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Wang Q, Guo P, Cheng W, Liu Y, Zhang Y, Huo P, Feng S, Zhang W. An efficient and universal In silico screening strategy for acquisition of high-affinity Aptamer and its application in analytical utility. Talanta 2024; 269:125535. [PMID: 38091739 DOI: 10.1016/j.talanta.2023.125535] [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: 06/25/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024]
Abstract
Numerous aptamers against various targets have been identified through the technology of systematic evolution of ligands by exponential enrichment (SELEX), but the affinity of these aptamers are often insufficient due to the limitations of SELEX. Therefore, a more rational in silico screening strategy (ISS) was developed for efficient screening of high affinity aptamers, which took shape complementarity and thermodynamic stability into consideration. Neuron specific enolase (NSE), a tumor marker, was selected as the target molecule. In the screening process, three aptamer candidates with good shape complementarity, lower ΔG values, and higher ZDOCK scores were produced. The dissociation constant (Kd) of these candidates to NSE was determined to be 10.13 nM, 14.82 nM, and 2.76 nM, respectively. Each of them exhibited higher affinity to NSE than the parent aptamer (Kd = 23.83 nM). Finally, an antibody-free fluorescence aptasensor assay, based on the aptamer with the highest affinity, P-5C8G, was conducted, resulting in a limit of detection (LOD) value of 1.8 nM, which was much lower than the parental aptamer (P, LOD = 12.6 nM). The proposed ISS approach provided an efficient and universal strategy to improve the aptamer to have a high affinity and good analytical utility.
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Affiliation(s)
- Qionglin Wang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China
| | - Pengbo Guo
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China
| | - Weyland Cheng
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China
| | - Yuchun Liu
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China
| | - Yaodong Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China
| | - Peng Huo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Shubin Feng
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China.
| | - Wancun Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450018, China.
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Moradi M, Mohabatkar H, Behbahani M, Dini G. Application of G-quadruplex aptamer conjugated MSNs to deliver ampicillin for suppressing S. aureus biofilm on mice bone. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Yunussova N, Sypabekova M, Zhumabekova Z, Matkarimov B, Kanayeva D. A Novel ssDNA Aptamer Targeting Carcinoembryonic Antigen: Selection and Characterization. BIOLOGY 2022; 11:biology11101540. [PMID: 36290442 PMCID: PMC9598387 DOI: 10.3390/biology11101540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/20/2022]
Abstract
One of the major causes of a drastically shorter life expectancy and one of the most prevalent diseases in the world today is cancer. Given the data on the rise in cancer cases throughout the world, it is obvious that, despite the diagnostic techniques currently being used, there is a pressing need to develop precise and sensitive techniques for early diagnosis of the disease. A high degree of affinity and specificity towards particular targets is maintained by the short nucleic acid molecules known as aptamers. Aptamers outperform antibodies due to their unique benefits, such as their simplicity in synthesis and modification, lack of toxicity, and long-term stability. Utilizing an accurate recognition element and a robust signal transduction mechanism, molecular diagnostics can be extremely sensitive and specific. In this study, development of new single-stranded DNA aptamers against CEA for use in cancer diagnostics was accomplished using SELEX and NGS methods. As a result of 12 iterative SELEX rounds, nine aptamer candidates against CEA were developed. NGS comparative analysis revealed that round twelve had an enriched number of aptamers that were specifically bound, as opposed to round eight. Among the selected nine sequences characterized by bioinformatics analysis and ELONA, an aptamer sequence with the highest specificity and affinity for the target protein was identified and further examined. Aptamer sequence (6) was screened in a concentration-dependent assay, specificity analysis was performed, and its potential secondary and tertiary structures were predicted, which enabled us to test one of the possible putative interactions with CEA. Finally, aptamer sequence (6) labelled with a Cy5 fluorescent tag was used in confocal microscopy to observe its binding towards the CEA expressed in HT-29 human colon adenocarcinoma cell line.
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Affiliation(s)
- Nigara Yunussova
- Ph.D. Program in Life Sciences, Nazarbayev University, 53 Kabanbay Batyr Ave., Astana 010000, Kazakhstan
| | - Marzhan Sypabekova
- National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Ave., Astana 010000, Kazakhstan
| | - Zhazira Zhumabekova
- M.Sc. Program in Biological Sciences, Nazarbayev University, 53 Kabanbay Batyr Ave., Astana 010000, Kazakhstan
| | - Bakhyt Matkarimov
- National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Ave., Astana 010000, Kazakhstan
| | - Damira Kanayeva
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, 53 Kabanbay Batyr Ave., Astana 010000, Kazakhstan
- Correspondence:
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Bimetallic organic framework Cu/UiO-66 mediated "fluorescence turn-on" method for ultrasensitive and rapid detection of carcinoembryonic antigen (CEA). Anal Chim Acta 2021; 1183:339000. [PMID: 34627512 DOI: 10.1016/j.aca.2021.339000] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/22/2021] [Accepted: 08/26/2021] [Indexed: 12/28/2022]
Abstract
Carcinoembryonic antigen (CEA) is a key serum tumor marker which is overexpressed in all types of adenocarcinomas. Therefore, establish the ultrasensitive, accurate and rapid method for CEA detection is essential for reducing the mortality of cancer. Here, a bimetallic organic framework Cu/UiO-66 was synthesized through the simple two-step hydrothermal method and used to construct a "fluorescence turn-on" analytical method for CEA detection. Cu/UiO-66 can adsorb CEA aptamers modified with FAM (CEA/FAM-Apt) and take place photoinduced electron transfer (PET) between Cu/UiO-66 and FAM, resulting in the fluorescence of the FAM is quenched. When CEA is present, CEA and CEA/FAM-Apt are tightly combined, making CEA/FAM-Apt far away from the Cu/UiO-66 surface. As a result, the fluorescence intensity of the system was significantly restored. Under optimal conditions, the proposed "fluorescence turn-on" method can detect CEA as low as 0.01 ng mL-1 in a range of 0.01-0.3 ng mL-1. Besides, this analytical method owns good selectivity, reproducibility and serum applicability, which provides a new platform for the direct detection of clinical diagnosis-related markers.
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Behbahani M, Mohabatkar H, Hosseini B. In silico design of quadruplex aptamers against the spike protein of SARS-CoV-2. INFORMATICS IN MEDICINE UNLOCKED 2021; 26:100757. [PMID: 34664030 PMCID: PMC8514331 DOI: 10.1016/j.imu.2021.100757] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022] Open
Abstract
Nucleic acid aptamers are short sequences of nucleic acid ligands that bind to a specific target molecule. Aptamers are experimentally nominated using the well-designed SELEX (systematic evolution of ligands by exponential enrichment) method. Here, we designed a new method for diagnosis and blocking SARS-CoV-2 based on G-quadruplex aptamer. This aptamer was developed against the receptor-binding domain (RBD) region of the spike protein. In the current study, ten quadruplex DNA aptamers entitled AP1, AP2, AP3, AP4, AP5, AP6, AP7, AP8, AP9, and AP10 were designed in silico and had high HADDOCK scores. One quadruplex aptamer sequence (AP1) was selected based on the interaction with RBD of SARS-CoV-2. Results showed that AP1 aptamer could be used as an agent in the diagnosis and therapy of SARS-CoV-2, although more works are still needed.
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Affiliation(s)
- Mandana Behbahani
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jareeb St., Isfahan, 81746-73441, Iran
| | - Hassan Mohabatkar
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jareeb St., Isfahan, 81746-73441, Iran
| | - Barumand Hosseini
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jareeb St., Isfahan, 81746-73441, Iran
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In silico approach for Post-SELEX DNA aptamers: A mini-review. J Mol Graph Model 2021; 105:107872. [PMID: 33765525 DOI: 10.1016/j.jmgm.2021.107872] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 02/07/2023]
Abstract
Aptamers are short oligonucleotides that possess high specificity and affinity against their target. Generated via Systematic Evolution of Ligands by Exponential Enrichment, (SELEX) in vitro, they were screened and enriched. This review covering the study utilizing bioinformatics tools to analyze primary sequence, secondary and tertiary structure prediction, as well as docking simulation for various aptamers and their ligand interaction. Literature was pooled from Web of Science (WoS) and Scopus databases until December 18, 2020 using specific search string related to DNA aptamers, in silico, structure prediction, and docking simulation. Out of 330 published articles, 38 articles were assessed in the analysis based on the predefined inclusion and exclusion criteria. It was found that Mfold and RNA Composer web server is the most popular tool in secondary and tertiary structure prediction of DNA aptamers, respectively. Meanwhile, in docking simulation, ZDOCK and AutoDock are preferred to analyze binding interaction in the aptamer-ligand complex. This review reports a brief framework of recent developments of in silico approaches that provide predictive structural information of ssDNA aptamer.
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Khoshbin Z, Housaindokht MR, Izadyar M, Bozorgmehr MR, Verdian A. Recent advances in computational methods for biosensor design. Biotechnol Bioeng 2020; 118:555-578. [PMID: 33135778 DOI: 10.1002/bit.27618] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/25/2020] [Accepted: 10/29/2020] [Indexed: 01/20/2023]
Abstract
Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost-effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast-growing field of biomedicine and biotechnology branches. Experimental efforts have led to valuable successes in the field of biosensor design; however, some deficiencies restrict their utilization for this purpose. Computational design of biosensors is introduced as a promising key to eliminate the gap. A set of reliable structure prediction of the biosensor segments, their stability, and accurate descriptors of molecular interactions are required to computationally design biosensors. In this review, we provide a comprehensive insight into the progress of computational methods to guide the design and development of biosensors, including molecular dynamics simulation, quantum mechanics calculations, molecular docking, virtual screening, and a combination of them as the hybrid methodologies. By relying on the recent advances in the computational methods, an opportunity emerged for them to be complementary or an alternative to the experimental methods in the field of biosensor design.
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Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Izadyar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
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Nur Topkaya S, Cetin AE. Electrochemical Aptasensors for Biological and Chemical Analyte Detection. ELECTROANAL 2020. [DOI: 10.1002/elan.202060388] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Seda Nur Topkaya
- Izmir Katip Celebi University Faculty of Pharmacy, Department of Analytical Chemistry 35620, Cigli Izmir TURKEY
| | - Arif E. Cetin
- Izmir Biomedicine and Genome Center 35330, Balcova Izmir TURKEY
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Navien TN, Thevendran R, Hamdani HY, Tang TH, Citartan M. In silico molecular docking in DNA aptamer development. Biochimie 2020; 180:54-67. [PMID: 33086095 DOI: 10.1016/j.biochi.2020.10.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/23/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022]
Abstract
Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that exhibit binding affinity and specificity against a wide variety of target molecules. Compared to RNA aptamers, DNA aptamers are much more stable and therefore are widely adopted in a number of applications especially in diagnostics. The tediousness and rigor associated with certain steps of the SELEX intensify the efforts to adopt in silico molecular docking approaches together with in vitro SELEX procedures in developing DNA aptamers. Inspired by these endeavors, we carry out an overview of the in silico molecular docking approaches in DNA aptamer generation, by detailing the stepwise procedures as well as shedding some light on the various softwares used. The in silico maturation strategy and the limitations of the in silico approaches are also underscored.
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Affiliation(s)
- Tholasi Nadhan Navien
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Ramesh Thevendran
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Hazrina Yusof Hamdani
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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Construction of electrochemical aptasensor of carcinoembryonic antigen based on toehold-aided DNA recycling signal amplification. Bioelectrochemistry 2020; 133:107492. [PMID: 32120323 DOI: 10.1016/j.bioelechem.2020.107492] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 01/20/2023]
Abstract
Carcinoembryonic antigen (CEA), serves as a broad-spectrum tumor marker, and plays an important role in reflecting the existence, therapeutic evaluation, development, monitoring and prognosis of many types of cancer. An electrochemical aptasensor was designed for CEA detection based on toehold-aided DNA recycling. A partially hybridized Probe-4 (i.e. P2/P3/P4) was self-assembled on the surface of a gold electrode serving as the sensing platform. For CEA detection, CEA can bind with aptamer and free probe-1 (P1) can hybridize with P4, triggering toehold-aided DNA recycling. This enables the hybridization of more probe-5 (P5) (labeled with methylene blue (MB)) with P4, causing more methylene blue (MB) to be brought close to the electrode surface. An amplified current signal was thus generated due to more MB in the electrode surface. The proposed design showed good linearity between current response and log CEA concentration ranging from 0.1 to 50 ng·mL-1, with a detection limit of 20 pg mL-1. This aptasensor also showed high specificity for CEA detection, and was successfully used in spiked biological samples.
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