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Aslan Y, Atabay M, Chowdhury HK, Göktürk I, Saylan Y, Inci F. Aptamer-Based Point-of-Care Devices: Emerging Technologies and Integration of Computational Methods. BIOSENSORS 2023; 13:bios13050569. [PMID: 37232930 DOI: 10.3390/bios13050569] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
Recent innovations in point-of-care (POC) diagnostic technologies have paved a critical road for the improved application of biomedicine through the deployment of accurate and affordable programs into resource-scarce settings. The utilization of antibodies as a bio-recognition element in POC devices is currently limited due to obstacles associated with cost and production, impeding its widespread adoption. One promising alternative, on the other hand, is aptamer integration, i.e., short sequences of single-stranded DNA and RNA structures. The advantageous properties of these molecules are as follows: small molecular size, amenability to chemical modification, low- or nonimmunogenic characteristics, and their reproducibility within a short generation time. The utilization of these aforementioned features is critical in developing sensitive and portable POC systems. Furthermore, the deficiencies related to past experimental efforts to improve biosensor schematics, including the design of biorecognition elements, can be tackled with the integration of computational tools. These complementary tools enable the prediction of the reliability and functionality of the molecular structure of aptamers. In this review, we have overviewed the usage of aptamers in the development of novel and portable POC devices, in addition to highlighting the insights that simulations and other computational methods can provide into the use of aptamer modeling for POC integration.
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Affiliation(s)
- Yusuf Aslan
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Maryam Atabay
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Hussain Kawsar Chowdhury
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Ilgım Göktürk
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Yeşeren Saylan
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Fatih Inci
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
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2
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A Polyclonal Aptamer Library for the Specific Binding of the Gut Bacterium Roseburia intestinalis in Mixtures with Other Gut Microbiome Bacteria and Human Stool Samples. Int J Mol Sci 2022; 23:ijms23147744. [PMID: 35887092 PMCID: PMC9317077 DOI: 10.3390/ijms23147744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 02/07/2023] Open
Abstract
Roseburia intestinalis has received attention as a potential probiotic bacterium. Recent studies have demonstrated that changes in its intestinal abundance can cause various diseases, such as obesity, enteritis and atherosclerosis. Probiotic administration or fecal transplantation alter the structure of the intestinal flora, offering possibilities for the prevention and treatment of these diseases. However, current monitoring methods, such as 16S rRNA sequencing, are complex and costly and require specialized personnel to perform the tests, making it difficult to continuously monitor patients during treatment. Hence, the rapid and cost-effective quantification of intestinal bacteria has become an urgent problem to be solved. Aptamers are of emerging interest because their stability, low immunogenicity and ease of modification are attractive properties for a variety of applications. We report a FluCell-SELEX polyclonal aptamer library specific for R. intestinalis isolated after seven evolution rounds, that can bind and label this organism for fluorescence microscopy and binding assays. Moreover, R. intestinalis can be distinguished from other major intestinal bacteria in complex defined mixtures and in human stool samples. We believe that this preliminary evidence opens new avenues towards aptamer-based electronic biosensors as new powerful and inexpensive diagnostic tools for the relative quantitative monitoring of R. intestinalis in gut microbiomes.
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3
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Bialy RM, Mainguy A, Li Y, Brennan JD. Functional nucleic acid biosensors utilizing rolling circle amplification. Chem Soc Rev 2022; 51:9009-9067. [DOI: 10.1039/d2cs00613h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.
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Affiliation(s)
- Roger M. Bialy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Alexa Mainguy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Yingfu Li
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D. Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
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4
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Ajamgard M, Sardroodi JJ, Ebrahimzadeh AR, Kamelabad MR. Molecular dynamics simulation study of gold nanosheet as drug delivery vehicles for anti-HIV-1 aptamers. Comput Biol Chem 2021; 95:107595. [PMID: 34739903 DOI: 10.1016/j.compbiolchem.2021.107595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/25/2021] [Accepted: 10/21/2021] [Indexed: 11/15/2022]
Abstract
The adsorption process of three aptamers with gold nanosheet (GNS) as a drug carrier has been investigated with the help of molecular dynamics simulations. The sequencing of the considered aptamers are as (CUUCAUUGUAACUUCUCAUAAUUUCCCGAGGCUUUUACUUUCGGGGUCCU) and (CCGGGUCGUCCCCUACGGGGACUAAAGACUGUGUCCAACCGCCCUCGCCU) for AP1 and AP2, respectively. AP3 is a muted version of AP1 in which nucleotide positions 4, 6, 18, 28 and 39 have C4A, U6G, A18G, G28A, and U39C mutations. At positions 24, and 40, a deletion mutation is seen to eliminate U24 and U40 bases. These aptamers are inhibitors for HIV-1 protease and can be candidates as potential pharmaceutics for treatment of AIDS in the future. The interactions between considered aptamers and GNS have been analyzed in detail with help of structural and energetic properties. These analyses showed that all three aptamers could well adsorb on GNS. Overall, the final results show that the adsorption of AP2 on the GNS is more favorable than other considered ones and consequently GNS can be considered as a device in order to immobilize these aptamers.
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Affiliation(s)
- Marzieh Ajamgard
- Molecular Simulation Laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran; Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran; Molecular Sciences and Engineering Research Group (MSERG), Iran
| | - Jaber Jahanbin Sardroodi
- Molecular Simulation Laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran; Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran; Molecular Sciences and Engineering Research Group (MSERG), Iran.
| | - Alireza Rastkar Ebrahimzadeh
- Molecular Simulation Laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran; Department of Physics, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran; Molecular Sciences and Engineering Research Group (MSERG), Iran
| | - Mahrokh Rezaei Kamelabad
- Molecular Simulation Laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran; Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran; Molecular Sciences and Engineering Research Group (MSERG), Iran
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5
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Recent Advancements in Aptamer-Based Surface Plasmon Resonance Biosensing Strategies. BIOSENSORS-BASEL 2021; 11:bios11070233. [PMID: 34356703 PMCID: PMC8301862 DOI: 10.3390/bios11070233] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022]
Abstract
Surface plasmon resonance (SPR) can track molecular interactions in real time, and is a powerful as well as widely used biological and chemical sensing technique. Among the different SPR-based sensing applications, aptamer-based SPR biosensors have attracted significant attention because of their simplicity, feasibility, and low cost for target detection. Continuous developments in SPR aptasensing research have led to the emergence of abundant technical and design concepts. To understand the recent advances in SPR for biosensing, this paper reviews SPR-based research from the last seven years based on different sensing-type strategies and sub-directions. The characteristics of various SPR-based applications are introduced. We hope that this review will guide the development of SPR aptamer sensors for healthcare.
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Zhang XH, Wang W, Chen X. Selection and identification of an ssDNA aptamer to NB4 cell. J Clin Lab Anal 2021; 35:e23718. [PMID: 33522630 PMCID: PMC8059720 DOI: 10.1002/jcla.23718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 01/09/2021] [Accepted: 01/15/2021] [Indexed: 11/17/2022] Open
Abstract
This study was to find the aptamers with high affinity and specificity binding to acute promyelocytic leukemia (APL) NB4 cell line. These aptamers targeted NB4 cells were selected from a random single‐stranded DNA (ssDNA) library of systematic evolution of ligands by exponential enrichment (CELL‐SELEX). The binding rate of FITC‐ssDNA library and NB4 cells was monitored using flow cytometry and fluorescence microscope. After cloned and sequenced, the structure, specificity, and affinity of these candidate aptamers were further analyzed. After a total of 19 rounds of selection, the ssDNA library was enriched and the BR (19.9%) of the 16th round was 12 times of the first round (1.6%). Three enriched aptamers were obtained from 21 positive clones of the 16th round, and the predicted secondary structures of these aptamers were mainly stem‐loop. The aptamer CX9 had the highest affinity, and the equilibrium dissociation constant (Kd) was 16.2 nM. The fluorescence intensity of CX9 binding to NB4 cells was stronger than HL60 and K562 cells under fluorescence microscopy. The study indicates that aptamer CX9 exhibits high affinity and specificity with NB4 cells and lay a foundation for the rapid diagnostic method to detect APL with fluorescence‐labeled aptamer.
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Affiliation(s)
- Xian-Hui Zhang
- Department of Laboratory Medicine, Children's Hospital of Shanxi Province, Taiyuan, China
| | - Wei Wang
- Department of Laboratory Medicine, Shanxi Provincial People's Hospital, Taiyuan, China
| | - Xin Chen
- Department of Laboratory Medicine, The 908th Hospital of Chinese PLA Joint Logistics Support Force, Nanchang, China
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7
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Selection and identification of diethylstilbestrol-specific aptamers based on magnetic-bead SELEX. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105354] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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8
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Mayo ML, Eberly JO, Crocker FH, Indest KJ. Modeling a synthetic aptamer-based riboswitch biosensor sensitive to low hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) concentrations. PLoS One 2020; 15:e0241664. [PMID: 33253235 PMCID: PMC7703952 DOI: 10.1371/journal.pone.0241664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/19/2020] [Indexed: 11/18/2022] Open
Abstract
RNA aptamers are relatively short nucleic acid sequences that bind targets with high affinity, and when combined with a riboswitch that initiates translation of a fluorescent reporter protein, can be used as a biosensor for chemical detection in various types of media. These processes span target binding at the molecular scale to fluorescence detection at the macroscale, which involves a number of intermediate rate-limiting physical (e.g., molecular conformation change) and biochemical changes (e.g., reaction velocity), which together complicate assay design. Here we describe a mathematical model developed to aid environmental detection of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) using the DsRed fluorescent reporter protein, but is general enough to potentially predict fluorescence from a broad range of water-soluble chemicals given the values of just a few kinetic rate constants as input. If we expose a riboswitch test population of Escherichia coli bacteria to a chemical dissolved in media, then the model predicts an empirically distinct, power-law relationship between the exposure concentration and the elapsed time of exposure. This relationship can be used to deduce an exposure time that meets or exceeds the optical threshold of a fluorescence detection device and inform new biosensor designs.
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Affiliation(s)
- Michael L. Mayo
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, United States of America
- * E-mail:
| | - Jed O. Eberly
- Central Agricultural Research Center, Montana State University, Moccasin, MT, United States of America
| | - Fiona H. Crocker
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, United States of America
| | - Karl J. Indest
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, United States of America
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9
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Han Y, Yang W, Luo X, He X, Zhao H, Tang W, Yue T, Li Z. Carbon dots based ratiometric fluorescent sensing platform for food safety. Crit Rev Food Sci Nutr 2020; 62:244-260. [PMID: 32876496 DOI: 10.1080/10408398.2020.1814197] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Food safety has become a major global concern and the rapid detection of food nutritional ingredients and contaminants has aroused much more attention. Nanomaterials-based fluorescent sensing holds great potential in designing highly sensitive and selective detection strategies for food safety analysis. Carbon dots (CDs) possess tremendous prospects in fluorescent sensing food ingredients and contaminants due to their superior properties of chemical and photostability, highly fluorescence with tunability, and no/low-toxicity. Numerous endeavors are demanded to contribute to overcoming the challenge of lower sensitivity and selectivity of the sensors interfered by various components in intricate food matrices to ensure food safety and human health. Nanohybrid CDs based ratiometric fluorescent sensing with self-calibration is regarded as an efficient strategy for the CDs based sensors for the specific recognition of target analyte in the food matrices. This work is devoted to reviewing the development of nanohybrid CDs based ratiometric fluorescent sensing platform and the perspectives of the platform for food safety. The applications of nanohybrid CDs in sensing are summarized and the sensing mechanisms are briefly discussed.
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Affiliation(s)
- Yong Han
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Weixia Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Xueli Luo
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Xie He
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Haiping Zhao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Wenzhi Tang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China.,Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, Shaanxi, PR China
| | - Zhonghong Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China.,Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, Shaanxi, PR China
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10
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Ajamgard M, Sardroodi JJ, Ebrahimzadeh AR. A Molecular Dynamics Study of the Inhibition of Monomeric HIV‐1 Protease as An Alternative to Overcome Drug Resistance by RNA Aptamers as A Therapeutic Tool. ChemistrySelect 2020. [DOI: 10.1002/slct.202000990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Marzieh Ajamgard
- Department of ChemistryFaculty of Basic SciencesAzarbaijan Shahid Madani University Tabriz Iran
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11
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Mutreja R, Baba SA, Navani NK. Nucleic Acid Aptamers as Emerging Tools for Diagnostics and Theranostics. Methods Mol Biol 2020; 2054:201-221. [PMID: 31482458 DOI: 10.1007/978-1-4939-9769-5_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aptamers are ssDNA or RNA sequences (20-80 nucleotides) generated in vitro by SELEX (Systematic Evolution of Ligands using EXponential enrichment) against diverse range of targets from small molecules to bacteria, viruses, and even eukaryotic cells. Aptamers, also known as chemical bodies, bind to their respective targets with tunable affinity and specificity, making aptamers as potent probes for diagnostics and excellent ligands for drug delivery in therapeutics. In this chapter, we have described the methods for generating DNA aptamers against proteins and their use in theranostics.
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Affiliation(s)
- Ruchi Mutreja
- Chemical Biology Lab, Department of Biotechnology, Indian Institute of Technology, Roorkee, Roorkee, India
| | - Shahnawaz Ahmad Baba
- Chemical Biology Lab, Department of Biotechnology, Indian Institute of Technology, Roorkee, Roorkee, India
| | - Naveen Kumar Navani
- Chemical Biology Lab, Department of Biotechnology, Indian Institute of Technology, Roorkee, Roorkee, India.
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12
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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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13
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Yesselman JD, Eiler D, Carlson ED, Gotrik MR, d'Aquino AE, Ooms AN, Kladwang W, Carlson PD, Shi X, Costantino DA, Herschlag D, Lucks JB, Jewett MC, Kieft JS, Das R. Computational design of three-dimensional RNA structure and function. NATURE NANOTECHNOLOGY 2019; 14:866-873. [PMID: 31427748 PMCID: PMC7324284 DOI: 10.1038/s41565-019-0517-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 06/24/2019] [Indexed: 05/30/2023]
Abstract
RNA nanotechnology seeks to create nanoscale machines by repurposing natural RNA modules. The field is slowed by the current need for human intuition during three-dimensional structural design. Here, we demonstrate that three distinct problems in RNA nanotechnology can be reduced to a pathfinding problem and automatically solved through an algorithm called RNAMake. First, RNAMake discovers highly stable single-chain solutions to the classic problem of aligning a tetraloop and its sequence-distal receptor, with experimental validation from chemical mapping, gel electrophoresis, solution X-ray scattering and crystallography with 2.55 Å resolution. Second, RNAMake automatically generates structured tethers that integrate 16S and 23S ribosomal RNAs into single-chain ribosomal RNAs that remain uncleaved by ribonucleases and assemble onto messenger RNA. Third, RNAMake enables the automated stabilization of small-molecule binding RNAs, with designed tertiary contacts that improve the binding affinity of the ATP aptamer and improve the fluorescence and stability of the Spinach RNA in cell extracts and in living Escherichia coli cells.
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Affiliation(s)
- Joseph D Yesselman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Eiler
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | - Erik D Carlson
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Michael R Gotrik
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Anne E d'Aquino
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
| | - Alexandra N Ooms
- Department of Cancer Genetics & Genomics, Stanford University School of Medicine, Stanford, CA, USA
| | - Wipapat Kladwang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul D Carlson
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Xuesong Shi
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - David A Costantino
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemistry, Stanford University School of Medicine, Stanford, CA, USA
- Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University, Stanford, CA, USA
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Physics, Stanford University, Stanford, CA, USA.
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14
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Proximity ligation assay induced hairpin to DNAzyme structure switching for entropy-driven amplified detection of thrombin. Anal Chim Acta 2019; 1064:104-111. [DOI: 10.1016/j.aca.2019.03.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/02/2019] [Accepted: 03/04/2019] [Indexed: 12/31/2022]
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15
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Eberly JO, Mayo ML, Carr MR, Crocker FH, Indest KJ. Detection of hexahydro-1,3-5-trinitro-1,3,5-triazine (RDX) with a microbial sensor. J GEN APPL MICROBIOL 2019; 65:145-150. [PMID: 30700648 DOI: 10.2323/jgam.2018.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Explosives such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) are common contaminants found in soil and groundwater at military facilities worldwide, but large-scale monitoring of these contaminants at low concentrations is difficult. Biosensors that incorporate aptamers with high affinity and specificity for a target are a novel way of detecting these compounds. This work describes novel riboswitch-based biosensors for detecting RDX. The performance of the RDX riboswitch was characterized in Escherichia coli using a range of RDX concentrations from 0-44 μmol l-1. Fluorescence was induced at RDX concentrations as low as 0.44 μmol l-1. The presence of 4.4 μmol l-1 RDX induced an 8-fold increase in fluorescence and higher concentrations did not induce a statistically significant increase in response.
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Affiliation(s)
- Jed O Eberly
- U.S. Army Engineer Research and Development Center, Environmental Laboratory.,Montana State University, Central Ag Research Center
| | - Michael L Mayo
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Matthew R Carr
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Fiona H Crocker
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Karl J Indest
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
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16
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Hirose K, Tsuchida M, Asakura H, Wakui K, Yoshimoto K, Iida K, Sato M, Shibukawa M, Suganuma M, Saito S. A single-round selection of selective DNA aptamers for mammalian cells by polymer-enhanced capillary transient isotachophoresis. Analyst 2018; 142:4030-4038. [PMID: 28875191 DOI: 10.1039/c7an00909g] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A single-round DNA aptamer selection for mammalian cells was successfully achieved for the first time using a capillary electrophoresis (CE)-based methodology called polymer-enhanced capillary transient isotachophoresis (PectI). The PectI separation yielded a single peak for the human lung cancer cell line (PC-9) complexed with DNA aptamer candidates, which was effectively separated from a free randomized DNA library peak, ensuring no contamination from free DNA in the PC-9-DNA aptamer complex fraction. The DNA aptamer candidates obtained after a single-round selection employing counter selection with HL-60 were proven to bind selectively and form kinetically stable complexes with PC-9 cells. Interestingly, most aptamer candidates showed high binding ability (Kd = 70-350 nM) with different extents of binding on the cell surface. These facts proved that a single-round selection for mammalian cells by PectI is feasible to obtain various types of aptamer candidates, which have high-affinity even for non-overexpressed but unique targets on the cell surface in addition to overexpressed targets.
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Affiliation(s)
- Kazuki Hirose
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan.
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17
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Saha S, Hetzke T, Prisner TF, Sigurdsson ST. Noncovalent spin-labeling of RNA: the aptamer approach. Chem Commun (Camb) 2018; 54:11749-11752. [PMID: 30276367 DOI: 10.1039/c8cc05597a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the first example of site-directed spin-labeling of unmodified RNA, a pyrrolidine-nitroxide derivative of tetramethylrosamine (TMR) was shown to bind with high affinity to the malachite green (MG) aptamer, as determined by continuous-wave (CW) electron paramagnetic resonance (EPR), pulsed electron-electron double resonance (PELDOR) and fluorescence spectroscopies.
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Affiliation(s)
- Subham Saha
- Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland.
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18
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Kaur H, Bruno JG, Kumar A, Sharma TK. Aptamers in the Therapeutics and Diagnostics Pipelines. Theranostics 2018; 8:4016-4032. [PMID: 30128033 PMCID: PMC6096388 DOI: 10.7150/thno.25958] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/16/2018] [Indexed: 12/17/2022] Open
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides that can selectively bind to small molecular ligands or protein targets with high affinity and specificity, by acquiring unique three-dimensional structures. Aptamers have the advantage of being highly specific, relatively small in size, non-immunogenic and can be easily stabilized by chemical modifications, thus allowing expansion of their diagnostic and therapeutic potential. Since the invention of aptamers in the early 1990s, great efforts have been made to make them clinically relevant for diseases like macular degeneration, cancer, thrombosis and inflammatory diseases. Furthermore, owing to the aforementioned advantages and unique adaptability of aptamers to point-of-care platforms, aptamer technology has created a stable niche in the field of in vitro diagnostics by enhancing the speed and accuracy of diagnoses. The aim of this review is to give an overview on aptamers, highlight the inherent therapeutic and diagnostic opportunities and challenges associated with them and present various aptamers that have reached therapeutic clinical trials, diagnostic markets or that have immediate translational potential for therapeutics and diagnostics applications.
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Affiliation(s)
| | - John G. Bruno
- Operational Technologies Corporation, 4100 NW Loop 410, Suite 100, San Antonio, Texas 78229, USA
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Tarun Kumar Sharma
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute (THSTI), Faridabad-121001, Haryana, India
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19
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Kalra P, Dhiman A, Cho WC, Bruno JG, Sharma TK. Simple Methods and Rational Design for Enhancing Aptamer Sensitivity and Specificity. Front Mol Biosci 2018; 5:41. [PMID: 29868605 PMCID: PMC5966647 DOI: 10.3389/fmolb.2018.00041] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/13/2018] [Indexed: 12/27/2022] Open
Abstract
Aptamers are structured nucleic acid molecules that can bind to their targets with high affinity and specificity. However, conventional SELEX (Systematic Evolution of Ligands by EXponential enrichment) methods may not necessarily produce aptamers of desired affinity and specificity. Thus, to address these questions, this perspective is intended to suggest some approaches and tips along with novel selection methods to enhance evolution of aptamers. This perspective covers latest novel innovations as well as a broad range of well-established approaches to improve the individual binding parameters (aptamer affinity, avidity, specificity and/or selectivity) of aptamers during and/or post-SELEX. The advantages and limitations of individual aptamer selection methods and post-SELEX optimizations, along with rational approaches to overcome these limitations are elucidated in each case. Further the impact of chosen selection milieus, linker-systems, aptamer cocktails and detection modules utilized in conjunction with target-specific aptamers, on the overall assay performance are discussed in detail, each with its own advantages and limitations. The simple variations suggested are easily available for facile implementation during and/or post-SELEX to develop ultrasensitive and specific assays. Finally, success studies of established aptamer-based assays are discussed, highlighting how they utilized some of the suggested methodologies to develop commercially successful point-of-care diagnostic assays.
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Affiliation(s)
- Priya Kalra
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India.,Faculty of Pharmacy, Uttarakhand Technical University, Dehradun, India
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - John G Bruno
- Operational Technologies Corporation, San Antonio, TX, United States
| | - Tarun K Sharma
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, India.,AptaBharat Innovation Private Limited, Translational Health Science and Technology Institute Incubator, Faridabad, India
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20
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Biondi E, Benner SA. Artificially Expanded Genetic Information Systems for New Aptamer Technologies. Biomedicines 2018; 6:E53. [PMID: 29747381 PMCID: PMC6027400 DOI: 10.3390/biomedicines6020053] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/04/2018] [Accepted: 05/06/2018] [Indexed: 01/04/2023] Open
Abstract
Directed evolution was first applied to diverse libraries of DNA and RNA molecules a quarter century ago in the hope of gaining technology that would allow the creation of receptors, ligands, and catalysts on demand. Despite isolated successes, the outputs of this technology have been somewhat disappointing, perhaps because the four building blocks of standard DNA and RNA have too little functionality to have versatile binding properties, and offer too little information density to fold unambiguously. This review covers the recent literature that seeks to create an improved platform to support laboratory Darwinism, one based on an artificially expanded genetic information system (AEGIS) that adds independently replicating nucleotide “letters” to the evolving “alphabet”.
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Affiliation(s)
- Elisa Biondi
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL 32615, USA.
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL 32615, USA.
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21
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Grijalvo S, Alagia A, Jorge AF, Eritja R. Covalent Strategies for Targeting Messenger and Non-Coding RNAs: An Updated Review on siRNA, miRNA and antimiR Conjugates. Genes (Basel) 2018; 9:E74. [PMID: 29415514 PMCID: PMC5852570 DOI: 10.3390/genes9020074] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 12/11/2022] Open
Abstract
Oligonucleotide-based therapy has become an alternative to classical approaches in the search of novel therapeutics involving gene-related diseases. Several mechanisms have been described in which demonstrate the pivotal role of oligonucleotide for modulating gene expression. Antisense oligonucleotides (ASOs) and more recently siRNAs and miRNAs have made important contributions either in reducing aberrant protein levels by sequence-specific targeting messenger RNAs (mRNAs) or restoring the anomalous levels of non-coding RNAs (ncRNAs) that are involved in a good number of diseases including cancer. In addition to formulation approaches which have contributed to accelerate the presence of ASOs, siRNAs and miRNAs in clinical trials; the covalent linkage between non-viral vectors and nucleic acids has also added value and opened new perspectives to the development of promising nucleic acid-based therapeutics. This review article is mainly focused on the strategies carried out for covalently modifying siRNA and miRNA molecules. Examples involving cell-penetrating peptides (CPPs), carbohydrates, polymers, lipids and aptamers are discussed for the synthesis of siRNA conjugates whereas in the case of miRNA-based drugs, this review article makes special emphasis in using antagomiRs, locked nucleic acids (LNAs), peptide nucleic acids (PNAs) as well as nanoparticles. The biomedical applications of siRNA and miRNA conjugates are also discussed.
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Affiliation(s)
- Santiago Grijalvo
- Institute of Advanced Chemistry of Catalonia (IQAC, CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Adele Alagia
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Andreia F Jorge
- Coimbra Chemistry Centre, (CQC), Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal.
| | - Ramon Eritja
- Institute of Advanced Chemistry of Catalonia (IQAC, CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
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22
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Yang KA, Chun H, Zhang Y, Pecic S, Nakatsuka N, Andrews AM, Worgall TS, Stojanovic MN. High-Affinity Nucleic-Acid-Based Receptors for Steroids. ACS Chem Biol 2017; 12:3103-3112. [PMID: 29083858 DOI: 10.1021/acschembio.7b00634] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Artificial receptors for hydrophobic molecules usually have moderate affinities and limited selectivities. We describe three new classes of high affinity hydrophobic receptors for nonaromatic steroids based on deoxyribonucleotides, obtained through five high stringency selections coupled with tailored counter-selections. The isolation of multiple classes of high affinity steroid receptors demonstrates the surprising breadth of moderately sized hydrophobic binding motifs (<40 nucleotides) available to natural nucleic acids. Studies of interactions with analogs indicate that two classes, four-way junctions and 4XGN motifs, comprise receptors with shapes that prevent binding of specific steroid conjugates used in counter-selections. Furthermore, they strongly prefer nonhydroxylated steroid cores, which is typical for hydrophobic receptors. The third new class accommodates hydroxyl groups in high-affinity, high-selectivity binding pockets, thus reversing the preferences of the first two classes. The high-affinity binding of aptamers to targets efficiently inhibits double-helix formation in the presence of the complementary oligonucleotides. The high affinity of some of these receptors and tailored elimination of binding through counter-selections ensures that these new aptamers will enable clinical chemistry applications.
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Affiliation(s)
| | - Hyosun Chun
- School
of Computer Science and Engineering, Seoul National University, Seoul 08826, Korea
| | | | | | - Nako Nakatsuka
- California
NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Anne M. Andrews
- California
NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, Los
Angeles, California 90095, United States
- Department
of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience
and Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles, Los Angeles, California 90095, United States
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23
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Liu Z, Zhang Y, Xie Y, Sun Y, Bi K, Cui Z, Zhao L, Fan W. An aptamer-based colorimetric sensor for streptomycin and its application in food inspection. Chem Res Chin Univ 2017. [DOI: 10.1007/s40242-017-7029-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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24
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Ignatov D, Johansson J. RNA-mediated signal perception in pathogenic bacteria. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28792118 DOI: 10.1002/wrna.1429] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/11/2017] [Accepted: 05/11/2017] [Indexed: 11/09/2022]
Abstract
Bacterial pathogens encounter several different environments during an infection, many of them possibly being detrimental. In order to sense its surroundings and adjust the gene expression accordingly, different regulatory schemes are undertaken. With these, the bacterium appropriately can differentiate between various environmental cues to express the correct virulence factor at the appropriate time and place. An attractive regulator device is RNA, which has an outstanding ability to alter its structure in response to external stimuli, such as metabolite concentration or alterations in temperature, to control its downstream gene expression. This review will describe the function of riboswitches and thermometers, with a particular emphasis on regulatory RNAs being important for bacterial pathogenicity. WIREs RNA 2017, 8:e1429. doi: 10.1002/wrna.1429 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Dmitriy Ignatov
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Jörgen Johansson
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
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25
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Das S, Purkayastha P. Selective Binding of Thioflavin T in Sequence-Exchanged Single Strand DNA Oligomers and Further Interaction with Phospholipid Membranes. ChemistrySelect 2017. [DOI: 10.1002/slct.201700194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shrabanti Das
- Department of Chemical Sciences; Indian Institute of Science Education and Research (IISER) Kolkata; Mohanpur 741246, WB India
| | - Pradipta Purkayastha
- Department of Chemical Sciences; Indian Institute of Science Education and Research (IISER) Kolkata; Mohanpur 741246, WB India
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26
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Jung IY, Kim JS, Choi BR, Lee K, Lee H. Hydrogel Based Biosensors for In Vitro Diagnostics of Biochemicals, Proteins, and Genes. Adv Healthc Mater 2017; 6. [PMID: 28371450 DOI: 10.1002/adhm.201601475] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/16/2017] [Indexed: 12/22/2022]
Abstract
Hydrogel-based biosensors have drawn considerable attention due to their various advantages over conventional detection systems. Recent studies have shown that hydrogel biosensors can be excellent alternative systems to detect a wide range of biomolecules, including small biochemicals, pathogenic proteins, and disease specific genes. Due to the excellent physical properties of hydrogels such as the high water content and stimuli-responsive behavior of cross-linked network structures, this system can offer substantial improvement for the design of novel detection systems for various diagnostic applications. The other main advantage of hydrogels is the role of biomimetic three-dimensional (3D) matrix immobilizing enzymes and aptamers within the detection systems, which enhances their stability. This provides ideal reaction conditions for enzymes and aptamers to interact with substrates within the aqueous environment of the hydrogel. In this review, we have highlighted various novel detection approaches utilizing the outstanding properties of the hydrogel. This review summarizes the recent progress of hydrogel-based biosensors and discusses their future perspectives and clinical limitations to overcome.
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Affiliation(s)
- Il Young Jung
- College of PharmacyGraduate School of Pharmaceutical SciencesEwha Womans University Seoul 03760 Republic of Korea
| | - Ji Su Kim
- College of PharmacyGraduate School of Pharmaceutical SciencesEwha Womans University Seoul 03760 Republic of Korea
| | - Bo Ram Choi
- College of PharmacyGraduate School of Pharmaceutical SciencesEwha Womans University Seoul 03760 Republic of Korea
| | - Kyuri Lee
- College of PharmacyGraduate School of Pharmaceutical SciencesEwha Womans University Seoul 03760 Republic of Korea
| | - Hyukjin Lee
- College of PharmacyGraduate School of Pharmaceutical SciencesEwha Womans University Seoul 03760 Republic of Korea
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27
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Warfield BM, Anderson PC. Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state. PLoS One 2017; 12:e0176229. [PMID: 28437473 PMCID: PMC5402969 DOI: 10.1371/journal.pone.0176229] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/08/2017] [Indexed: 11/18/2022] Open
Abstract
RNA aptamers are oligonucleotides that bind with high specificity and affinity to target ligands. In the absence of bound ligand, secondary structures of RNA aptamers are generally stable, but single-stranded and loop regions, including ligand binding sites, lack defined structures and exist as ensembles of conformations. For example, the well-characterized theophylline-binding aptamer forms a highly stable binding site when bound to theophylline, but the binding site is unstable and disordered when theophylline is absent. Experimental methods have not revealed at atomic resolution the conformations that the theophylline aptamer explores in its unbound state. Consequently, in the present study we applied 21 microseconds of molecular dynamics simulations to structurally characterize the ensemble of conformations that the aptamer adopts in the absence of theophylline. Moreover, we apply Markov state modeling to predict the kinetics of transitions between unbound conformational states. Our simulation results agree with experimental observations that the theophylline binding site is found in many distinct binding-incompetent states and show that these states lack a binding pocket that can accommodate theophylline. The binding-incompetent states interconvert with binding-competent states through structural rearrangement of the binding site on the nanosecond to microsecond timescale. Moreover, we have simulated the complete theophylline binding pathway. Our binding simulations supplement prior experimental observations of slow theophylline binding kinetics by showing that the binding site must undergo a large conformational rearrangement after the aptamer and theophylline form an initial complex, most notably, a major rearrangement of the C27 base from a buried to solvent-exposed orientation. Theophylline appears to bind by a combination of conformational selection and induced fit mechanisms. Finally, our modeling indicates that when Mg2+ ions are present the population of binding-competent aptamer states increases more than twofold. This population change, rather than direct interactions between Mg2+ and theophylline, accounts for altered theophylline binding kinetics.
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Affiliation(s)
- Becka M. Warfield
- Department of Physical Sciences, University of Washington, Bothell, Washington, United States of America
| | - Peter C. Anderson
- Department of Physical Sciences, University of Washington, Bothell, Washington, United States of America
- * E-mail:
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28
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Desrosiers A, Vallée-Bélisle A. Nature-inspired DNA switches: applications in medicine. Nanomedicine (Lond) 2017; 12:175-179. [DOI: 10.2217/nnm-2016-0349] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Arnaud Desrosiers
- Laboratory of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, Québec, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, Québec H3C 3J7, Canada
| | - Alexis Vallée-Bélisle
- Laboratory of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, Québec, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, Québec H3C 3J7, Canada
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29
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Mazumdar D, Lan T, Lu Y. "Dipstick" Colorimetric Detection of Metal Ions Based on Immobilization of DNAzyme and Gold Nanoparticles onto a Lateral Flow Device. Methods Mol Biol 2017; 1571:389-406. [PMID: 28281269 DOI: 10.1007/978-1-4939-6848-0_24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Real-time, on-site detection and quantification of different trace analytes is a challenge that requires both searching a general class of molecules to recognize a broad range of contaminants and translating this recognition to easily detectable signals. Functional nucleic acids, which include DNAzymes (DNA with catalytic activity) and aptamers (nucleic acids that bind an analyte), are ideal candidates for the target recognition. These nucleic acids can be selected by a combinatorial biology method called in vitro selection to interact with a particular analyte with high specificity and sensitivity. Furthermore, they can be incorporated into sensors by attaching signaling molecules. Due to the high extinction coefficients and distance-dependent optical properties, metallic nanoparticles such as the commonly used gold nanoparticles have been shown to be very attractive in converting analyte-specific functional DNA into colorimetric sensors. DNAzyme directed assembly of gold nanoparticles has been used to make colorimetric sensors for metal ions such as lead, uranium, and copper. To make the operation even easier and less vulnerable to operator's errors, dipstick tests have been constructed. Here, we describe protocols for the preparation of DNAzyme-linked gold nanoparticles (AuNP) that are then immobilized on to lateral flow devices to make easy-to-use dipstick tests for metal ions.
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Affiliation(s)
| | - Tian Lan
- Glucosentient Inc., 60 Hazelwood Drive, Champaign, IL, 61820, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, A 322 Chemical and Life Sciences Building, 600 S. Mathews Ave., Urbana, IL, 61801, USA.
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30
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Yoo CH, Jung S, Bae J, Kim G, Ihm J, Lee J. DNA aptamer release from the DNA-SWNT hybrid by protein recognition. Chem Commun (Camb) 2016; 52:2784-7. [PMID: 26763942 DOI: 10.1039/c5cc07726e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we show the formation of the complex between a DNA aptamer and a single-walled carbon nanotube (SWNT) and its reaction with its target protein. The aptamer, which is specifically bound with thrombin, the target protein in this study, easily wraps and disperses the SWNT by noncovalent π-π stacking.
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Affiliation(s)
- Chang-Hyuk Yoo
- School of Mechanical and Aerospace Engineering, Seoul National University, Seoul 151-742, Republic of Korea. and Inter-Semiconductor Research Center, Seoul National University, Seoul 151-742, Republic of Korea
| | - Seungwon Jung
- School of Mechanical and Aerospace Engineering, Seoul National University, Seoul 151-742, Republic of Korea. and Inter-Semiconductor Research Center, Seoul National University, Seoul 151-742, Republic of Korea and Center for Biomicrosystems, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
| | - Jaehyun Bae
- FPRD and Department of Physics and Astronomy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Gunn Kim
- Department of Physics, Sejong University, Seoul 143-747, Republic of Korea
| | - Jisoon Ihm
- FPRD and Department of Physics and Astronomy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Junghoon Lee
- School of Mechanical and Aerospace Engineering, Seoul National University, Seoul 151-742, Republic of Korea. and Inter-Semiconductor Research Center, Seoul National University, Seoul 151-742, Republic of Korea
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31
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Melaine F, Coilhac C, Roupioz Y, Buhot A. A nanoparticle-based thermo-dynamic aptasensor for small molecule detection. NANOSCALE 2016; 8:16947-16954. [PMID: 27714066 DOI: 10.1039/c6nr04868d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Small molecules (MW < 1000 Da) represent a large class of biomarkers of interest. Recently, a new class of biosensors has been emerging thanks to the recognition properties of aptamers, short DNA or RNA single strands, selected against such small molecular targets. Among them, an adenosine-specific aptamer has been largely described and used due to its remarkable affinity to this small target (KD = 6 μM). In this paper, we achieved the proof-of-principle of an aptasensor based on the thermodynamic follow-up of adenosine binding with engineered split-aptamer sequences. The detection is carried out by surface plasmon resonance imaging of split-aptamer micro-arrays, while signal amplification is ensured by gold nanoparticles (AuNPs). This original approach based on DNA sequence engineering and AuNP conjugation enabled us to reach limits of detection (LOD) 200 times lower than the KD measured in solution with the native aptamer (LOD = 30 nM).
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Affiliation(s)
- Feriel Melaine
- Université Grenoble Alpes, INAC, SPrAM, F-38000 Grenoble, France. and CEA, INAC, SPrAM, F-38000 Grenoble, France and CNRS, SPrAM, F-38000 Grenoble, France
| | - Clothilde Coilhac
- Université Grenoble Alpes, INAC, SPrAM, F-38000 Grenoble, France. and CEA, INAC, SPrAM, F-38000 Grenoble, France and CNRS, SPrAM, F-38000 Grenoble, France
| | - Yoann Roupioz
- Université Grenoble Alpes, INAC, SPrAM, F-38000 Grenoble, France. and CEA, INAC, SPrAM, F-38000 Grenoble, France and CNRS, SPrAM, F-38000 Grenoble, France
| | - Arnaud Buhot
- Université Grenoble Alpes, INAC, SPrAM, F-38000 Grenoble, France. and CEA, INAC, SPrAM, F-38000 Grenoble, France and CNRS, SPrAM, F-38000 Grenoble, France
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32
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Shen Q, Peng C, Zhan Y, Fan L, Wang M, Zhou Q, Liu J, Lv X, Tang Q, Li J, Huang X, Xia J. Aptamer-polymer functionalized silicon nanosubstrates for enhanced recovered circulating tumor cell viability and in vitro chemosensitivity testing. Int J Nanomedicine 2016; 11:2133-46. [PMID: 27274239 PMCID: PMC4876848 DOI: 10.2147/ijn.s103569] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Selection of the optimal chemotherapy regimen for an individual cancer patient is challenging. The existing chemosensitivity tests are costly, time-consuming, and not amenable to wide utilization within a clinic. This limitation might be addressed by the recently proposed use of circulating tumor cells (CTCs), which provide an opportunity to noninvasively monitor response to therapy. Over the past few decades, various techniques were developed to capture and recover CTCs, but these techniques were often limited by a capture and recovery performance tradeoff between high viability and high efficiency. In this work, we used anti-epithelial cell adhesion molecule coated aptamer–poly (N-isopropylacrylamide) functionalized silicon nanowire substrates to capture and release epithelial cell adhesion molecule-positive CTCs at 32°C and 4°C, respectively. Then, we applied the nuclease to digest the aptamer to release the captured CTCs (near or at the end of the polymer brush), which cannot be released by heating/cooling process. High viability and purity CTCs could be achieved by decreasing the heating/cooling cycles and enzymatic treatment rounds. Furthermore, the time-saving process is helpful to maintain the morphology and enhance vitality of the recovered CTCs and is beneficial to the subsequent cell culture in vitro. We validated the feasibility of chemosensitivity testing based on the recovered HCC827 cells using an adenosine triphosphate–tumor chemosensitivity assay, and the results suggested that our method can determine which agent and what concentration have the best chemosensitivity for the culturing recovered CTCs. So, the novel method capable of a highly effective capture and recovery of high viability CTCs will pave the way for chemosensitivity testing.
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Affiliation(s)
- Qinglin Shen
- Department of Oncology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China; Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Caixia Peng
- Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China; Central Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Yan Zhan
- Department of Oncology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Liang Fan
- Department of Oncology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Mengyi Wang
- Department of Oncology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Qing Zhou
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Jue Liu
- Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China; Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Xiaojuan Lv
- Department of Oncology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Qiu Tang
- Department of Oncology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Jun Li
- Department of Oncology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China; Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Xiaodong Huang
- Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Jiahong Xia
- Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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Leach JC, Wang A, Ye K, Jin S. A RNA-DNA Hybrid Aptamer for Nanoparticle-Based Prostate Tumor Targeted Drug Delivery. Int J Mol Sci 2016; 17:380. [PMID: 26985893 PMCID: PMC4813238 DOI: 10.3390/ijms17030380] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 12/03/2022] Open
Abstract
The side effects of radio- and chemo-therapy pose long-term challenges on a cancer patient’s health. It is, therefore, highly desirable to develop more effective therapies that can specifically target carcinoma cells without damaging normal and healthy cells. Tremendous efforts have been made in the past to develop targeted drug delivery systems for solid cancer treatment. In this study, a new aptamer, A10-3-J1, which recognizes the extracellular domain of the prostate specific membrane antigen (PSMA), was designed. A super paramagnetic iron oxide nanoparticle-aptamer-doxorubicin (SPIO-Apt-Dox) was fabricated and employed as a targeted drug delivery platform for cancer therapy. This DNA RNA hybridized aptamer antitumor agent was able to enhance the cytotoxicity of targeted cells while minimizing collateral damage to non-targeted cells. This SPIO-Apt-Dox nanoparticle has specificity to PSMA+ prostate cancer cells. Aptamer inhibited nonspecific uptake of membrane-permeable doxorubic to the non-target cells, leading to reduced untargeted cytotoxicity and endocytic uptake while enhancing targeted cytotoxicity and endocytic uptake. The experimental results indicate that the drug delivery platform can yield statistically significant effectiveness being more cytotoxic to the targeted cells as opposed to the non-targeted cells.
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Affiliation(s)
- John C Leach
- Department of Biomedical Engineering, College of Engineering, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Andrew Wang
- Ocean Nanotech, 2143 Worth Lane, Springdale, AR 72764, USA.
| | - Kaiming Ye
- Department of Biomedical Engineering, College of Engineering, University of Arkansas, Fayetteville, AR 72701, USA.
- Department of Biomedical Engineering, Thomas J. Watson School of Engineering and Applied Sciences, State University of New York in Binghamton, Binghamton, NY 13902, USA.
| | - Sha Jin
- Department of Biomedical Engineering, College of Engineering, University of Arkansas, Fayetteville, AR 72701, USA.
- Department of Biomedical Engineering, Thomas J. Watson School of Engineering and Applied Sciences, State University of New York in Binghamton, Binghamton, NY 13902, USA.
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Champanhac C, Teng IT, Cansiz S, Zhang L, Wu X, Zhoa Z, Fu T, Tan W. Development of a panel of DNA Aptamers with High Affinity for Pancreatic Ductal Adenocarcinoma. Sci Rep 2015; 5:16788. [PMID: 26603187 PMCID: PMC4658478 DOI: 10.1038/srep16788] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/09/2015] [Indexed: 12/12/2022] Open
Abstract
Pancreatic cancer costs nearly 40,000 lives in the U.S. each year and has one of the
lowest survival rates among cancers. Effective treatment of pancreatic ductal
adenocarcinoma is hindered by lack of a reliable biomarker. To address this
challenge, aptamers were selected by cell-SELEX (Systematic Evolution of Ligands by
EXponential enrichment) targeting human pancreatic ductal adenocarcinoma (PL45).
Five promising aptamers presenting low Kd values and good specificity
were generated. Among these five aptamers, one was tailored into a nanostructure
carrying a high drug payload for specific drug delivery. The results show a
viability of almost 80% for negative cells while only 50% of the target cells
remained alive after 48 h incubation. These results lead to the
conclusion that further research could reveal protein biomarkers specific to
pancreatic adenocarcinoma, with probes available for early detection.
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Affiliation(s)
- Carole Champanhac
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - I-Ting Teng
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Sena Cansiz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Liqin Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Xiaoqiu Wu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Zilong Zhoa
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Ting Fu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Weihong Tan
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, USA.,Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
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35
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Günay KA, Klok HA. Identification of Soft Matter Binding Peptide Ligands Using Phage Display. Bioconjug Chem 2015; 26:2002-15. [PMID: 26275106 DOI: 10.1021/acs.bioconjchem.5b00377] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Phage display is a powerful tool for the selection of highly affine, short peptide ligands. While originally primarily used for the identification of ligands to proteins, the scope of this technique has significantly expanded over the past two decades. Phage display nowadays is also increasingly applied to identify ligands that selectively bind with high affinity to a broad range of other substrates including natural and biological polymers as well as a variety of low-molecular-weight organic molecules. Such peptides are of interest for various reasons. The ability to selectively and with high affinity bind to the substrate of interest allows the conjugation or immobilization of, e.g., nanoparticles or biomolecules, or generally, facilitates interactions at materials interfaces. On the other hand, presentation of peptide ligands that selectively bind to low-molecular-weight organic materials is of interest for the development of sensor surfaces. The aim of this article is to highlight the opportunities provided by phage display for the identification of peptide ligands that bind to synthetic or natural polymer substrates or to small organic molecules. The article will first provide an overview of the different peptide ligands that have been identified by phage display that bind to these "soft matter" targets. The second part of the article will discuss the different characterization techniques that allow the determination of the affinity of the identified ligands to the respective substrates.
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Affiliation(s)
- Kemal Arda Günay
- École Polytechnique Fédérale de Lausanne (EPFL) , Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
| | - Harm-Anton Klok
- École Polytechnique Fédérale de Lausanne (EPFL) , Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
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36
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Vanschoenbeek K, Vanbrabant J, Hosseinkhani B, Vermeeren V, Michiels L. Aptamers targeting different functional groups of 17β-estradiol. J Steroid Biochem Mol Biol 2015; 147:10-6. [PMID: 25465478 DOI: 10.1016/j.jsbmb.2014.10.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/17/2014] [Accepted: 10/20/2014] [Indexed: 11/16/2022]
Abstract
Aptamers, short synthetic ssDNA or RNA molecules with a specific three-dimensional structure, are promising recognition elements in biosensor technology. In vitro generation of aptamers with high sensitivity and specificity toward a broad range of analytes has been achieved using the systematic evolution of ligands by exponential enrichment (SELEX) process. This iterative pathway of aptamer generation consists of sequential positive and counterselection steps. The present research aimed to select two sets of ssDNA aptamers which both are able to bind to different functional groups on the cyclopentanoperhydrophenanthrene ring of 17β-estradiol (E2). By repetitively switching between positive selection steps using E2 as target molecule and counterselection steps with nortestosterone as countermolecule, aptamers were successfully selected against the hydroxylated aromatic A ring of E2. Additionally, an aptamer which binds the upper segments of the B, C and D ring of the cyclopentanoperhydrophenanthrene ring of E2 was generated after repetitively swapping between positive selection steps with E2 as target molecule and counterselection steps with dexamethasone as countermolecule. Epitope specificity of the aptamers was demonstrated by evaluating their binding responses toward a number of steroid hormones structurally related to E2. The selected aptamers with affinities for different functional groups of E2 can potentially be applied to develop a cross-reactive aptasensor. This aptasensor introduces a promising tool for the future of in-field real-time monitoring of a wide range of steroid hormones.
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Affiliation(s)
| | - Jeroen Vanbrabant
- Hasselt University, BIOMED, Martelarenlaan 42, 3500 Hasselt, Belgium.
| | | | | | - Luc Michiels
- Hasselt University, BIOMED, Martelarenlaan 42, 3500 Hasselt, Belgium.
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37
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Anandhakumar C, Kizaki S, Bando T, Pandian GN, Sugiyama H. Advancing Small-Molecule-Based Chemical Biology with Next-Generation Sequencing Technologies. Chembiochem 2014; 16:20-38. [DOI: 10.1002/cbic.201402556] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Indexed: 12/24/2022]
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38
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Green NS, Norton ML. Interactions of DNA with graphene and sensing applications of graphene field-effect transistor devices: a review. Anal Chim Acta 2014; 853:127-142. [PMID: 25467454 DOI: 10.1016/j.aca.2014.10.023] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 10/11/2014] [Accepted: 10/14/2014] [Indexed: 02/06/2023]
Abstract
Graphene field-effect transistors (GFET) have emerged as powerful detection platforms enabled by the advent of chemical vapor deposition (CVD) production of the unique atomically thin 2D material on a large scale. DNA aptamers, short target-specific oligonucleotides, are excellent sensor moieties for GFETs due to their strong affinity to graphene, relatively short chain-length, selectivity, and a high degree of analyte variability. However, the interaction between DNA and graphene is not fully understood, leading to questions about the structure of surface-bound DNA, including the morphology of DNA nanostructures and the nature of the electronic response seen from analyte binding. This review critically evaluates recent insights into the nature of the DNA graphene interaction and its affect on sensor viability for DNA, small molecules, and proteins with respect to previously established sensing methods. We first discuss the sorption of DNA to graphene to introduce the interactions and forces acting in DNA based GFET devices and how these forces can potentially affect the performance of increasingly popular DNA aptamers and even future DNA nanostructures as sensor substrates. Next, we discuss the novel use of GFETs to detect DNA and the underlying electronic phenomena that are typically used as benchmarks for characterizing the analyte response of these devices. Finally, we address the use of DNA aptamers to increase the selectivity of GFET sensors for small molecules and proteins and compare them with other, state of the art, detection methods.
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Affiliation(s)
- Nathaniel S Green
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, WV 25755, United States
| | - Michael L Norton
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, WV 25755, United States.
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39
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Sharma AK, Plant JJ, Rangel AE, Meek KN, Anamisis AJ, Hollien J, Heemstra JM. Fluorescent RNA labeling using self-alkylating ribozymes. ACS Chem Biol 2014; 9:1680-4. [PMID: 24896502 DOI: 10.1021/cb5002119] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The ability to fluorescently label specific RNA sequences is of significant utility for both in vitro and live cell applications. Currently, most RNA labeling methods utilize RNA-nucleic acid or RNA-protein molecular recognition. However, in the search for improved RNA labeling methods, harnessing the small-molecule recognition capabilities of RNA is rapidly emerging as a promising alternative. Along these lines, we propose a novel strategy in which a ribozyme acts to promote self-alkylation with a fluorophore, providing a robust, covalent linkage between the RNA and the fluorophore. Here we describe the selection and characterization of ribozymes that promote self-labeling with fluorescein iodoacetamide (FIA). Kinetic studies reveal a second-order rate constant that is on par with those of other reactions used for biomolecular labeling. Additionally, we demonstrate that labeling is specific to the ribozyme sequences, as FIA does not react nonspecifically with RNA.
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Affiliation(s)
- Ashwani K. Sharma
- Department of Chemistry and the Center
for Cell and Genome Science and ‡Department of Biology
and the Center for Cell and Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Joshua J. Plant
- Department of Chemistry and the Center
for Cell and Genome Science and ‡Department of Biology
and the Center for Cell and Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Alexandra E. Rangel
- Department of Chemistry and the Center
for Cell and Genome Science and ‡Department of Biology
and the Center for Cell and Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Kirsten N. Meek
- Department of Chemistry and the Center
for Cell and Genome Science and ‡Department of Biology
and the Center for Cell and Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - April J. Anamisis
- Department of Chemistry and the Center
for Cell and Genome Science and ‡Department of Biology
and the Center for Cell and Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Julie Hollien
- Department of Chemistry and the Center
for Cell and Genome Science and ‡Department of Biology
and the Center for Cell and Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Jennifer M. Heemstra
- Department of Chemistry and the Center
for Cell and Genome Science and ‡Department of Biology
and the Center for Cell and Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
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40
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Feng C, Dai S, Wang L. Optical aptasensors for quantitative detection of small biomolecules: a review. Biosens Bioelectron 2014; 59:64-74. [PMID: 24690563 DOI: 10.1016/j.bios.2014.03.014] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/27/2014] [Accepted: 03/06/2014] [Indexed: 01/16/2023]
Abstract
Aptasensors are aptamer-based biosensors with excellent recognition capability towards a wide range of targets. Specially, there have been ever-growing interests in the development of aptasensors for the detection of small molecules. This phenomenon is contributed to two reasons. On one hand, small biomolecules play an important role in living organisms with many kinds of biological function, such as antiarrhythmic effect and vasodilator activity of adenosine. On the other hand, the concentration of small molecules can be an indicator for disease diagnosis, for example, the concentration of ATP is closely associated with cell injury and cell viability. As a potential analysis tool in the construction of aptasensors, optical analysis has attracted much more interest of researchers due to its high sensitivity, quick response and simple operation. Besides, it promises the promotion of aptasensors in performance toward a new level. Review the development of optical aptasensors for small biomolecules will give readers an overall understanding of its progress and provide some theoretical guidelines for its future development. Hence, we give a mini-review on the advance of optical aptasensors for small biomolecules. This review focuses on recent achievements in the design of various optical aptasensors for small biomolecules, containing fluorescence aptasensors, colorimetric aptasensors, chemiluminescence aptasensors and other optical aptasensors.
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Affiliation(s)
- Chunjing Feng
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China
| | - Shuang Dai
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China
| | - Lei Wang
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China.
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41
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Abstract
Isolating a particular strand of DNA from a double stranded DNA duplex is an important step in aptamer generation as well as many other biotechnology applications. Here we describe a microfluidic, flow-through, dialysis device for isolating single-stranded DNA (ssDNA) from double-stranded DNA (dsDNA). The device consists of two channels fabricated in polydimethylsiloxane (PDMS) separated by a track etched polycarbonate membrane (800 nm pore size). To isolate ssDNA, dual-biotin labelled dsDNA was immobilized onto streptavidin-coated polystyrene beads. Alkaline treatment was used to denature dsDNA, releasing the non-biotinylated ssDNA. In the flow-through dialysis device the liberated ssDNA was able to cross the membrane and was collected in an outlet channel. The complementary sequence bound to the bead was unable to cross the membrane and was directed to a waste channel. The effect of NaOH concentration and flow rate on purity and yield were compared. >95% ssDNA purity was achieved at 25 mM NaOH. However, lower flow rates were necessary to achieve ssDNA yields approaching the 50% theoretical maximum of the concurrent-flow device. Under optimized conditions the microfluidic isolation achieved even higher purity ssDNA than analogous manual procedures.
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Affiliation(s)
- Yixiao Sheng
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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42
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In vitro selection with artificial expanded genetic information systems. Proc Natl Acad Sci U S A 2013; 111:1449-54. [PMID: 24379378 DOI: 10.1073/pnas.1311778111] [Citation(s) in RCA: 233] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Artificially expanded genetic information systems (AEGISs) are unnatural forms of DNA that increase the number of independently replicating nucleotide building blocks. To do this, AEGIS pairs are joined by different arrangements of hydrogen bond donor and acceptor groups, all while retaining their Watson-Crick geometries. We report here a unique case where AEGIS DNA has been used to execute a systematic evolution of ligands by exponential enrichment (SELEX) experiment. This AEGIS-SELEX was designed to create AEGIS oligonucleotides that bind to a line of breast cancer cells. AEGIS-SELEX delivered an AEGIS aptamer (ZAP-2012) built from six different kinds of nucleotides (the standard G, A, C, and T, and the AEGIS nonstandard P and Z nucleotides, the last having a nitro functionality not found in standard DNA). ZAP-2012 has a dissociation constant of 30 nM against these cells. The affinity is diminished or lost when Z or P (or both) is replaced by standard nucleotides and compares well with affinities of standard GACT aptamers selected against cell lines using standard SELEX. The success of AEGIS-SELEX relies on various innovations, including (i) the ability to synthesize GACTZP libraries, (ii) polymerases that PCR amplify GACTZP DNA with little loss of the AEGIS nonstandard nucleotides, and (iii) technologies to deep sequence GACTZP DNA survivors. These results take the next step toward expanding the power and utility of SELEX and offer an AEGIS-SELEX that could possibly generate receptors, ligands, and catalysts having sequence diversities nearer to that displayed by proteins.
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43
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Yang J, Bowser MT. Capillary electrophoresis-SELEX selection of catalytic DNA aptamers for a small-molecule porphyrin target. Anal Chem 2013; 85:1525-30. [PMID: 23234289 DOI: 10.1021/ac302721j] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) has previously been used to select aptamers for large-molecule targets such as proteins, lipopolysaccharides, and peptides. For the first time, we have performed CE-SELEX selection for a small-molecule target, N-methyl mesoporphyrin (NMM), with a molecular weight of only 580 g/mol. DNA aptamers with high-nanomolar to low-micromolar dissociation constants were achieved after only three rounds of selection. This corresponds to an >50-fold improvement in affinity over the random library. Two out of eight randomly chosen aptamers were found to catalyze the metal insertion reaction of mesoporphyrin with 1.7- and 2.0-fold rate enhancements, respectively.
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Affiliation(s)
- Jing Yang
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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Martín ME, García-Hernández M, García-Recio EM, Gómez-Chacón GF, Sánchez-López M, González VM. DNA aptamers selectively target Leishmania infantum H2A protein. PLoS One 2013; 8:e78886. [PMID: 24205340 PMCID: PMC3804487 DOI: 10.1371/journal.pone.0078886] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/16/2013] [Indexed: 02/08/2023] Open
Abstract
Parasites of the genus Leishmania produce leishmaniasis which affects millions people around the world. Understanding the molecular characteristics of the parasite can increase the knowledge about the mechanisms underlying disease development and progression. Thus, the study of the molecular features of histones has been considered of particular interest because Leishmania does not condense the chromatin during mitosis and, consequently, a different role for these proteins in the biology of the parasite can be expected. Furthermore, the sequence divergences in the amino and in the carboxy-terminal domains of the kinetoplastid core histones convert them in potential diagnostic and/or therapeutics targets. Aptamers are oligonucleotide ligands that are selected in vitro by their affinity and specificity for the target as a consequence of the particular tertiary structure that they are able to acquire depending on their sequence. Development of high-affinity molecules with the ability to recognize specifically Leishmania histones is essential for the progress of this kind of study. Two aptamers which specifically recognize Leishmania infantum H2A histone were cloned from a previously obtained ssDNA enriched population. These aptamers were sequenced and subjected to an in silico analysis. ELONA, slot blot and Western blot were performed to establish aptamer affinity and specificity for LiH2A histone and ELONA assays using peptides corresponding to overlapped sequences of LiH2A were made mapping the aptamers:LiH2A interaction. As "proofs of concept", aptamers were used to determine the number of parasites in an ELONA platform and to purify LiH2A from complex mixtures. The aptamers showed different secondary structures among them; however, both of them were able to recognize the same peptides located in a side of the protein. In addition, we demonstrate that these aptamers are useful for LiH2A identification and also may be of potential application as diagnostic system and as a laboratory tool with purification purpose.
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Affiliation(s)
- M. Elena Martín
- Departamento de Bioquímica-Investigación, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Ramón y Cajal, Madrid, Spain
| | | | - Eva M. García-Recio
- Departamento de Bioquímica-Investigación, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Ramón y Cajal, Madrid, Spain
| | | | | | - Víctor M. González
- Departamento de Bioquímica-Investigación, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Ramón y Cajal, Madrid, Spain
- * E-mail:
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45
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Rouah-Martin E, Mehta J, van Dorst B, de Saeger S, Dubruel P, Maes BUW, Lemiere F, Goormaghtigh E, Daems D, Herrebout W, van Hove F, Blust R, Robbens J. Aptamer-based molecular recognition of lysergamine, metergoline and small ergot alkaloids. Int J Mol Sci 2012; 13:17138-59. [PMID: 23242153 PMCID: PMC3546743 DOI: 10.3390/ijms131217138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 11/26/2012] [Accepted: 12/05/2012] [Indexed: 11/16/2022] Open
Abstract
Ergot alkaloids are mycotoxins produced by fungi of the genus Claviceps, which infect cereal crops and grasses. The uptake of ergot alkaloid contaminated cereal products can be lethal to humans and animals. For food safety assessment, analytical techniques are currently used to determine the presence of ergot alkaloids in food and feed samples. However, the number of samples which can be analyzed is limited, due to the cost of the equipment and the need for skilled personnel. In order to compensate for the lack of rapid tests for the detection of ergot alkaloids, the aim of this study was to develop a specific recognition element for ergot alkaloids, which could be further applied to produce a colorimetric reaction in the presence of these toxins. As recognition elements, single-stranded DNA ligands were selected by using an iterative selection procedure named SELEX, i.e., Systematic Evolution of Ligands by EXponential enrichment. After several selection cycles, the resulting aptamers were cloned and sequenced. A surface plasmon resonance analysis enabled determination of the dissociation constants of the complexes of aptamers and lysergamine. Dissociation constants in the nanomolar range were obtained with three selected aptamers. One of the selected aptamers, having a dissociation constant of 44 nM, was linked to gold nanoparticles and it was possible to produce a colorimetric reaction in the presence of lysergamine. This system could also be applied to small ergot alkaloids in an ergot contaminated flour sample.
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Affiliation(s)
- Elsa Rouah-Martin
- Laboratory of Systemic Physiological and Ecotoxicological Research (SPHERE), Department of Biology, University of Antwerp, Groenenborgerlaan 171, Antwerp B-2020, Belgium; E-Mails: (J.M.); (B.V.D.); (R.B.)
- Institute of Agricultural and Fisheries Research (ILVO), Ankerstraat 1, Oostende B-8400, Belgium; E-Mail:
| | - Jaytry Mehta
- Laboratory of Systemic Physiological and Ecotoxicological Research (SPHERE), Department of Biology, University of Antwerp, Groenenborgerlaan 171, Antwerp B-2020, Belgium; E-Mails: (J.M.); (B.V.D.); (R.B.)
- Institute of Agricultural and Fisheries Research (ILVO), Ankerstraat 1, Oostende B-8400, Belgium; E-Mail:
| | - Bieke van Dorst
- Laboratory of Systemic Physiological and Ecotoxicological Research (SPHERE), Department of Biology, University of Antwerp, Groenenborgerlaan 171, Antwerp B-2020, Belgium; E-Mails: (J.M.); (B.V.D.); (R.B.)
- Institute of Agricultural and Fisheries Research (ILVO), Ankerstraat 1, Oostende B-8400, Belgium; E-Mail:
| | - Sarah de Saeger
- Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, Ghent B-9000, Belgium; E-Mail:
| | - Peter Dubruel
- Polymer Chemistry and Biomaterials Group, Ghent University, campus Sterre S4, Krijgslaan 281, Ghent B-9000, Belgium; E-Mail:
| | - Bert U. W. Maes
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerp B-2020, Belgium; E-Mails: (B.U.W.M.); (F.L.); (D.D.); (W.H.)
| | - Filip Lemiere
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerp B-2020, Belgium; E-Mails: (B.U.W.M.); (F.L.); (D.D.); (W.H.)
| | - Erik Goormaghtigh
- Structural Biology and Bioinformatics Center, Free University of Brussels (ULB), campus de la Plaine, CP206/02, boulevard du Triomphe, Brussels B-1050, Belgium; E-Mail:
| | - Devin Daems
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerp B-2020, Belgium; E-Mails: (B.U.W.M.); (F.L.); (D.D.); (W.H.)
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerp B-2020, Belgium; E-Mails: (B.U.W.M.); (F.L.); (D.D.); (W.H.)
| | - François van Hove
- Mycothèque de l’Université catholique de Louvain (BCCMTM/MUCL), Mycology, Applied Microbiology, Earth and Life Institute (ELI), Université catholique de Louvain (UCL), Croix du Sud 2 boîte L7.05.06, Louvain-la-Neuve B-1348, Belgium; E-Mail:
| | - Ronny Blust
- Laboratory of Systemic Physiological and Ecotoxicological Research (SPHERE), Department of Biology, University of Antwerp, Groenenborgerlaan 171, Antwerp B-2020, Belgium; E-Mails: (J.M.); (B.V.D.); (R.B.)
| | - Johan Robbens
- Institute of Agricultural and Fisheries Research (ILVO), Ankerstraat 1, Oostende B-8400, Belgium; E-Mail:
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Cho S, Lee BR, Cho BK, Kim JH, Kim BG. In vitro selection of sialic acid specific RNA aptamer and its application to the rapid sensing of sialic acid modified sugars. Biotechnol Bioeng 2012; 110:905-13. [PMID: 23042406 DOI: 10.1002/bit.24737] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/17/2012] [Accepted: 09/21/2012] [Indexed: 11/07/2022]
Abstract
Sialic acids (SAs) are located on the terminal positions of glycan on a cell surface, which play important role in the spread and metastasis of cancer cells and infection of pathogen. For their detection and diagnosis, the finding of SA specific ligand is an essential prerequisite. Here, RNA aptamer for N-acetylneuraminic acid (Neu5Ac), a representative of SAs, with the high affinity of 1.35 nM and the selectivity was screened by in vitro selection method. The strong binding of the screened aptamer was enough to protect the hydrolysis of Neu5Ac by neuraminidase with the stoichiometry of 1:1 molar ratio. For the rapid detection of SAs, the RNA aptamer was further engineered to the aptazyme sensor by conjugating with a ribozyme following the characterization of selected aptamer by RNase footprinting assay. Without additional desialylation, modification, or/and purification processes, the aptazyme indicated high catalytic activities in the presence of Neu5Ac over 20 µM in several minutes. Also, we observed that the aptazyme sensor shows high sensitivities to Neu5Ac-conjugated sugars as well as Neu5Ac monomer, but not in non-Neu5Ac modified sugars. The aptamer for Neu5Ac can support valuable tools in a wide range of bioanalytical applications as well as biosensors.
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Affiliation(s)
- Suhyung Cho
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Seoul, Republic of Korea
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Challenges and opportunities for small molecule aptamer development. J Nucleic Acids 2012; 2012:748913. [PMID: 23150810 PMCID: PMC3488411 DOI: 10.1155/2012/748913] [Citation(s) in RCA: 286] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/08/2012] [Indexed: 12/14/2022] Open
Abstract
Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
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Abstract
Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
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Pednekar PP, Jadhav KR, Kadam VJ. Aptamer-dendrimer bioconjugate: a nanotool for therapeutics, diagnosis, and imaging. Expert Opin Drug Deliv 2012; 9:1273-88. [PMID: 22897588 DOI: 10.1517/17425247.2012.716421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Aptamers hold great promise as molecular tool in biomedical applications due to the therapeutic utility exhibited by their target specificity and sensitivity. Although current development of aptamer is hindered by its probable in vivo degradation, inefficient immobilization on probe surface, and generation of low detection signal, bioconjugation with nanomaterials can feasibly solve these problems. Nanostructures such as dendrimers, with multivalency and nonimmunogenicity, bioconjugated with aptamers have opened newer vistas for better pharmaceutical applications of aptamers. AREAS COVERED This review covers brief overview of aptamers and dendrimers, with specific focus on recent progresses of aptamer-dendrimer (Apt-D) bioconjugate in areas of targeted drug delivery, diagnosis, and molecular imaging along with the discussion on the currently available conjugates, using their in vitro and in vivo results. EXPERT OPINION The novel Apt-D bioconjugates have led to advances in targeting cancer cell, have amplified biosensing, and offered in vivo cell imaging. Because of the unique properties and applications, Apt-D bioconjugate propose an exciting future. However, further research in synthesis of new target-specific aptamers and their conjugation with dendrimers is required to establish full potential of Apt-D bioconjugate.
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Affiliation(s)
- Priti P Pednekar
- University of Mumbai, Bharati Vidyapeeth's College of Pharmacy, Department of Pharmaceutics, CBD Belapur, Sector-8, Navi-Mumbai-400614, India.
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Vinkenborg JL, Mayer G, Famulok M. Aptamer-based affinity labeling of proteins. Angew Chem Int Ed Engl 2012; 51:9176-80. [PMID: 22865679 DOI: 10.1002/anie.201204174] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Indexed: 12/20/2022]
Abstract
A most able label: Labeled aptamers can be cross-linked to their target structures in a light-dependent and highly specific manner as a result of a new strategy termed aptamer-based affinity labeling (ABAL) of proteins. The aptamer-protein complexes can be enriched in vitro, from a cellular lysate and from the surface of living cells, opening new ways to study aptamer interactions in biological contexts.
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