1
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Wang J, Chen D, Huang W, Yang N, Yuan Q, Yang Y. Aptamer-functionalized field-effect transistor biosensors for disease diagnosis and environmental monitoring. EXPLORATION (BEIJING, CHINA) 2023; 3:20210027. [PMID: 37933385 PMCID: PMC10624392 DOI: 10.1002/exp.20210027] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 03/10/2023] [Indexed: 11/08/2023]
Abstract
Nano-biosensors that are composed of recognition molecules and nanomaterials have been extensively utilized in disease diagnosis, health management, and environmental monitoring. As a type of nano-biosensors, molecular specificity field-effect transistor (FET) biosensors with signal amplification capability exhibit prominent advantages including fast response speed, ease of miniaturization, and integration, promising their high sensitivity for molecules detection and identification. With intrinsic characteristics of high stability and structural tunability, aptamer has become one of the most commonly applied biological recognition units in the FET sensing fields. This review summarizes the recent progress of FET biosensors based on aptamer functionalized nanomaterials in medical diagnosis and environmental monitoring. The structure, sensing principles, preparation methods, and functionalization strategies of aptamer modified FET biosensors were comprehensively summarized. The relationship between structure and sensing performance of FET biosensors was reviewed. Furthermore, the challenges and future perspectives of FET biosensors were also discussed, so as to provide support for the future development of efficient healthcare management and environmental monitoring devices.
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Affiliation(s)
- Jingfeng Wang
- College of Chemistry and Molecular Sciences, Institute of Molecular MedicineRenmin Hospital of Wuhan University, School of Microelectronics, Wuhan UniversityWuhanChina
| | - Duo Chen
- College of Chemistry and Molecular Sciences, Institute of Molecular MedicineRenmin Hospital of Wuhan University, School of Microelectronics, Wuhan UniversityWuhanChina
| | - Wanting Huang
- College of Chemistry and Molecular Sciences, Institute of Molecular MedicineRenmin Hospital of Wuhan University, School of Microelectronics, Wuhan UniversityWuhanChina
| | - Nianjun Yang
- Department of Chemistry, Insititute of Materials ResearchHasselt UniversityHasseltBelgium
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical EngineeringHunan UniversityChangshaChina
| | - Yanbing Yang
- College of Chemistry and Molecular Sciences, Institute of Molecular MedicineRenmin Hospital of Wuhan University, School of Microelectronics, Wuhan UniversityWuhanChina
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2
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Aparna GM, Tetala KKR. Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays. Biomolecules 2023; 13:biom13040602. [PMID: 37189350 DOI: 10.3390/biom13040602] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Microarrays are one of the trailblazing technologies of the last two decades and have displayed their importance in all the associated fields of biology. They are widely explored to screen, identify, and gain insights on the characteristics traits of biomolecules (individually or in complex solutions). A wide variety of biomolecule-based microarrays (DNA microarrays, protein microarrays, glycan microarrays, antibody microarrays, peptide microarrays, and aptamer microarrays) are either commercially available or fabricated in-house by researchers to explore diverse substrates, surface coating, immobilization techniques, and detection strategies. The aim of this review is to explore the development of biomolecule-based microarray applications since 2018 onwards. Here, we have covered a different array of printing strategies, substrate surface modification, biomolecule immobilization strategies, detection techniques, and biomolecule-based microarray applications. The period of 2018–2022 focused on using biomolecule-based microarrays for the identification of biomarkers, detection of viruses, differentiation of multiple pathogens, etc. A few potential future applications of microarrays could be for personalized medicine, vaccine candidate screening, toxin screening, pathogen identification, and posttranslational modifications.
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3
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Effect of hydrophobic groups on adsorption of arginine-based amino acids to solid surfaces in water. Struct Chem 2022. [DOI: 10.1007/s11224-022-02090-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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4
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Banu K, Mondal B, Rai B, Monica N, Hanumegowda R. Prospects for the application of aptamer based assay platforms in pathogen detection. Biocybern Biomed Eng 2022. [DOI: 10.1016/j.bbe.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Jiang W, Jones JC, Shankavaram U, Sproull M, Camphausen K, Krauze AV. Analytical Considerations of Large-Scale Aptamer-Based Datasets for Translational Applications. Cancers (Basel) 2022; 14:2227. [PMID: 35565358 PMCID: PMC9105298 DOI: 10.3390/cancers14092227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 11/17/2022] Open
Abstract
The development and advancement of aptamer technology has opened a new realm of possibilities for unlocking the biocomplexity available within proteomics. With ultra-high-throughput and multiplexing, alongside remarkable specificity and sensitivity, aptamers could represent a powerful tool in disease-specific research, such as supporting the discovery and validation of clinically relevant biomarkers. One of the fundamental challenges underlying past and current proteomic technology has been the difficulty of translating proteomic datasets into standards of practice. Aptamers provide the capacity to generate single panels that span over 7000 different proteins from a singular sample. However, as a recent technology, they also present unique challenges, as the field of translational aptamer-based proteomics still lacks a standardizing methodology for analyzing these large datasets and the novel considerations that must be made in response to the differentiation amongst current proteomic platforms and aptamers. We address these analytical considerations with respect to surveying initial data, deploying proper statistical methodologies to identify differential protein expressions, and applying datasets to discover multimarker and pathway-level findings. Additionally, we present aptamer datasets within the multi-omics landscape by exploring the intersectionality of aptamer-based proteomics amongst genomics, transcriptomics, and metabolomics, alongside pre-existing proteomic platforms. Understanding the broader applications of aptamer datasets will substantially enhance current efforts to generate translatable findings for the clinic.
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Affiliation(s)
- Will Jiang
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, 9000 Rockville Pike, Building 10, CRC, Bethesda, MD 20892, USA; (W.J.); (U.S.); (M.S.); (K.C.)
| | - Jennifer C. Jones
- Translational Nanobiology Section, Laboratory of Pathology, NIH/NCI/CCR, Bethesda, MD 20892, USA;
| | - Uma Shankavaram
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, 9000 Rockville Pike, Building 10, CRC, Bethesda, MD 20892, USA; (W.J.); (U.S.); (M.S.); (K.C.)
| | - Mary Sproull
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, 9000 Rockville Pike, Building 10, CRC, Bethesda, MD 20892, USA; (W.J.); (U.S.); (M.S.); (K.C.)
| | - Kevin Camphausen
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, 9000 Rockville Pike, Building 10, CRC, Bethesda, MD 20892, USA; (W.J.); (U.S.); (M.S.); (K.C.)
| | - Andra V. Krauze
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, 9000 Rockville Pike, Building 10, CRC, Bethesda, MD 20892, USA; (W.J.); (U.S.); (M.S.); (K.C.)
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6
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Development of novel aptasensor for ultra-sensitive detection of myoglobin via electrochemical signal amplification of methylene blue using poly (styrene)-block-poly (acrylic acid) amphiphilic copolymer. Talanta 2022; 237:122950. [PMID: 34736676 DOI: 10.1016/j.talanta.2021.122950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 01/25/2023]
Abstract
Amplification of electrochemical signal in order to betterment of limit of detection in determination of biomarkers has an important role in early detection of some dangerous diseases such as cancers. For this purpose, in this research, two types of poly (styrene)-block-poly (acrylic acid) amphiphilic copolymer (PS61-b-PAA596 and PS596-b-PAA61) were synthesized by controlled radical polymerization method via reversible addition-fragmentation chain transfer polymerization (RAFT) technique. Chemical structure of block copolymers was confirmed by FT-IR spectroscopy and their surface morphology was assessed by scanning electron microscopy (SEM). Self-assembly of these block copolymers into polymeric vesicles (polymersomes), loading and release efficiency of methylene blue as an electroactive indicator were investigated in DMF and THF solvents. On the basis of our findings PS61-b-PAA596 has better capability for loading and release of MB than PS596-b-PAA61. Then the obtained methylene blue-loaded polymersome successfully used for development of an aptasensor toward determination of trace amounts of myoglobin. The proposed aptasensor showed a wide linear range from 1.0 aM to 1.0 μM with an ultra-low detection limit of 0.73 aM. Applying this amplification strategy, determination of myoglobin in real samples was successfully performed.
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7
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Cerqueira SM, Fernandes R, Moreira FT, Sales MGF. Development of an electrochemical biosensor for Galectin-3 detection in point-of-care. Microchem J 2021. [DOI: 10.1016/j.microc.2021.105992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Khodadadi E, Mahjoub S, Arabi MS, Najafzadehvarzi H, Nasirian V. Fabrication and evaluation of aptamer-conjugated paclitaxel-loaded magnetic nanoparticles for targeted therapy on breast cancer cells. Mol Biol Rep 2021; 48:2105-2116. [PMID: 33635469 DOI: 10.1007/s11033-021-06199-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/28/2021] [Indexed: 11/30/2022]
Abstract
Targeted drug delivery vehicles make it possible to deliver anti-cancer drugs to the cells or tissues of interest. Aptamers are peptide or oligonucleotide molecules that can serve as targeting elements of drug carriers. In the current study, we evaluated the capacity of an aptamer-based drug carrier to deliver Paclitaxel (PTX) to cancer cells. After being synthesized, SPIONs@PTX-SYL3C aptamer was characterized using different methods, including differential light scattering (DLS), infrared spectroscopy (FTIR), Transmission electron microscopy (TEM), X-ray diffraction (XRD), Thermal gravimetric analysis (TGA), and vibrating sample magnetometer (VSM). Encapsulation efficiency (EE) and loading efficiency (LE) were also evaluated. The carrier was applied on 4T1, MCF 7, and MCF-10A breast cell lines to evaluate its drug delivery potency and specificity. EE and LE were calculated to be 77.6% and 7.76%, respectively. MTT results revealed that aptameric SPIONs@PTX was more toxic than non-aptameric SPIONs@PTX. Flowcytometry analysis and DAPI staining confirmed that SPIONs@PTX-Aptamer had higher cell internalization rate when compared to non-targeted SPIONs@PTX. Our results indicate that aptamer-conjugated SPIONs@PTX has a good capacity in recognizing its target cells and inhibiting their growth and division.
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Affiliation(s)
- Emad Khodadadi
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran
| | - Soleiman Mahjoub
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran. .,Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran.
| | - Mehdi Sheikh Arabi
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
| | - Hossein Najafzadehvarzi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.,Department of Pharmacology, Babol University of Medical Sciences, Babol, Iran
| | - Vahid Nasirian
- Department of Chemistry and Physics, Louisiana State University in Shreveport, Shreveport, LA, 71115, USA
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9
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Designing of peptide aptamer targeting the receptor-binding domain of spike protein of SARS-CoV-2: an in silico study. Mol Divers 2021; 26:157-169. [PMID: 33389440 PMCID: PMC7778502 DOI: 10.1007/s11030-020-10171-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022]
Abstract
Short synthetic peptide molecules which bind to a specific target protein with a high affinity to exert its function are known as peptide aptamers. The high specificity of aptamers with small-molecule targets (metal ions, dyes and theophylline; ATP) is within 1 pM and 1 μM range, whereas with the proteins (thrombin, CD4 and antibodies) it is in the nanomolar range (which is equivalent to monoclonal antibodies). The recently identified coronavirus (SARS-CoV-2) genome encodes for various proteins, such as envelope, membrane, nucleocapsid, and spike protein. Among these, the protein necessary for the virus to enter inside the host cell is spike protein. The work focuses on designing peptide aptamer targeting the spike receptor-binding domain of SARS-CoV-2. The peptide aptamer has been designed by using bacterial Thioredoxin A as the scaffold protein and an 18-residue-long peptide. The tertiary structure of the peptide aptamer is modeled and docked to spike receptor-binding domain of SARS CoV2. Molecular dynamic simulation has been done to check the stability of the aptamer and receptor-binding domain complex. It was observed that the aptamer binds to spike receptor-binding domain of SARS-CoV-2 in a similar pattern as that of ACE2. The aptamer-receptor-binding domain complex was found to be stable in a 100 ns molecular dynamic simulation. The aptamer is also predicted to be non-antigenic, non-allergenic, non-hemolytic, non-inflammatory, water-soluble with high affinity toward ACE2 than serum albumin. Thus, peptide aptamer can be a novel approach for the therapeutic treatment for SARS-CoV-2.
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10
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Lietard J, Somoza MM. Spotting, Transcription and In Situ Synthesis: Three Routes for the Fabrication of RNA Microarrays. Comput Struct Biotechnol J 2019; 17:862-868. [PMID: 31321002 PMCID: PMC6612525 DOI: 10.1016/j.csbj.2019.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/04/2019] [Accepted: 06/08/2019] [Indexed: 12/11/2022] Open
Abstract
DNA microarrays have become commonplace in the last two decades, but the synthesis of other nucleic acids biochips, most importantly RNA, has only recently been developed to a similar extent. RNA microarrays can be seen as organized surfaces displaying a potentially very large number of unique sequences and are of invaluable help in understanding the complexity of RNA structure and function as they allow the probing and treatment of each of the many different sequences simultaneously. Three approaches have emerged for the fabrication of RNA microarrays. The earliest examples used a direct, manual or mechanical, deposition of pre-synthesized, purified RNA oligonucleotides onto the surface in a process called spotting. In a second approach, pre-spotted or in situ-synthesized DNA microarrays are employed as templates for the transcription of RNA, subsequently or immediately captured on the surface. Finally, a third approach attempts to mirror the phosphoramidite-based protocols for in situ synthesis of high-density DNA arrays in order to produce in situ synthesized RNA microarrays. In this mini-review, we describe the chemistry and the engineering behind the fabrications methods, underlining the advantages and shortcomings of each, and illustrate how versatile these platforms can be by presenting some of their applications.
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11
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Hierarchical mechanism of amino acid sensing by the T-box riboswitch. Nat Commun 2018; 9:1896. [PMID: 29760498 PMCID: PMC5951919 DOI: 10.1038/s41467-018-04305-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/16/2018] [Indexed: 11/08/2022] Open
Abstract
In Gram-positive bacteria, T-box riboswitches control gene expression to maintain the cellular pools of aminoacylated tRNAs essential for protein biosynthesis. Co-transcriptional binding of an uncharged tRNA to the riboswitch stabilizes an antiterminator, allowing transcription read-through, whereas an aminoacylated tRNA does not. Recent structural studies have resolved two contact points between tRNA and Stem-I in the 5' half of the T-box riboswitch, but little is known about the mechanism empowering transcriptional control by a small, distal aminoacyl modification. Using single-molecule fluorescence microscopy, we have probed the kinetic and structural underpinnings of tRNA binding to a glycyl T-box riboswitch. We observe a two-step mechanism where fast, dynamic recruitment of tRNA by Stem-I is followed by ultra-stable anchoring by the downstream antiterminator, but only without aminoacylation. Our results support a hierarchical sensing mechanism wherein dynamic global binding of the tRNA body is followed by localized readout of its aminoacylation status by snap-lock-based trapping.
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12
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Wu X, Shaikh AB, Yu Y, Li Y, Ni S, Lu A, Zhang G. Potential Diagnostic and Therapeutic Applications of Oligonucleotide Aptamers in Breast Cancer. Int J Mol Sci 2017; 18:ijms18091851. [PMID: 28841163 PMCID: PMC5618500 DOI: 10.3390/ijms18091851] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 08/23/2017] [Accepted: 08/23/2017] [Indexed: 12/18/2022] Open
Abstract
Breast cancer is one of the most common causes of cancer related deaths in women. Currently, with the development of early detection, increased social awareness and kinds of treatment options, survival rate has improved in nearly every type of breast cancer patients. However, about one third patients still have increased chances of recurrence within five years and the five-year relative survival rate in patients with metastasis is less than 30%. Breast cancer contains multiple subtypes. Each subtype could cause distinct clinical outcomes and systemic interventions. Thereby, new targeted therapies are of particular importance to solve this major clinical problem. Aptamers, often termed “chemical antibodies”, are functionally similar to antibodies and have demonstrated their superiority of recognizing target with high selectivity, affinity and stability. With these intrinsic properties, aptamers have been widely studied in cancer biology and some are in clinical trials. In this review, we will firstly discuss about the global impacts and mechanisms of breast cancer, then briefly highlight applications of aptamers that have been developed for breast cancer and finally summarize various challenges in clinical translation of aptamers.
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Affiliation(s)
| | - Atik Badshah Shaikh
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Yuanyuan Yu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Yongshu Li
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Shuaijian Ni
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Aiping Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Ge Zhang
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
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Ruan M, Seydou M, Noel V, Piro B, Maurel F, Barbault F. Molecular Dynamics Simulation of a RNA Aptasensor. J Phys Chem B 2017; 121:4071-4080. [PMID: 28363022 DOI: 10.1021/acs.jpcb.6b12544] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-stranded RNA aptamers have emerged as novel biosensor tools. However, the immobilization procedure of the aptamer onto a surface generally induces a loss of affinity. To understand this molecular process, we conducted a complete simulation study for the Flavin mononucleotide aptamer for which experimental data are available. Several molecular dynamics simulations (MD) of the Flavin in complex with its RNA aptamer were conducted in solution, linked with six thymidines (T6) and, finally, immobilized on an hexanol-thiol-functionalized gold surface. First, we demonstrated that our MD computations were able to reproduce the experimental solution structure and to provide a meaningful estimation of the Flavin free energy of binding. We also demonstrated that the T6 linkage, by itself, does not generate a perturbation of the Flavin recognition process. From the simulation of the complete biosensor system, we observed that the aptamer stays oriented parallel to the surface at a distance around 36 Å avoiding, this way, interaction with the surface. We evidenced a structural reorganization of the Flavin aptamer binding mode related to the loss of affinity and induced by an anisotropic distribution of sodium cationic densities. This means that ionic diffusion is different between the surface and the aptamer than above this last one. We suggest that these findings might be extrapolated to other nucleic acids systems for the future design of biosensors with higher efficiency and selectivity.
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Affiliation(s)
- Min Ruan
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France.,School of Materials and Metallurgy, Hubei Polytechnic University , Huangshi, Hubei, China
| | - Mahamadou Seydou
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - Vincent Noel
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - Benoit Piro
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - François Maurel
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - Florent Barbault
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
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Microarrays as Model Biosensor Platforms to Investigate the Structure and Affinity of Aptamers. J Nucleic Acids 2016; 2016:9718612. [PMID: 27042344 PMCID: PMC4794571 DOI: 10.1155/2016/9718612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/17/2016] [Indexed: 01/10/2023] Open
Abstract
Immobilization of nucleic acid aptamer recognition elements selected free in solution onto the surface of biosensor platforms has proven challenging. This study investigated the binding of multiple aptamer/target pairs immobilized on a commercially available microarray as a model system mimicking biosensor applications. The results indicate a minimum distance (linker length) from the surface and thymine nucleobase linker provides reproducible binding across varying conditions. An indirect labeling method, where the target was labeled with a biotin followed by a brief Cy3-streptavidin incubation, provided a higher signal-to-noise ratio and over two orders of magnitude improvement in limit of detection, compared to direct Cy3-protein labeling. We also showed that the affinities of the aptamer/target interaction can change between direct and indirect labeling and conditions to optimize for the highest fluorescence intensity will increase the sensitivity of the assay but will not change the overall affinity. Additionally, some sequences which did not initially bind demonstrated binding when conditions were optimized. These results, in combination with studies demonstrating enhanced binding in nonselection buffers, provided insights into the structure and affinity of aptamers critical for biosensor applications and allowed for generalizations in starting conditions for researchers wishing to investigate aptamers on a microarray surface.
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15
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Martin JA, Mirau PA, Chushak Y, Chávez JL, Naik RR, Hagen JA, Kelley-Loughnane N. Single-Round Patterned DNA Library Microarray Aptamer Lead Identification. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2015; 2015:137489. [PMID: 26075138 PMCID: PMC4446497 DOI: 10.1155/2015/137489] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 04/22/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
A method for identifying an aptamer in a single round was developed using custom DNA microarrays containing computationally derived patterned libraries incorporating no information on the sequences of previously reported thrombin binding aptamers. The DNA library was specifically designed to increase the probability of binding by enhancing structural complexity in a sequence-space confined environment, much like generating lead compounds in a combinatorial drug screening library. The sequence demonstrating the highest fluorescence intensity upon target addition was confirmed to bind the target molecule thrombin with specificity by surface plasmon resonance, and a novel imino proton NMR/2D NOESY combination was used to screen the structure for G-quartet formation. We propose that the lack of G-quartet structure in microarray-derived aptamers may highlight differences in binding mechanisms between surface-immobilized and solution based strategies. This proof-of-principle study highlights the use of a computational driven methodology to create a DNA library rather than a SELEX based approach. This work is beneficial to the biosensor field where aptamers selected by solution based evolution have proven challenging to retain binding function when immobilized on a surface.
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Affiliation(s)
- Jennifer A. Martin
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, MD 20817, USA
| | - Peter A. Mirau
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USA
| | - Yaroslav Chushak
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, MD 20817, USA
| | - Jorge L. Chávez
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
- UES Inc., 4401 Dayton-Xenia Road, Dayton, Dayton, OH 45433, USA
| | - Rajesh R. Naik
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USA
| | - Joshua A. Hagen
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
| | - Nancy Kelley-Loughnane
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
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16
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Aptamer Microarrays—Current Status and Future Prospects. MICROARRAYS 2015; 4:115-32. [PMID: 27600216 PMCID: PMC4996391 DOI: 10.3390/microarrays4020115] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/09/2015] [Accepted: 03/18/2015] [Indexed: 12/16/2022]
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17
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Kadioglu O, Malczyk AH, Greten HJ, Efferth T. Aptamers as a novel tool for diagnostics and therapy. Invest New Drugs 2015; 33:513-20. [PMID: 25637166 DOI: 10.1007/s10637-015-0213-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/21/2015] [Indexed: 11/27/2022]
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides that are capable of binding small molecules, proteins, or nucleotides with high specificity. They show a stable conformation and high binding affinity for their target molecules. There are numerous applications for aptamers in biotechnology, molecular diagnostics and targeted therapy of diseases. Their production is cheap, and they generally display lower immunogenicity than monoclonal antibodies. In the present review, we give an introduction to the preparation of aptamers and provide examples for their use in biotechnology, diagnostics and therapy of diseases.
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Affiliation(s)
- Onat Kadioglu
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Staudinger Weg 5, 55128, Mainz, Germany
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18
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High efficiency acetylcholinesterase immobilization on DNA aptamer modified surfaces. Molecules 2014; 19:4986-96. [PMID: 24756130 PMCID: PMC6271157 DOI: 10.3390/molecules19044986] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/08/2014] [Accepted: 04/11/2014] [Indexed: 11/17/2022] Open
Abstract
We report here the in vitro selection of DNA aptamers for electric eel acetylcholinesterase (AChE). One selected aptamer sequence (R15/19) has a high affinity towards the enzyme (Kd=157±42 pM). Characterization of the aptamer showed its binding is not affected by low ionic strength (~20 mM), however significant reduction in affinity occurred at high ionic strength (~1.2 M). In addition, this aptamer does not inhibit the catalytic activity of AChE that we exploit through immobilization of the DNA on a streptavidin-coated surface. Subsequent immobilization of AChE by the aptamer results in a 4-fold higher catalytic activity when compared to adsorption directly on to plastic.
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19
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Thiviyanathan V, Gorenstein DG. Aptamers and the next generation of diagnostic reagents. Proteomics Clin Appl 2014; 6:563-73. [PMID: 23090891 DOI: 10.1002/prca.201200042] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 09/17/2012] [Accepted: 09/20/2012] [Indexed: 01/06/2023]
Abstract
Antibodies have been extensively used as capture and detection reagents in diagnostic applications of proteomics-based technologies. Proteomic assays need high sensitivity and specificity, a wide dynamic range for detection, and accurate, reproducible quantification with small confidence values. However, several inherent limitations of monoclonal antibodies in meeting the emerging challenges of proteomics led to the development of a new class of oligonucleotide-based reagents. Natural and derivatized nucleic acid aptamers are emerging as promising alternatives to monoclonal antibodies. Aptamers can be effectively used to simultaneously detect thousands of proteins in multiplex discovery platforms, where antibodies often fail due to cross-reactivity problems. Through chemical modification, vast range of additional functional groups can be added at any desired position in the oligonucleotide sequence, therefore the best features of small molecule drugs, proteins, and antibodies can be brought together into aptamers, making aptamers the most versatile reagent in proteomics. In this review, we discuss the recent developments in aptamer technology, including new selection methods and the aptamers' application in proteomics.
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Affiliation(s)
- Varatharasa Thiviyanathan
- Centers for Proteomics & Systems Biology, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX, USA
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20
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Franssen-van Hal NLW, van der Putte P, Hellmuth K, Matysiak S, Kretschy N, Somoza MM. Optimized light-directed synthesis of aptamer microarrays. Anal Chem 2013; 85:5950-7. [PMID: 23672295 PMCID: PMC3686109 DOI: 10.1021/ac400746j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
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Aptamer microarrays are a promising
high-throughput method for
ultrasensitive detection of multiple analytes, but although much is
known about the optimal synthesis of oligonucleotide microarrays used
in hybridization-based genomics applications, the bioaffinity interactions
between aptamers and their targets is qualitatively different and
requires significant changes to synthesis parameters. Focusing on
streptavidin-binding DNA aptamers, we employed light-directed in situ
synthesis of microarrays to analyze the effects of sequence fidelity,
linker length, surface probe density, and substrate functionalization
on detection sensitivity. Direct comparison with oligonucleotide hybridization
experiments indicates that aptamer microarrays are significantly more
sensitive to sequence fidelity and substrate functionalization and
have different optimal linker length and surface probe density requirements.
Whereas microarray hybridization probes generate maximum signal with
multiple deletions, aptamer sequences with the same deletion rate
result in a 3-fold binding signal reduction compared with the same
sequences synthesized for maximized sequence fidelity. The highest
hybridization signal was obtained with dT 5mer linkers, and the highest
aptamer signal was obtained with dT 11mers, with shorter aptamer linkers
significantly reducing the binding signal. The probe hybridization
signal was found to be more sensitive to molecular crowding, whereas
the aptamer probe signal does not appear to be constrained within
the density of functional surface groups commonly used to synthesize
microarrays.
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21
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Radom F, Jurek PM, Mazurek MP, Otlewski J, Jeleń F. Aptamers: molecules of great potential. Biotechnol Adv 2013; 31:1260-74. [PMID: 23632375 DOI: 10.1016/j.biotechadv.2013.04.007] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/27/2013] [Accepted: 04/19/2013] [Indexed: 01/08/2023]
Abstract
Aptamers emerged over 20 years ago as a class of nucleic acids able to recognize specific targets. Today, aptamer-related studies constitute a large and important field of biotechnology. Functional oligonucleotides have proved to be a versatile tool in biomedical research due to the ease of synthesis, a wide range of potentially recognized molecular targets and the simplicity of selection. Similarly to antibodies, aptamers can be used to detect or isolate specific molecules, as well as to act as targeting and therapeutic agents. In this review we present different approaches to aptamer application in nanobiotechnology, diagnostics and medicine.
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Affiliation(s)
- Filip Radom
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
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22
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Abstract
IMPORTANCE OF THE FIELD Therapeutic aptamers are synthetic, structured oligonucleotides that bind to a very broad range of targets with high affinity and specificity. They are an emerging class of targeting ligand that show great promise for treating a number of diseases. A series of aptamers currently in various stages of clinical development highlights the potential of aptamers for therapeutic applications. AREAS COVERED IN THIS REVIEW This review covers in vitro selection of oligonucleotide ligands, called aptamers, from a combinatorial library using the Systematic Evolution of Ligands by Exponential Enrichment process as well as the other known strategies for finding aptamers against various targets. WHAT THE READER WILL GAIN Readers will gain an understanding of the highly useful strategies for successful aptamer discovery. They may also be able to combine two or more of the presented strategies for their aptamer discovery projects. TAKE HOME MESSAGE Although many processes are available for discovering aptamers, it is not easy to discover an aptamer candidate that is ready to move toward pharmaceutical drug development. It is also apparent that there have been relatively few therapeutic advances and clinical trials undertaken due to the small number of companies that participate in aptamer development.
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23
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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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24
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Vinkenborg JL, Mayer G, Famulok M. Aptamer-basierte Affinitätsmarkierung von Proteinen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204174] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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25
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Johnson A, Song Q, Ko Ferrigno P, Bueno PR, Davis JJ. Sensitive Affimer and Antibody Based Impedimetric Label-Free Assays for C-Reactive Protein. Anal Chem 2012; 84:6553-60. [DOI: 10.1021/ac300835b] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Anthony Johnson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1
3TA, United Kingdom
| | - Qifeng Song
- Wellcome
Trust/EPSRC/Leeds Medical
Engineering Centre, Leeds Institute of Molecular Medicine, Wellcome
Trust Brenner Building, St James’s University Hospital, Leeds LS9 7TF, United Kingdom
| | - Paul Ko Ferrigno
- Wellcome
Trust/EPSRC/Leeds Medical
Engineering Centre, Leeds Institute of Molecular Medicine, Wellcome
Trust Brenner Building, St James’s University Hospital, Leeds LS9 7TF, United Kingdom
| | - Paulo R. Bueno
- Instituto de Química (Institute
of Chemistry, Physical Chemistry Department), Universidade Estadual Paulista (São Paulo State University, UNESP), CP 355, 14800-900, Araraquara, São Paulo, Brazil
| | - Jason J. Davis
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1
3TA, United Kingdom
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26
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Walter JG, Stahl F, Scheper T. Aptamers as affinity ligands for downstream processing. Eng Life Sci 2012. [DOI: 10.1002/elsc.201100197] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Johanna-Gabriela Walter
- Institut für Technische Chemie; Leibniz Universität Hannover; Callinstr. 3; 30167; Hannover; Germany
| | - Frank Stahl
- Institut für Technische Chemie; Leibniz Universität Hannover; Callinstr. 3; 30167; Hannover; Germany
| | - Thomas Scheper
- Institut für Technische Chemie; Leibniz Universität Hannover; Callinstr. 3; 30167; Hannover; Germany
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27
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Lübbecke M, Walter JG, Stahl F, Scheper T. Aptamers as detection molecules on reverse phase protein microarrays for the analysis of cell lysates. Eng Life Sci 2012. [DOI: 10.1002/elsc.201100100] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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28
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Facing current quantification challenges in protein microarrays. J Biomed Biotechnol 2012; 2012:831347. [PMID: 22619499 PMCID: PMC3348655 DOI: 10.1155/2012/831347] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 02/07/2012] [Accepted: 02/08/2012] [Indexed: 12/28/2022] Open
Abstract
The proteome is highly variable and differs from cell to cell. The reasons are posttranslational modifications, splice variants, and polymorphisms. Techniques like next-generation sequencing can only give an inadequate picture of the protein status of a cell. Protein microarrays are able to track these changes on the level they occur: the proteomic level. Therefore, protein microarrays are powerful tools for relative protein quantification, to unveil new interaction partners and to track posttranslational modifications. This papers gives an overview on current protein microarray techniques and discusses recent advances in relative protein quantification.
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29
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Protein-imprinted materials: rational design, application and challenges. Anal Bioanal Chem 2012; 403:2173-83. [PMID: 22367246 DOI: 10.1007/s00216-012-5840-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 02/01/2012] [Accepted: 02/03/2012] [Indexed: 02/07/2023]
Abstract
Protein imprinting is a promising tool for generating artificial biomimetic receptors with antibody-like specific recognition sites. Recently, protein-imprinted materials, as potential antibody substitutes, have attracted much attention in many fields, for example chemical sensors, chromatographic stationary phases, and artificial enzymes, owing to their long-term storage stability, potential re-usability, resistance to harsh environment, and low cost. In this critical review, we focus our discussion on the rational preparation of protein-imprinted materials in terms of choice of template, functional monomer, crosslinker, and polymerization format. In addition, several highlighted applications of protein-imprinted materials are emphasized, not only in well-known fields but also in some unique fields, for example proteomics and tissue engineering. Finally, we propose challenges arising from the intrinsic properties of protein imprinting, for example obtaining the template, heterogeneous binding, and extrinsic competition, for example immobilized aptamers.
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30
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Srinivas RL, Chapin SC, Doyle PS. Aptamer-functionalized microgel particles for protein detection. Anal Chem 2011; 83:9138-45. [PMID: 22017663 DOI: 10.1021/ac202335u] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Highly sensitive and multiplexed detection of clinically relevant proteins in biologically complex samples is crucial for the advancement of clinical proteomics. In recent years, aptamers have emerged as useful tools for protein analysis due to their specificity and affinity for protein targets as well as their compatibility with particle-based detection systems. In this study, we demonstrate the highly sensitive detection of human α-thrombin on encoded hydrogel microparticles functionalized with an aptamer capture sequence. We use static imaging and microfluidic flow-through analysis techniques to evaluate the detection capabilities of the microgels in sandwich-assay formats that utilize both aptamers and antibodies for the reporting of target-binding events. Buffers and reagent concentrations were optimized to provide maximum reaction efficiency while still maintaining an assay with a simple workflow that can be easily adapted to the multiplexed detection of other clinically relevant proteins. The three-dimensional, nonfouling hydrogel immobilization scaffold used in this work provides three logs of dynamic range, with a limit of detection of 4 pM using a single aptamer capture species and without the need for spacers or signal amplification.
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Affiliation(s)
- Rathi L Srinivas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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31
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Zhu G, Lübbecke M, Walter JG, Stahl F, Scheper T. Characterization of Optimal Aptamer-Microarray Binding Chemistry and Spacer Design. Chem Eng Technol 2011. [DOI: 10.1002/ceat.201000551] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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32
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Aptamer-based radioimmunotherapy: the feasibility and prospect in cancer therapy. J Radioanal Nucl Chem 2011. [DOI: 10.1007/s10967-011-1340-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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33
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Human thrombin detection through a sandwich aptamer microarray: interaction analysis in solution and in solid phase. SENSORS 2011; 11:9426-41. [PMID: 22163703 PMCID: PMC3231252 DOI: 10.3390/s111009426] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 09/27/2011] [Accepted: 09/28/2011] [Indexed: 01/30/2023]
Abstract
We have developed an aptamer-based microarray for human thrombin detection exploiting two non-overlapping DNA thrombin aptamers recognizing different exosites of the target protein. The 15-mer aptamer (TBA1) binds the fibrinogen-binding site, whereas the 29-mer aptamer (TBA2) binds the heparin binding domain. Extensive analysis on the complex formation between human thrombin and modified aptamers was performed by Electrophoresis Mobility Shift Assay (EMSA), in order to verify in solution whether the chemical modifications introduced would affect aptamers/protein recognition. The validated system was then applied to the aptamer microarray, using the solid phase system devised by the solution studies. Finally, the best procedure for Sandwich Aptamer Microarray (SAM) and the specificity of the sandwich formation for the developed aptasensor for human thrombin were optimized.
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34
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Abstract
Aptamers are single-stranded structured oligonucleotides (DNA or RNA) that can bind to a wide range of targets ("apatopes") with high affinity and specificity. These nucleic acid ligands, generated from pools of random-sequence by an in vitro selection process referred to as systematic evolution of ligands by exponential enrichment (SELEX), have now been identified as excellent tools for chemical biology, therapeutic delivery, diagnosis, research, and monitoring therapy in real-time imaging. Today, aptamers represent an interesting class of modern Pharmaceuticals which with their low immunogenic potential mimic extend many of the properties of monoclonal antibodies in diagnostics, research, and therapeutics. More recently, chimeric aptamer approach employing many different possible types of chimerization strategies has generated more stable and efficient chimeric aptamers with aptamer-aptamer, aptamer-nonaptamer biomacromolecules (siRNAs, proteins) and aptamer-nanoparticle chimeras. These chimeric aptamers when conjugated with various biomacromolecules like locked nucleic acid (LNA) to potentiate their stability, biodistribution, and targeting efficiency, have facilitated the accurate targeting in preclinical trials. We developed LNA-aptamer (anti-nucleolin and EpCAM) complexes which were loaded in iron-saturated bovine lactofeerin (Fe-blf)-coated dopamine modified surface of superparamagnetic iron oxide (Fe3O4) nanoparticles (SPIONs). This complex was used to deliver the specific aptamers in tumor cells in a co-culture model of normal and cancer cells. This review focuses on the chimeric aptamers, currently in development that are likely to find future practical applications in concert with other therapeutic molecules and modalities.
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Affiliation(s)
- Jagat R Kanwar
- Nanomedicine Laboratory of Immunology and Molecular Biomedical Research (LIMBR), Centre for Biotechnology and Interdisciplinary Biosciences (BioDeakin), Institute for Technology and Research Innovation (ITRI), Geelong Technology Precinct (GTP), Deakin University, Victoria, Australia.
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35
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Matylla-Kulinska K, Boots JL, Zimmermann B, Schroeder R. Finding aptamers and small ribozymes in unexpected places. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:73-91. [PMID: 21853532 DOI: 10.1002/wrna.105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The discovery of the catalytic properties of RNAs was a milestone for our view of how life emerged and forced us to reformulate many of our dogmas. The urge to grasp the whole spectrum of potential activities of RNA molecules stimulated two decades of fervent research resulting in a deep understanding of RNA-based phenomena. Most ribozymes were discovered by serendipity during the analysis of chemical processes, whereas RNA aptamers were identified through meticulous design and selection even before their discovery in nature. The desire to obtain aptamers led to the development of sophisticated technology and the design of efficient strategies. With the new notion that transcriptomes cover a major part of genomes and determine the identity of cells, it is reasonable to speculate that many more aptamers and ribozymes are awaiting their discovery in unexpected places. Now, in the genomic era with the development of powerful bioinformatics and sequencing methods, we are overwhelmed with tools for studying the genomes of all living and possibly even extinct organisms. Genomic SELEX (systematic evolution of ligands by exponential enrichment) coupled with deep sequencing and sophisticated computational analysis not only gives access to unexplored parts of sequenced genomes but also allows screening metagenomes in an unbiased manner.
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Affiliation(s)
- Katarzyna Matylla-Kulinska
- Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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36
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Bogomolova A, Aldissi M. Real-time aptamer quantum dot fluorescent flow sensor. Biosens Bioelectron 2011; 26:4099-103. [PMID: 21515039 DOI: 10.1016/j.bios.2011.04.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 03/21/2011] [Accepted: 04/01/2011] [Indexed: 11/30/2022]
Abstract
The goal of this work was to develop and test a novel real-time biosensing approach which can be adapted to either environmental or clinical monitoring of biological pathogens. We have developed a working prototype of a real-time aptamer-based fluorescent flow sensor. The sensor utilizes a competitive displacement approach to measure the binding of the analyte, which keeps the nonspecific binding below detectable levels. The complex of surface-immobilized DNA aptamer with fluorescent complementary oligonucleotide releases the oligonucleotide upon binding with a specific target, which is translated by a decrease in fluorescence. Bright and stable fluorescence of quantum dots is utilized for prolonged detection of the analyte in flow conditions. The real-time sensor prototype is developed with previously characterized ATP-specific aptamer and is capable of specifically detecting 0.1 mM of ATP in biological buffer, with a quantitative response up to 5 mM. The developed prototype is portable and easy to use and its design allows further miniaturization and multiplexing. The developed real-time sensing approach can be adapted to a variety of targets of environmental and clinical significance.
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Affiliation(s)
- Anastasia Bogomolova
- Smart Polymers Research Corporation, 108 4th Street, Belleair Beach, FL 33786, USA
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37
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38
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39
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Optical detection systems using immobilized aptamers. Biosens Bioelectron 2011; 26:3725-36. [PMID: 21419619 DOI: 10.1016/j.bios.2011.02.031] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/16/2011] [Accepted: 02/18/2011] [Indexed: 11/24/2022]
Abstract
Advances in the development and the applications of optical biosensing systems based on immobilized aptamers are presented. These nucleic acid sequences have been used as new molecular recognition elements to develop heterogeneous assays, biosensors and microarrays. Among different detection modes that have been employed, optical ones which are described here are among the most used. Since their first report in 1996, numerous optical detection systems using aptamers and mainly based on fluorescence have been developed. Two main approaches have been used: label-based (using fluorophore, luminophore, enzyme, nanoparticles) or aptamer label-free detection systems (e.g. surface plasmon resonance, optical resonance). Most methods are based on a labeling approach. Some targets can be optically detected using not only colorimetry, chemiluminescence or the most developed fluorescence mode but also more recent non conventional optical methods such as surface plasmon-coupled directional emission (SPCDE). The first SPCDE-based aptasensor for thrombin detection has recently been reported in 2009. Aptasensors based on surface-enhanced Raman scattering spectroscopy (SERS) which presents advantages compared to fluorescence have also been described. Different label-free techniques have recently been shown to be suitable for developing performant aptasensors or aptamer-based microarrays, such as surface plasmon resonance (SPR), diffraction grating, evanescent-field-coupled (EFC) waveguide-mode, optical resonance or Brewster angle straddle interferometry (BASI). Important advances have been realized on optical aptamer-based detection systems that appear as highly efficient devices with enormous potential.
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40
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Abstract
In less than 40 years, aptamers have consolidated their role in biosensor development. Chemically related to nucleic acid probes, production of aptamers against targets of various sizes and compositions places them as ideal capture elements, alternative to more consolidated molecules such as antibodies. Thanks to their chemical simplicity and production, as well as their unique characteristics, aptamers have been successfully integrated in several innovative approaches. The incorporation of aptamers into the existing microarray technologies has lead to the reporting of various detection strategies, including direct fluorescence detection of fluorescent reporters, fluorescence anisotropy, FRET, SPR imaging, and electrochemical detection.
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Affiliation(s)
- Eva Baldrich
- Instituto de Microelectrónica de Barcelona (IMB-CNM), Barcelona, Spain.
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41
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Ye BF, Zhao YJ, Li TT, Xie ZY, Gu ZZ. Aptamer-based suspension array indexed by structural color and shape. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm14009d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Xie S, Walton SP. Development of a dual-aptamer-based multiplex protein biosensor. Biosens Bioelectron 2010; 25:2663-8. [PMID: 20547050 PMCID: PMC2891049 DOI: 10.1016/j.bios.2010.04.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 04/24/2010] [Accepted: 04/26/2010] [Indexed: 11/28/2022]
Abstract
Parallel biosensors for proteins are becoming more essential for the thorough and systematic investigation of complex biological processes. These tools also enable improved clinical diagnoses relative to single-protein analyses due to their greater information content. If implemented correctly, affinity-based techniques can provide unique advantages in terms of sensitivity and flexibility. Aptamers are increasingly being used as the affinity reagents of choice for protein biosensing applications. Here, we describe the development and characterization of an aptamer-based method for parallel protein analyses that relies on recognition of the target protein by two unique aptamers targeting different epitopes on the protein. Our results show that the technique achieved simultaneous and quantitative detection of thrombin and platelet-derived growth factor-BB (PDGF-BB) with high specificity both in buffered solutions and in serum samples.
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Affiliation(s)
- Shengnan Xie
- Applied Biomolecular Engineering Laboratory of the Cellular and Biomolecular Laboratory, Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, 48824, USA
| | - S. Patrick Walton
- Applied Biomolecular Engineering Laboratory of the Cellular and Biomolecular Laboratory, Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, 48824, USA
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43
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Abstract
Aptamers are nucleic acid sequences synthesized through in vitro selection and amplification technique, possessing a broader range of applications in therapeutics, biosensing, diagnostics, and research. Aptamers offer a number of advantages over their antibodies counterpart, one of them is their ability to undergo chemical derivatization to increase their life in the body fluids and bioavailability in animals. Although aptamers were discovered in 1990s, they have become one of the most widely investigated molecules, with a huge number of publications in the last decade. This article presents an overview of the advancements that have been made in aptamers. We mainly focused on articles published since 2005.
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Affiliation(s)
- Muhammad Ali Syed
- Department of Biosciences, Comsats Institute of Information Technology, Islamabad, Pakistan.
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44
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Tuleuova N, Jones CN, Yan J, Ramanculov E, Yokobayashi Y, Revzin A. Development of an aptamer beacon for detection of interferon-gamma. Anal Chem 2010; 82:1851-7. [PMID: 20121141 DOI: 10.1021/ac9025237] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Traditional antibody-based affinity sensing strategies employ multiple reagents and washing steps and are unsuitable for real-time detection of analyte binding. Aptamers, on the other hand, may be designed to monitor binding events directly, in real-time, without the need for secondary labels. The goal of the present study was to design an aptamer beacon for fluorescence resonance energy transfer (FRET)-based detection of interferon-gamma (IFN-gamma)--an important inflammatory cytokine. Variants of DNA aptamer modified with biotin moieties and spacers were immobilized on avidin-coated surfaces and characterized by surface plasmon resonance (SPR). The SPR studies showed that immobilization of aptamer via the 3' end resulted in the best binding IFN-gamma (K(d) = 3.44 nM). This optimal aptamer variant was then used to construct a beacon by hybridizing fluorophore-labeled aptamer with an antisense oligonucleotide strand carrying a quencher. SPR studies revealed that IFN-gamma binding with an aptamer beacon occurred within 15 min of analyte introduction--suggesting dynamic replacement of the quencher-complementary strand by IFN-gamma molecules. To further highlight biosensing applications, aptamer beacon molecules were immobilized inside microfluidic channels and challenged with varying concentration of analyte. Fluorescence microscopy revealed low fluorescence in the absence of analyte and high fluorescence after introduction of IFN-gamma. Importantly, unlike traditional antibody-based immunoassays, the signal was observed directly upon binding of analyte without the need for multiple washing steps. The surface immobilized aptamer beacon had a linear range from 5 to 100 nM and a lower limit of detection of 5 nM IFN-gamma. In conclusion, we designed a FRET-based aptamer beacon for monitoring of an inflammatory cytokine-IFN-gamma. In the future, this biosensing strategy will be employed to monitor dynamics of cytokine production by the immune cells.
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Affiliation(s)
- Nazgul Tuleuova
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA
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45
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Densmore D, Hsiau THC, Kittleson JT, DeLoache W, Batten C, Anderson JC. Algorithms for automated DNA assembly. Nucleic Acids Res 2010; 38:2607-16. [PMID: 20335162 PMCID: PMC2860133 DOI: 10.1093/nar/gkq165] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Generating a defined set of genetic constructs within a large combinatorial space provides a powerful method for engineering novel biological functions. However, the process of assembling more than a few specific DNA sequences can be costly, time consuming and error prone. Even if a correct theoretical construction scheme is developed manually, it is likely to be suboptimal by any number of cost metrics. Modular, robust and formal approaches are needed for exploring these vast design spaces. By automating the design of DNA fabrication schemes using computational algorithms, we can eliminate human error while reducing redundant operations, thus minimizing the time and cost required for conducting biological engineering experiments. Here, we provide algorithms that optimize the simultaneous assembly of a collection of related DNA sequences. We compare our algorithms to an exhaustive search on a small synthetic dataset and our results show that our algorithms can quickly find an optimal solution. Comparison with random search approaches on two real-world datasets show that our algorithms can also quickly find lower-cost solutions for large datasets.
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Affiliation(s)
- Douglas Densmore
- Department of Fuel Synthesis, Joint BioEnergy Institute, 5885 Hollis St., Fourth Floor, Emeryville CA 94608, USA.
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46
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Xie S, Moya C, Bilgin B, Jayaraman A, Walton SP. Emerging affinity-based techniques in proteomics. Expert Rev Proteomics 2010; 6:573-83. [PMID: 19811078 DOI: 10.1586/epr.09.74] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Proteomes of interest, such as the human proteome, have such complexity that no single technique is adequate for the complete analysis of the constituents. Depending on the goal (e.g., identification of a novel protein vs measurement of the level of a known protein), the tools required can vary significantly. While existing methods provide valuable information, their limitations drive the development of complementary, innovative methods to achieve greater breadth of coverage, dynamic range or specificity of analysis. We will discuss affinity-based methods and their applications, focusing on their unique advantages. In addition, we will describe emerging methods with potential value to proteomics, as well as the challenges that remain for proteomic studies.
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Affiliation(s)
- Shengnan Xie
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA
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47
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Thiel KW, Giangrande PH. Therapeutic applications of DNA and RNA aptamers. Oligonucleotides 2009; 19:209-22. [PMID: 19653880 DOI: 10.1089/oli.2009.0199] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Structured single-stranded nucleic acids, or aptamers, bind target molecules with high affinity and specificity, which translates into unique therapeutic possibilities. Currently, aptamers can be identified to most proteins, including blood-clotting factors, cell-surface receptors, and transcription factors. Chemical modifications to the oligonucleotides enhance their pharmacokinetics and pharmacodynamics, thus extending their therapeutic potential. Several aptamers have entered the clinical pipeline for applications and diseases such as macular degeneration, coronary artery bypass graft surgery, and various types of cancer. Furthermore, the functional repertoire of aptamers has expanded with the descriptions of multivalent agonistic aptamers and aptamers-siRNA chimeras. This review highlights those aptamers and aptamer-based approaches with particular likelihood of achieving therapeutic application.
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Affiliation(s)
- Kristina W Thiel
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
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48
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Torres-Chavolla E, Alocilja EC. Aptasensors for detection of microbial and viral pathogens. Biosens Bioelectron 2009; 24:3175-82. [PMID: 19117748 PMCID: PMC7125720 DOI: 10.1016/j.bios.2008.11.010] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 11/14/2008] [Accepted: 11/17/2008] [Indexed: 12/01/2022]
Abstract
Aptamers are specific nucleic acid sequences that can bind to a wide range of non-nucleic acid targets with high affinity and specificity. These molecules are identified and selected through an in vitro process called SELEX (systematic evolution of ligands by exponential enrichment). Proteins are the most common targets in aptamer selection. In diagnostic and detection assays, aptamers represent an alternative to antibodies as recognition agents. Cellular detection is a promising area in aptamer research. One of its principal advantages is the ability to target and specifically differentiate microbial strains without having previous knowledge of the membrane molecules or structural changes present in that particular microorganism. The present review focuses on aptamers, SELEX procedures, and aptamer-based biosensors (aptasensors) for the detection of pathogenic microorganisms and viruses. Special emphasis is placed on nanoparticle-based platforms.
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Affiliation(s)
- Edith Torres-Chavolla
- Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA
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49
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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50
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Davis JJ, Tkac J, Humphreys R, Buxton AT, Lee TA, Ko Ferrigno P. Peptide Aptamers in Label-Free Protein Detection: 2. Chemical Optimization and Detection of Distinct Protein Isoforms. Anal Chem 2009; 81:3314-20. [DOI: 10.1021/ac802513n] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jason J. Davis
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, and Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Beckett Street, Leeds LS9 7TF
| | - Jan Tkac
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, and Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Beckett Street, Leeds LS9 7TF
| | - Rachel Humphreys
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, and Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Beckett Street, Leeds LS9 7TF
| | - Anthony T. Buxton
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, and Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Beckett Street, Leeds LS9 7TF
| | - Tracy A. Lee
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, and Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Beckett Street, Leeds LS9 7TF
| | - Paul Ko Ferrigno
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, and Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Beckett Street, Leeds LS9 7TF
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