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Görner A, Franz L, Çanak-Ipek T, Avci-Adali M, Marel AK. Development of an Aptamer-Based QCM-D Biosensor for the Detection of Thrombin Using Supported Lipid Bilayers as Surface Functionalization. BIOSENSORS 2024; 14:270. [PMID: 38920574 PMCID: PMC11201429 DOI: 10.3390/bios14060270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/02/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024]
Abstract
Biosensors play an important role in numerous research fields. Quartz crystal microbalances with dissipation monitoring (QCM-Ds) are sensitive devices, and binding events can be observed in real-time. In combination with aptamers, they have great potential for selective and label-free detection of various targets. In this study, an alternative surface functionalization for a QCM-D-based aptasensor was developed, which mimics an artificial cell membrane and thus creates a physiologically close environment for the binding of the target to the sensor. Vesicle spreading was used to form a supported lipid bilayer (SLB) of 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphethanolamine-N-(cap biotinyl) (biotin-PE). The SLB was then coated with streptavidin followed by applying a biotinylated aptamer against thrombin. SLB formation was investigated in terms of temperature and composition. Temperatures of 25 °C and below led to incomplete SLB formation, whereas a full bilayer was built at higher temperatures. We observed only a small influence of the content of biotinylated lipids in the mixture on the further binding of streptavidin. The functionalization of the sensor surface with the thrombin aptamer and the subsequent thrombin binding were investigated at different concentrations. The sensor could be reconstituted by incubation with a 5 M urea solution, which resulted in the release of the thrombin from the sensor surface. Thereafter, it was possible to rebind thrombin. Thrombin in spiked samples of human serum was successfully detected. The developed system can be easily applied to other target analytes using the desired aptamers.
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Affiliation(s)
- Anne Görner
- Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany; (A.G.); (L.F.)
| | - Leyla Franz
- Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany; (A.G.); (L.F.)
| | - Tuba Çanak-Ipek
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tübingen, 72076 Tübingen, Germany; (T.Ç.-I.); (M.A.-A.)
| | - Meltem Avci-Adali
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tübingen, 72076 Tübingen, Germany; (T.Ç.-I.); (M.A.-A.)
| | - Anna-Kristina Marel
- Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany; (A.G.); (L.F.)
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Zia A, Wu Y, Nguyen T, Wang X, Peter K, Ta HT. The choice of targets and ligands for site-specific delivery of nanomedicine to atherosclerosis. Cardiovasc Res 2021; 116:2055-2068. [PMID: 32077918 DOI: 10.1093/cvr/cvaa047] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/23/2019] [Accepted: 02/17/2020] [Indexed: 12/22/2022] Open
Abstract
As nanotechnologies advance into clinical medicine, novel methods for applying nanomedicine to cardiovascular diseases are emerging. Extensive research has been undertaken to unlock the complex pathogenesis of atherosclerosis. However, this complexity presents challenges to develop effective imaging and therapeutic modalities for early diagnosis and acute intervention. The choice of ligand-receptor system vastly influences the effectiveness of nanomedicine. This review collates current ligand-receptor systems used in targeting functionalized nanoparticles for diagnosis and treatment of atherosclerosis. Our focus is on the binding affinity and selectivity of ligand-receptor systems, as well as the relative abundance of targets throughout the development and progression of atherosclerosis. Antibody-based targeting systems are currently the most commonly researched due to their high binding affinities when compared with other ligands, such as antibody fragments, peptides, and other small molecules. However, antibodies tend to be immunogenic due to their size. Engineering antibody fragments can address this issue but will compromise their binding affinity. Peptides are promising ligands due to their synthetic flexibility and low production costs. Alongside the aforementioned binding affinity of ligands, the choice of target and its abundance throughout distinct stages of atherosclerosis and thrombosis is relevant to the intended purpose of the nanomedicine. Further studies to investigate the components of atherosclerotic plaques are required as their cellular and molecular profile shifts over time.
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Affiliation(s)
- Adil Zia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuao Wu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.,School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Tuan Nguyen
- School of Chemical Engineering, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Xiaowei Wang
- Baker Heart and Diabetes Institute, Melbourne, VIC 3000, Australia
| | - Karlheinz Peter
- Baker Heart and Diabetes Institute, Melbourne, VIC 3000, Australia
| | - Hang T Ta
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.,School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Woolloongabba, QLD 4102, Australia
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Ștefan G, Hosu O, De Wael K, Lobo-Castañón MJ, Cristea C. Aptamers in biomedicine: Selection strategies and recent advances. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.137994] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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4
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Ducongé F. Aptamers for Molecular Imaging. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00034-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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5
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Application of aptamers for in vivo molecular imaging and theranostics. Adv Drug Deliv Rev 2018; 134:94-106. [PMID: 30125606 DOI: 10.1016/j.addr.2018.08.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 07/06/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022]
Abstract
Nucleic acid aptamers are small three-dimensional structures of oligonucleotides selected to bind to a target of interest with high affinity and specificity. In vitro, aptamers already compete with antibodies to serve as imaging probes, e.g. for microscopy or flow cytometry. However, they are also increasingly used for in vivo molecular imaging. Accordingly, aptamers have been evaluated over the last twenty years in almost every imaging modality, including single photon emission computed tomography, positron emission tomography, magnetic resonance imaging, fluorescence imaging, echography, and x-ray computed tomography. This review focuses on the studies that were conducted in vivo with aptamer-based imaging probes. It also presents how aptamers have been recently used to develop new types of probes for multimodal imaging and theranostic applications.
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Ferreira IM, de Sousa Lacerda CM, Dos Santos SR, de Barros ALB, Fernandes SO, Cardoso VN, de Andrade ASR. Detection of bacterial infection by a technetium-99m-labeled peptidoglycan aptamer. Biomed Pharmacother 2017; 93:931-938. [PMID: 28715874 DOI: 10.1016/j.biopha.2017.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 10/19/2022] Open
Abstract
Nuclear medicine clinicians are still waiting for the optimal scintigraphic imaging agents capable of distinguishing between infection and inflammation, and between fungal and bacterial infections. Aptamers have several properties that make them suitable for molecular imaging. In the present study, a peptidoglycan aptamer (Antibac1) was labeled with 99mTc and evaluated by biodistribution studies and scintigraphic imaging in infection-bearing mice. Labeling with 99mTc was performed by the direct method and the complex stability was evaluated in saline, plasma and in the molar excess of cysteine. The biodistribution and scintigraphic imaging studies with the 99mTc-Antibac1 were carried out in two different experimental infection models: Bacterial-infected mice (S. aureus) and fungal-infected mice (C. albicans). A 99mTc radiolabeled library, consisting of oligonucleotides with random sequences, was used as a control for both models. Radiolabeling yields were superior to 90% and 99mTc-Antibac1 was highly stable in presence of saline, plasma, and cysteine up to 6h. Scintigraphic images of S. aureus infected mice at 1.5 and 3.0h after 99mTc-Antibac1 injection showed target to non-target ratios of 4.7±0.9 and 4.6±0.1, respectively. These values were statistically higher than those achieved for the 99mTc-library at the same time frames (1.6±0.4 and 1.7±0.4, respectively). Noteworthy, 99mTc-Antibac1 and 99mTc-library showed similar low target to non-target ratios in the fungal-infected model: 2.0±0.3 and 2.0±0.6for 99mTc-Antibac1 and 2.1±0.3 and 1.9 ± 0.6 for 99mTc-library, at the same times. These findings suggest that the 99mTc-Antibac1 is a feasible imaging probe to identify a bacterial infection focus. In addition, this radiolabeled aptamer seems to be suitable in distinguishing between bacterial and fungal infection.
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Affiliation(s)
- Iêda Mendes Ferreira
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Rua Professor Mário Werneck S/N°, Cidade Universitária, Campus da UFMG, 31120-970, Belo Horizonte, MG, Brazil.
| | - Camila Maria de Sousa Lacerda
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Rua Professor Mário Werneck S/N°, Cidade Universitária, Campus da UFMG, 31120-970, Belo Horizonte, MG, Brazil.
| | - Sara Roberta Dos Santos
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Rua Professor Mário Werneck S/N°, Cidade Universitária, Campus da UFMG, 31120-970, Belo Horizonte, MG, Brazil.
| | - André Luís Branco de Barros
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Cidade Universitária, Campus da UFMG, 31270-091, Belo Horizonte, MG, Brazil.
| | - Simone Odília Fernandes
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Cidade Universitária, Campus da UFMG, 31270-091, Belo Horizonte, MG, Brazil.
| | - Valbert Nascimento Cardoso
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Cidade Universitária, Campus da UFMG, 31270-091, Belo Horizonte, MG, Brazil.
| | - Antero Silva Ribeiro de Andrade
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Rua Professor Mário Werneck S/N°, Cidade Universitária, Campus da UFMG, 31120-970, Belo Horizonte, MG, Brazil.
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Santos SRD, de Sousa Lacerda CM, Ferreira IM, de Barros ALB, Fernandes SO, Cardoso VN, de Andrade ASR. Scintigraphic imaging of Staphylococcus aureus infection using 99mTc radiolabeled aptamers. Appl Radiat Isot 2017; 128:22-27. [PMID: 28683356 DOI: 10.1016/j.apradiso.2017.06.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/09/2017] [Accepted: 06/27/2017] [Indexed: 01/31/2023]
Abstract
Staphylococcus aureus is a specie of great medical importance associated with many infections as bacteremia and infective endocarditis as well as osteoarticular, skin and soft tissue, pleuropulmonary, and device related infections. Early identification of infectious foci is crucial for successful treatment. Scintigraphy could contribute to this purpose since specific radiotracers were available. Aptamers due to their high specificity have great potential for radiopharmaceuticals development. In the present study scintigraphic images of S. aureus infectious foci were obtained using specific S. aureus aptamers radiolabeled with 99mTc.
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Affiliation(s)
- Sara Roberta Dos Santos
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Rua Professor Mário Werneck S/No, Cidade Universitária-Campus da UFMG, 31120-970 Belo Horizonte, MG, Brazil.
| | - Camila Maria de Sousa Lacerda
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Rua Professor Mário Werneck S/No, Cidade Universitária-Campus da UFMG, 31120-970 Belo Horizonte, MG, Brazil.
| | - Iêda Mendes Ferreira
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Rua Professor Mário Werneck S/No, Cidade Universitária-Campus da UFMG, 31120-970 Belo Horizonte, MG, Brazil.
| | - André Luís Branco de Barros
- Departamento de Análises Clínicas e Toxicológicas - Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Cidade Universitária - Campus da UFMG, 31270-091 Belo Horizonte, MG, Brazil.
| | - Simone Odília Fernandes
- Departamento de Análises Clínicas e Toxicológicas - Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Cidade Universitária - Campus da UFMG, 31270-091 Belo Horizonte, MG, Brazil.
| | - Valbert Nascimento Cardoso
- Departamento de Análises Clínicas e Toxicológicas - Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Cidade Universitária - Campus da UFMG, 31270-091 Belo Horizonte, MG, Brazil.
| | - Antero Silva Ribeiro de Andrade
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Rua Professor Mário Werneck S/No, Cidade Universitária-Campus da UFMG, 31120-970 Belo Horizonte, MG, Brazil.
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Chen K, Stafford AR, Wu C, Yeh CH, Kim PY, Fredenburgh JC, Weitz JI. Exosite 2-Directed Ligands Attenuate Protein C Activation by the Thrombin–Thrombomodulin Complex. Biochemistry 2017; 56:3119-3128. [DOI: 10.1021/acs.biochem.7b00250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kai Chen
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Alan R. Stafford
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Chengliang Wu
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Calvin H. Yeh
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Paul Y. Kim
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - James C. Fredenburgh
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Jeffrey I. Weitz
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
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9
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de Sousa Lacerda CM, Ferreira IM, Dos Santos SR, de Barros ALB, Fernandes SO, Cardoso VN, de Andrade ASR. (1→3)-β-D-glucan aptamers labeled with technetium-99m: Biodistribution and imaging in experimental models of bacterial and fungal infection. Nucl Med Biol 2016; 46:19-24. [PMID: 27951452 DOI: 10.1016/j.nucmedbio.2016.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/18/2016] [Accepted: 11/24/2016] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Acid nucleic aptamers are RNA or DNA oligonucleotides capable of binding to a target molecule with high affinity and selectivity. These molecules are promising tools in nuclear medicine. Many aptamers have been used as targeting molecule of radiopharmaceuticals in preclinical studies. (1→3)-β-D-glucans are the main structural cell wall components of fungi and some bacteria. In the present study two radiolabeled (1→3)-β-D-glucan aptamers (seq6 and seq30) were evaluated to identity infectious foci caused by fungal or bacterial cells. METHODS Aptamer labeling with 99mTc was performed by the direct method and biodistribution studies were accomplished in Swiss mice (n=6) infected in the right thigh muscle with Staphylococcus aureus or Candida albicans. A 99mTc radiolabeled library consisting of oligonucleotides with random sequences was used as control. RESULTS There was a higher uptake of 99mTc radiolabeled aptamers in the infected thigh than in the left thigh muscle (non-infected) in the S. aureus infected animals. The target/non-target ratios were 3.17±0.22 for seq6 and 2.66±0.10 for seq30. These ratios were statistically higher than the value (1.54±0.05) found for the radiolabeled library (control). With regard to biodistribution, no statistical difference was verified between aptamers and control uptakes in the infection foci in the C. albicans infected animals. The target/non-target ratios were 1.53±0.03, 1.64±0.12 and 1.08±0.02 for radiolabeled library, seq6 and seq30, respectively. Scintigraphic imaging of infected foci using radiolabeled aptamers was possible only for S. aureus infected mice. CONCLUSIONS Seq6 and seq30 aptamers proved to be inefficient for diagnosis of C. albicans infection. Nevertheless, their applicability for diagnosis of S. aureus and other bacterial infections by scintigraphy should be further explored.
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Affiliation(s)
- Camila Maria de Sousa Lacerda
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Rua Professor Mário Werneck S/N°, Cidade Universitária-Campus da UFMG, Belo Horizonte, MG 31120-970, Brazil.
| | - Iêda Mendes Ferreira
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Rua Professor Mário Werneck S/N°, Cidade Universitária-Campus da UFMG, Belo Horizonte, MG 31120-970, Brazil.
| | - Sara Roberta Dos Santos
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Rua Professor Mário Werneck S/N°, Cidade Universitária-Campus da UFMG, Belo Horizonte, MG 31120-970, Brazil.
| | - André Luís Branco de Barros
- Departamento de Análises Clínicas e Toxicológicas-Faculdade de Farmácia, Universidade Federal de Minas Gerais, Cidade Universitária-Campus da UFMG, Belo Horizonte, MG 31270-091, Brazil.
| | - Simone Odília Fernandes
- Departamento de Análises Clínicas e Toxicológicas-Faculdade de Farmácia, Universidade Federal de Minas Gerais, Cidade Universitária-Campus da UFMG, Belo Horizonte, MG 31270-091, Brazil.
| | - Valbert Nascimento Cardoso
- Departamento de Análises Clínicas e Toxicológicas-Faculdade de Farmácia, Universidade Federal de Minas Gerais, Cidade Universitária-Campus da UFMG, Belo Horizonte, MG 31270-091, Brazil.
| | - Antero Silva Ribeiro de Andrade
- Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Rua Professor Mário Werneck S/N°, Cidade Universitária-Campus da UFMG, Belo Horizonte, MG 31120-970, Brazil.
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Gijs M, Aerts A, Impens N, Baatout S, Luxen A. Aptamers as radiopharmaceuticals for nuclear imaging and therapy. Nucl Med Biol 2015; 43:253-71. [PMID: 26746572 DOI: 10.1016/j.nucmedbio.2015.09.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/24/2015] [Accepted: 09/10/2015] [Indexed: 12/27/2022]
Abstract
Today, radiopharmaceuticals belong to the standard instrumentation of nuclear medicine, both in the context of diagnosis and therapy. The majority of radiopharmaceuticals consist of targeting biomolecules which are designed to interact with a disease-related molecular target. A plethora of targeting biomolecules of radiopharmaceuticals exists, including antibodies, antibody fragments, proteins, peptides and nucleic acids. Nucleic acids have some significant advantages relative to proteinaceous biomolecules in terms of size, production, modifications, possible targets and immunogenicity. In particular, aptamers (non-coding, synthetic, single-stranded DNA or RNA oligonucleotides) are of interest because they can bind a molecular target with high affinity and specificity. At present, few aptamers have been investigated preclinically for imaging and therapeutic applications. In this review, we describe the use of aptamers as targeting biomolecules of radiopharmaceuticals. We also discuss the chemical modifications which are needed to turn aptamers into valuable (radio-)pharmaceuticals, as well as the different radiolabeling strategies that can be used to radiolabel oligonucleotides and, in particular, aptamers.
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Affiliation(s)
- Marlies Gijs
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium; Cyclotron Research Centre, University of Liège, Liège, Belgium
| | - An Aerts
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
| | - Nathalie Impens
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
| | - André Luxen
- Cyclotron Research Centre, University of Liège, Liège, Belgium.
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Le TT, Scott S, Cass AEG. Streptavidin binding bifunctional aptamers and their interaction with low molecular weight ligands. Anal Chim Acta 2012; 761:143-8. [PMID: 23312325 DOI: 10.1016/j.aca.2012.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 11/04/2012] [Accepted: 11/09/2012] [Indexed: 02/07/2023]
Abstract
This paper describes the measurement of the binding affinities of two bifunctional RNA aptamers to their respective ligands. The aptamers comprise either a theophylline or malachite green binding sequence fused to a streptavidin binding sequence. These bifunctional aptamers are shown to bind simultaneously to both the small ligand and to streptavidin whether in free solution or on gold surfaces. Binding isotherms for both interactions were measured by different physiochemical techniques: surface plasmon resonance, fluorescence spectroscopy and dynamic light scattering. Both qualitatively and quantitatively there is little difference in binding affinities between the bifunctional aptamers and their monofunctional components. The respective K(d) values for streptavidin binding in the monofunctional aptamer and in the theophylline bifunctional aptamer were 12 nM and 65 nM, respectively whilst the K(d) values for theophylline binding in the monofunctional aptamer and the streptavidin bifunctional aptamer were 300 nM and 120 nM. These results are consistent with treating each aptamer sequence as a module that can be combined with others without significant loss of function. This allows for the use of streptavidin based immobilization strategies without either the cost of biotinylated dNTPs or the variable yields associated with the chemical biotinylation of RNA.
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Affiliation(s)
- Thao T Le
- Department of Chemistry, Imperial College London, SW7 2AZ, UK
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Soontornworajit B, Wang Y. Nucleic acid aptamers for clinical diagnosis: cell detection and molecular imaging. Anal Bioanal Chem 2010; 399:1591-9. [PMID: 21161512 DOI: 10.1007/s00216-010-4559-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 11/24/2010] [Accepted: 12/01/2010] [Indexed: 01/09/2023]
Abstract
Nucleic acid aptamers have recently attracted significant attention in the field of clinical diagnosis because they have numerous merits, such as high affinity, high specificity, small size, little immunogenicity, stable structures, and ease of synthesis. This review focuses on discussing the potential applications of aptamers in cell detection and molecular imaging. For the ex vivo cell detection, this review discusses the status of five strategies: endogenous nucleic acid analysis, flow cytometry analysis, nanoparticle-based cell sensing, microfluidic cell separation, and histological examination. This review also discusses in vivo molecular and cell imaging by introducing aptamer-based molecular imaging, cell imaging, and integrated imaging and therapy. On the basis of the status of these promising studies, this review summarizes several challenging issues and unmet needs that may require more effort or attention in the future.
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Affiliation(s)
- Boonchoy Soontornworajit
- Department of Chemical, Materials & Biomolecular Engineering, University of Connecticut, 191 Auditorium Road, Storrs, CT 06269-3222, USA
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Abstract
The era of ‘modern medicine’ has changed its name to ‘molecular medicine’, and reflects a new age based on personalized medicine utilizing molecular biomarkers in the diagnosis, staging and monitoring of therapy. Alzheimer’s disease has a classical biomarker determined at autopsy with the histologic staining of amyloid accumulation in the brain. Today we can diagnose Alzheimer’s disease using the same classical pathologic biomarker, but now using a noninvasive imaging probe to image the amyloid deposition in a patient and potentially provide treatment strategies and measure their effectiveness. Molecular medicine is the exploitation of biomarkers to detect disease before overt expression of pathology. Physicians can now find, fight and follow disease using imaging, and the need for other disease biomarkers is in high demand. This review will discuss the innovative physical and molecular biomarker probes now being developed for imaging systems and we will introduce the concepts needed for validation and regulatory acceptance of surrogate biomarkers in the detection and treatment of disease.
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Missailidis S, Perkins A. Update: aptamers as novel radiopharmaceuticals: their applications and future prospects in diagnosis and therapy. Cancer Biother Radiopharm 2007; 22:453-68. [PMID: 17803440 DOI: 10.1089/cbr.2007.357] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The production of biomaterials with the capacity to bind tightly and specifically to cell surface receptors of malignant cells can greatly benefit cancer diagnosis and treatment. Whereas antibodies have the ability to specifically recognize some tumor cell makers, their large size and immunogenecity markedly limit their value. The development of nuclease-resistant oligonucleotide agents, termed aptamers, offers an alternative to antibodies as targeting, diagnostic, and delivery agents. Using the systematic evolution of ligands by exponential enrichment (SELEX) methodology or other variations, one can select specific sequences that have appropriate binding affinities and specificities against clinically relevant markers from large libraries of oligonucleotide ligands. Aptamers have been found to bind their targets with high specificity and with dissociation constants in the subnanomolar or picomolar range. However, the possibility for the selected aptamers to be developed as targeting agents for diagnostic imaging or targeted radiotherapy purposes has yet to be realized. Peptide-coupling reactions between amino and carboxylic groups offer the possibility of labeling the aptamers with a number of chelators that, coupled with appropriate radionuclides, would generate novel targeted radiopharmaceuticals for the diagnosis and therapy of disease. The unparalleled combinatorial chemical diversity, small size, and modification ability of aptamers is expected to meet the criteria for robust, generic drug discovery technology and open new horizons for the development of future radiopharmaceuticals.
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Affiliation(s)
- Sotiris Missailidis
- Department of Chemistry, The Open University, Walton Hall, Milton Keynes, UK.
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Famulok M, Hartig JS, Mayer G. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem Rev 2007; 107:3715-43. [PMID: 17715981 DOI: 10.1021/cr0306743] [Citation(s) in RCA: 666] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael Famulok
- LIMES Institute, Program Unit Chemical Biology and Medicinal Chemistry, c/o Kekulé-Institut für Organische Chemie und Biochemie, Gerhard Domagk-Strasse 1, 53121 Bonn, Germany.
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Kretz CA, Stafford AR, Fredenburgh JC, Weitz JI. HD1, a thrombin-directed aptamer, binds exosite 1 on prothrombin with high affinity and inhibits its activation by prothrombinase. J Biol Chem 2006; 281:37477-85. [PMID: 17046833 DOI: 10.1074/jbc.m607359200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Incorporation of prothrombin into the prothrombinase complex is essential for rapid thrombin generation at sites of vascular injury. Prothrombin binds directly to anionic phospholipid membrane surfaces where it interacts with the enzyme, factor Xa, and its cofactor, factor Va. We demonstrate that HD1, a thrombin-directed aptamer, binds prothrombin and thrombin with similar affinities (K(d) values of 86 and 34 nm, respectively) and attenuates prothrombin activation by prothrombinase by over 90% without altering the activation pathway. HD1-mediated inhibition of prothrombin activation by prothrombinase is factor Va-dependent because (a) the inhibitory activity of HD1 is lost if factor Va is omitted from the prothrombinase complex and (b) prothrombin binding to immobilized HD1 is reduced by factor Va. These data suggest that HD1 competes with factor Va for prothrombin binding. Kinetic analyses reveal that HD1 produces a 2-fold reduction in the k(cat) for prothrombin activation by prothrombinase and a 6-fold increase in the K(m), highlighting the contribution of the factor Va-prothrombin interaction to prothrombin activation. As a high affinity, prothrombin exosite 1-directed ligand, HD1 inhibits prothrombin activation more efficiently than Hir(54-65)(SO(3)(-)). These findings suggest that exosite 1 on prothrombin exists as a proexosite only for ligands whose primary target is thrombin rather than prothrombin.
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Affiliation(s)
- Colin A Kretz
- Department of Medicine, McMaster University, and Henderson Research Centre, Hamilton, Ontario L8V 1C3, Canada
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Abstract
Nucleic acid molecules are designed to interact predominantly with proteins or complementary nucleic acids. Interaction of nucleic acids with carbohydrates, abundant constituents of glycoproteins and glycolipids, are not common in cells. Biomedical applications of nucleic acids targeted against oligosaccharides, which are involved in the function of receptors, immune answer, host interaction with invading infectious agents, and cancer metastasis, are feasible. In vitro selection of nucleic acids interacting with oligoand polysaccharides is a promising strategy to identify potential inhibitors of biochemical recognition processes in which carbohydrates are involved. Several RNA and DNA aptamers directed against carbohydrates have already been isolated and characterized. The results are summarized in this article, and an attempt is made to draw initial conclusions concerning the perspectives of the outlined approach.
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Affiliation(s)
- M Sprinzl
- Laboratorium für Biochemie, Universität Bayreuth, 95440 Bayreuth, Germany.
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Tavitian B. Oligonucleotides as radiopharmaceuticals. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2005:1-34. [PMID: 15524208 DOI: 10.1007/3-540-26809-x_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Affiliation(s)
- B Tavitian
- INSERM ERM 103 Service Hospitalier, Frédéric Joliot CEA Direction des Sciences du Vivant Direction de la Recherche Medicale, Orsay, France.
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Dellaire G, Nisman R, Eskiw CH, Bazett-Jones DP. In situ imaging and isolation of proteins using dsDNA oligonucleotides. Nucleic Acids Res 2004; 32:e165. [PMID: 15562000 PMCID: PMC534643 DOI: 10.1093/nar/gnh164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As proteomics initiatives mature, the need will arise for the multiple visualization of proteins and supramolecular complexes within their true context, in situ. Single-stranded DNA and RNA aptamers can be used for low resolution imaging of cellular receptors and cytoplasmic proteins by light microscopy (LM). These techniques, however, cannot be applied to the imaging of nuclear antigens as these single-stranded aptamers bind endogenous RNA and DNA with high affinity. To overcome this problem, we have developed a novel method for the in situ detection of proteins using double-stranded DNA oligonucleotides. To demonstrate this system we have utilized the prokaryotic DNA-binding proteins LacI and TetR as peptide tags to image fusion proteins in situ using dsDNA oligonucleotides encoding either the Lac or Tet operator. Using fluorescent and fluorogold dsDNA oligonucleotides, we localized within the nucleus a TetR-PML fusion protein within promyelocytic leukaemia protein (PML) bodies by LM and a LacI-SC35 fusion protein within nuclear speckles by correlative light and electron microscopy (LM/EM). Isolation of LacI-SC35 was also accomplished by using biotinylated dsDNA and streptavidin sepharose. The use of dsDNA oligonucleotides should complement existing aptamer in situ detection techniques by allowing the multiple detection and localization of nuclear proteins in situ and at high resolution.
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Affiliation(s)
- Graham Dellaire
- Programme in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
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Abstract
Nucleic acid aptamers are molecules that bind to their ligands with high affinity and specificity. Unlike other functional nucleic acids such as antisense oligonucleotides, ribozymes, or siRNAs, aptamers almost never exert their effects on the genetic level. They manipulate their target molecules such as gene products or epitopes directly and site specifically, leaving nontargeted protein functions intact. In a similar way to antibodies, aptamers bind to many different kinds of target molecules with high specificity and can be made to order, but as a result of their different biochemical nature and size they can also be used complementary to antibodies. In some cases, aptamers might be more suitable or more specific than antibody approaches or small molecules, both as scientific and biotechnological tools and as therapeutic agents. Recent examples of characterization of aptamers as tools for scientific research to study regulatory circuits, as tools in diagnostic or biosensor development, and as therapeutic agents are discussed.
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Affiliation(s)
- Martina Rimmele
- Research & Development, RiNA Netzwerk RNA Technologien GmbH, Takustrasse 3, 14195 Berlin, Germany.
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Abstract
BACKGROUND The systematic evolution of ligands by exponential enrichment (SELEX) technique is a combinatorial library approach in which DNA or RNA molecules (aptamers) are selected by their ability to bind their protein targets with high affinity and specificity, comparable to that of monoclonal antibodies. In contrast to antibodies conventionally selected in animals, aptamers are generated by an in vitro selection process, and can be directed against almost every target, including antigens like toxins or nonimmunogenic targets, against which conventional antibodies cannot be raised. METHODS Aptamers are ideal candidates for cytomics, as they can be attached to fluorescent reporters or nanoparticles in order to study biological function by fluorescence microscopy, by flow cytometry, or to quantify the concentration of their target in biological fluids or cells using ELISA, RIA, and Western blot assays. RESULTS We demonstrate the in vitro selection of anti-kinin B1 receptor aptamers that could be used to determine B1 receptor expression during inflammation processes. These aptamers specifically recognize their target in a Northern-Western blot assay, and bind to their target protein whenever they are exposed in the membrane. CONCLUSIONS Currently, aptamers are linked to fluorescent reporters. We discuss here the present status and future directions concerning the use of the SELEX technique in cytomics.
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Affiliation(s)
- Henning Ulrich
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
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Kuhnast B, Klussmann S, Hinnen F, Boisgard R, Rousseau B, Fürste JP, Tavitian B, Dollé F. Fluorine-18- and iodine-125-labelling of spiegelmers. J Labelled Comp Radiopharm 2003. [DOI: 10.1002/jlcr.781] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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