalska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Katarzyna Pels
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Wojciech Strzalka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
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