201
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Ocsoy I, Isiklan N, Cansiz S, Özdemir N, Tan W. ICG-conjugated Magnetic Graphene Oxide for Dual Photothermal and Photodynamic Therapy. RSC Adv 2016; 6:30285-30292. [PMID: 27774142 PMCID: PMC5070673 DOI: 10.1039/c6ra06798k] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Aptamer-functionalized magnetic graphene oxide conjugates loaded with indocyanine green (ICG) dye, or Apt@ICG@mGO, have been successfully developed for dual-targeted photothermal and photodynamic therapy. In general, a drug or its carrier or their dosage can be imprtant important issues in terms of toxicity. However, in this system, each component used is quite safe, biocompatibe and clean. For instance, ICG, a Food and Drug Administration (FDA) approved near-infrared (NIR) dye, serves as both a photothermal and photodynamic agent. It is immobilized on the surface of mGO via a physical interaction called "π-π stacking". The mGO, as a most biocomptible member of the carbo family, is selected for use as a platform for aptamer and ICG dye conjugation, as well as as a photothermal agent. The light in the near-infrared region (NIR) was chosen as a harmless light source for activating the agents for photothermal therapy (PTT) and photodynamic therapy (PDT). The magnetic properties of mGO are also used for separation of Apt@ICG@mGO conjugates from the reaction medium. Aptamer sgc8 acts as a targeting ligand to selectively and specifically bind to a protein on the membrane of cancer cell line CCRF-CEM. After the aptamer- functionalized ICG@mGO conjugates are incubated with target CEM cells at 37 °C for 2 hours, they are bound to cells or they may be internalized into the cell via endocytosis. More significantly, we demonstrated that the Apt@ICG@mGO conjugates produce heat for photothermal therapy (PTT) and singlet oxygen for photodynamic therapy (PDT) upon NIR laser irradiation at 808 nm. Thus, remarkably efficient cancer cell destructions with ~41% and ~60% and ~82% cell killing using 10, 50 and 100 ppm Apt@ICG@mGO, respectively are achieved in 5 min light exposure.
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Affiliation(s)
- Ismail Ocsoy
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611; Department of Analytical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, 38039 Turkey; Nanotechnology Research Center (ERNAM), Erciyes University, Kayseri, 38039 Turkey
| | - Nuran Isiklan
- Department of Chemistry, Science and Arts Faculty, Kırıkkale University, Kırıkkale, 7100 Turkey
| | - Sena Cansiz
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611
| | - Nalan Özdemir
- Department of Chemistry, Faculty of Science, Erciyes University, Kayseri, 38039 Turkey
| | - Weihong Tan
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611
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202
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Gu H, Duan N, Wu S, Hao L, Xia Y, Ma X, Wang Z. Graphene oxide-assisted non-immobilized SELEX of okdaic acid aptamer and the analytical application of aptasensor. Sci Rep 2016; 6:21665. [PMID: 26898784 PMCID: PMC4761938 DOI: 10.1038/srep21665] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/28/2016] [Indexed: 12/25/2022] Open
Abstract
Okadaic acid (OA) is a low-molecular-weight marine toxin from shellfish that causes abdominal pain, vomiting and diarrhea, i.e., diarrheic shellfish poisoning. In this study, a ssDNA aptamer that specifically binds to OA with high affinity was obtained via Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assisted by graphene oxide (GO). This aptamer was then applied to fabricate a novel direct competitive enzyme-linked aptamer assay (ELAA). At the optimized conditions, this ELAA method showed a low detection limit (LOD of 0.01 ng/mL), wide linear range (from 0.025 to 10 ng/mL), good recovery rate (92.86–103.34% in OA-spiked clam samples) and repeatability (RSD of 2.28–4.53%). The proposed method can be used to detect OA in seafood products with high sensitivity and can potentially be adapted for the determination of other small molecular analytes.
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Affiliation(s)
- Huajie Gu
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Nuo Duan
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Shijia Wu
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liling Hao
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Yu Xia
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Ma
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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203
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Kryza D, Debordeaux F, Azéma L, Hassan A, Paurelle O, Schulz J, Savona-Baron C, Charignon E, Bonazza P, Taleb J, Fernandez P, Janier M, Toulmé JJ. Ex Vivo and In Vivo Imaging and Biodistribution of Aptamers Targeting the Human Matrix MetalloProtease-9 in Melanomas. PLoS One 2016; 11:e0149387. [PMID: 26901393 PMCID: PMC4762761 DOI: 10.1371/journal.pone.0149387] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 02/01/2016] [Indexed: 02/07/2023] Open
Abstract
The human Matrix MetalloProtease-9 (hMMP-9) is overexpressed in tumors where it promotes the release of cancer cells thus contributing to tumor metastasis. We raised aptamers against hMMP-9, which constitutes a validated marker of malignant tumors, in order to design probes for imaging tumors in human beings. A chemically modified RNA aptamer (F3B), fully resistant to nucleases was previously described. This compound was subsequently used for the preparation of F3B-Cy5, F3B-S-acetylmercaptoacetyltriglycine (MAG) and F3B-DOTA. The binding properties of these derivatives were determined by surface plasmon resonance and electrophoretic mobility shift assay. Optical fluorescence imaging confirmed the binding to hMMP-9 in A375 melanoma bearing mice. Quantitative biodistribution studies were performed at 30 min, 1h and 2 h post injection of 99mTc-MAG-aptamer and 111In-DOTA-F3B. 99mTc radiolabeled aptamer specifically detected hMMP-9 in A375 melanoma tumors but accumulation in digestive tract was very high. Following i.v. injection of 111In-DOTA-F3B, high level of radioactivity was observed in kidneys and bladder but digestive tract uptake was very limited. Tumor uptake was significantly (student t test, p<0.05) higher for 111In-DOTA-F3B with 2.0%ID/g than for the 111In-DOTA-control oligonucleotide (0.7%ID/g) with tumor to muscle ratio of 4.0. Such difference in tumor accumulation has been confirmed by ex vivo scintigraphic images performed at 1h post injection and by autoradiography, which revealed the overexpression of hMMP-9 in sections of human melanomas. These results demonstrate that F3B aptamer is of interest for detecting hMMP-9 in melanoma tumor.
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Affiliation(s)
- David Kryza
- UNIV Lyon, Université Claude Bernard Lyon 1, LAGEP UMR 5007 CNRS, Villeurbanne, France
- Hospices Civils de Lyon, Imthernat plateform, Lyon, France
| | - Frédéric Debordeaux
- Université de Bordeaux, CNRS, INCIA, UMR 5287, Bordeaux, France
- Service de Médecine Nucléaire, CHU de Bordeaux, Bordeaux, France
| | - Laurent Azéma
- Inserm U1212, Bordeaux, France
- CNRS UMR5320, Pessac, France
- University of Bordeaux, ARNA Laboratory, Bordeaux, France
| | - Aref Hassan
- Inserm U1212, Bordeaux, France
- CNRS UMR5320, Pessac, France
- University of Bordeaux, ARNA Laboratory, Bordeaux, France
| | - Olivier Paurelle
- Inserm U1212, Bordeaux, France
- CNRS UMR5320, Pessac, France
- University of Bordeaux, ARNA Laboratory, Bordeaux, France
| | - Jürgen Schulz
- Université de Bordeaux, CNRS, INCIA, UMR 5287, Bordeaux, France
- Service de Médecine Nucléaire, CHU de Bordeaux, Bordeaux, France
| | | | - Elsa Charignon
- Hospices Civils de Lyon, Imthernat plateform, Lyon, France
| | | | - Jacqueline Taleb
- UNIV Lyon, Université Claude Bernard Lyon 1, LAGEP UMR 5007 CNRS, Villeurbanne, France
| | - Philippe Fernandez
- Université de Bordeaux, CNRS, INCIA, UMR 5287, Bordeaux, France
- Service de Médecine Nucléaire, CHU de Bordeaux, Bordeaux, France
| | - Marc Janier
- UNIV Lyon, Université Claude Bernard Lyon 1, LAGEP UMR 5007 CNRS, Villeurbanne, France
- Hospices Civils de Lyon, Imthernat plateform, Lyon, France
| | - Jean Jacques Toulmé
- Inserm U1212, Bordeaux, France
- CNRS UMR5320, Pessac, France
- University of Bordeaux, ARNA Laboratory, Bordeaux, France
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204
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Generation and characterization of novel DNA aptamers against coat protein of grouper nervous necrosis virus (GNNV) with antiviral activities and delivery potential in grouper cells. Antiviral Res 2016; 129:104-114. [PMID: 26892075 DOI: 10.1016/j.antiviral.2016.02.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/14/2016] [Accepted: 02/12/2016] [Indexed: 12/15/2022]
Abstract
Nervous necrosis virus (NNV) infected larvae and juveniles of more than 50 fish species, resulting in mortality rates of greater than 95%. However, there is no efficient method to control NNV infections. Aptamers generated by selective evolution of ligands by exponential enrichment (SELEX) are short, single-stranded nucleic acid oligomers. They display a high degree of affinity and specificity for many targets, such as viruses and viral proteins. In this study, three novel DNA aptamers (A5, A10, and B11) that specifically target the coat protein (CP) of grouper nervous necrosis virus (GNNV) were selected using SELEX. Secondary structures and minimum free energy (ΔG) predictions indicated that these aptamers could form stable, secondary stem-loop structures. Electrophoretic mobility shift assays, enzyme-linked immunosorbent assays, Kd measurements, the co-localization of tetramethylrhodamine (TAMRA) labeled-aptamers with the CP and flow cytometry analysis revealed that these aptamers could specifically bind the CP with high (nanomolar) affinities. In addition, competition analysis suggested the aptamers shared some common CP binding sites with the anti-CP antibody. Moreover, all three aptamers did not show any cytotoxic effects in vitro or in vivo, and anti-viral analysis indicated the selected aptamers could inhibit NNV infection in vitro and in vivo. Compared with controls, mortality of GNNV-infected fish decreased by 40% and 80% after 10 days infection, when the GNNV was pre-incubated with the 1000 nM A10 and B11, respectively. TAMRA-labeled aptamers could bind to NNV virions and directly enter NNV-infected cells, suggesting they could be used as tracers to study the mechanism of viral infection, as well as for targeted therapy. This is the first time that aptamers targeting a viral protein of marine fish have been generated and characterized. These aptamers hold promise as diagnostic, therapeutic, and targeted drug delivery agents for controlling NNV infections.
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205
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Schumacher S, Seitz H. Quality control of antibodies for assay development. N Biotechnol 2016; 33:544-50. [PMID: 26873787 DOI: 10.1016/j.nbt.2016.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 01/12/2016] [Accepted: 02/03/2016] [Indexed: 01/19/2023]
Abstract
Antibodies are used as powerful tools in basic research, for example, in biomarker identification, and in various forms for diagnostics, for example, identification of allergies or autoimmune diseases. Due to their robustness and ease of handling, immunoassays are favourite methods for investigation of various biological or medical questions. Nevertheless in many cases, additional analyses such as mass spectrometry are used to validate or confirm the results of immunoassays. To minimize the workload and to increase confidence in immunoassays, there are urgent needs for antibodies which are both highly specific and well validated. Unfortunately many commercially available antibodies are neither well characterized nor fully tested for cross-reactivities. Adequate quality control and validation of an antibody is time-consuming and can be frustrating. Such validation needs to be performed for every assay/application. However, where an antibody validation is successful, a highly specific and stable reagent will be on hand. This article describes the validation processes of antibodies, including some often neglected factors, as well as unspecific binding to other sample compounds in a multiparameter diagnostic assay. The validation consists of different immunological methods, with important assay controls, and is performed in relation to the development of a diagnostic test.
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Affiliation(s)
- Sarah Schumacher
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics und Bioprocesses, Am Mühlenberg 13, 14476 Potsdam, Germany; Humboldt University Berlin, Department of Biology, Invalidenstr. 110, 10115 Berlin, Germany
| | - Harald Seitz
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics und Bioprocesses, Am Mühlenberg 13, 14476 Potsdam, Germany.
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206
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Dirkzwager RM, Kinghorn AB, Richards JS, Tanner JA. APTEC: aptamer-tethered enzyme capture as a novel rapid diagnostic test for malaria. Chem Commun (Camb) 2016; 51:4697-700. [PMID: 25692283 DOI: 10.1039/c5cc00438a] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report the rapid diagnosis of malaria by aptamer-tethered enzyme capture (APTEC) whereby an aptamer captures biomarker Plasmodium falciparum lactate dehydrogenase (PfLDH) then activity is measured colorimetrically. The robust test was sensitive (limit of detection = 4.9 ng mL(-1)) and could reliably diagnose malaria in clinical blood samples.
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Affiliation(s)
- Roderick M Dirkzwager
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R..
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207
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Wen Y, Li L, Wang L, Xu L, Liang W, Ren S, Liu G. Biomedical Applications of DNA-Nanomaterials Based on Metallic Nanoparticles and DNA Self-Assembled Nanostructures. CHINESE J CHEM 2016. [DOI: 10.1002/cjoc.201500849] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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208
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Methods for assembling B-cell lymphoma specific and internalizing aptamer-siRNA nanoparticles via the sticky bridge. Methods Mol Biol 2016; 1297:169-85. [PMID: 25896003 DOI: 10.1007/978-1-4939-2562-9_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Structured functional RNA entities, including aptamers and siRNAs, have amazing versatility in structure and function. These molecules can serve as powerful, attractive building blocks for the bottom-up assembly of complex nanostructures. Here, we describe novel cell-type specific and internalizing B-cell activating factor receptor (BAFF-R) aptamer-siRNA delivery systems for B-cell lymphoma therapy, in which both the aptamer and the Dicer substrate siRNA (DsiRNA) portions are conjugated through a "sticky bridge." The BAFF-R is overexpressed on the surface of B-cell malignancies, allowing binding and internalization of the aptamer-stick-siRNA nanoparticles. STAT3 siRNAs are encapsulated within the nanoparticles delivered by the BAFF-R aptamers and are localized to the cytoplasm, resulting in robust gene silencing of STAT3 mRNAs in a variety of B-cell lines. Moreover, these nanoparticles do not induce cell proliferation and apoptosis. Collectively, aptamer-mediated delivery strategies provide a toolset to become a more widely used therapeutic modality for the treatment of diseases.
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209
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Jolly P, Damborsky P, Madaboosi N, Soares RRG, Chu V, Conde JP, Katrlik J, Estrela P. DNA aptamer-based sandwich microfluidic assays for dual quantification and multi-glycan profiling of cancer biomarkers. Biosens Bioelectron 2015; 79:313-9. [PMID: 26720920 DOI: 10.1016/j.bios.2015.12.058] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/11/2015] [Accepted: 12/18/2015] [Indexed: 12/19/2022]
Abstract
Two novel sandwich-based immunoassays for prostate cancer (PCa) diagnosis are reported, in which the primary antibody for capture is replaced by a DNA aptamer. The assays, which can be performed in parallel, were developed in a microfluidic device and tested for the detection of free Prostate Specific Antigen (fPSA). A secondary antibody (Aptamer-Antibody Assay) or a lectin (Aptamer-Lectin Assay) is used to quantify, by chemiluminescence, both the amount of fPSA and its glycosylation levels. The use of aptamers enables a more reliable, selective and controlled sensing of the analyte. The dual approach provides sensitive detection of fPSA along with selective fPSA glycoprofiling, which is of significant importance in the diagnosis and prognosis of PCa, as tumor progression is associated with changes in fPSA glycosylation. With these approaches, we can potentially detect 0.5 ng/mL of fPSA and 3 ng/mL of glycosylated fPSA using Sambucus nigra (SNA) lectin, both within the relevant clinical range. The approach can be applied to a wide range of biomarkers, thus providing a good alternative to standard antibody-based immunoassays with significant impact in medical diagnosis and prognosis.
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Affiliation(s)
- Pawan Jolly
- Department of Electronic & Electrical Engineering, University of Bath, Bath BA2 7AY, United Kingdom.
| | - Pavel Damborsky
- Department of Glycobiotechnology, Center for Glycomics, Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 84105, Slovakia.
| | - Narayanan Madaboosi
- INESC-MN - Microsystems and Nanotechnologies, R. Alves Redol 9, 1000-029 Lisboa, Portugal.
| | - Ruben R G Soares
- INESC-MN - Microsystems and Nanotechnologies, R. Alves Redol 9, 1000-029 Lisboa, Portugal; Department of Bioengineering, Instituto Superior Técnico, University of Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Virginia Chu
- INESC-MN - Microsystems and Nanotechnologies, R. Alves Redol 9, 1000-029 Lisboa, Portugal.
| | - João P Conde
- INESC-MN - Microsystems and Nanotechnologies, R. Alves Redol 9, 1000-029 Lisboa, Portugal; Department of Bioengineering, Instituto Superior Técnico, University of Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Jaroslav Katrlik
- Department of Glycobiotechnology, Center for Glycomics, Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 84105, Slovakia.
| | - Pedro Estrela
- Department of Electronic & Electrical Engineering, University of Bath, Bath BA2 7AY, United Kingdom.
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210
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Hollenstein M. DNA Catalysis: The Chemical Repertoire of DNAzymes. Molecules 2015; 20:20777-804. [PMID: 26610449 PMCID: PMC6332124 DOI: 10.3390/molecules201119730] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 12/24/2022] Open
Abstract
Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as gene silencing agents, the scope of DNAzymes has rapidly expanded into diverse fields, including biosensing, diagnostics, logic gate operations, and the development of novel synthetic and biological tools. In this review, an overview of all the different chemical reactions catalyzed by DNAzymes is given with an emphasis on RNA cleavage and the use of non-nucleosidic substrates. The use of modified nucleoside triphosphates (dN*TPs) to expand the chemical space to be explored in selection experiments and ultimately to generate DNAzymes with an expanded chemical repertoire is also highlighted.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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211
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Li Q, Wang YD, Shen GL, Tang H, Yu RQ, Jiang JH. Split aptamer mediated endonuclease amplification for small-molecule detection. Chem Commun (Camb) 2015; 51:4196-9. [PMID: 25672262 DOI: 10.1039/c5cc00390c] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A novel, highly sensitive split aptamer mediated endonuclease amplification strategy for the construction of aptameric sensors is reported.
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Affiliation(s)
- Qing Li
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China.
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212
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Peters G, Coussement P, Maertens J, Lammertyn J, De Mey M. Putting RNA to work: Translating RNA fundamentals into biotechnological engineering practice. Biotechnol Adv 2015; 33:1829-44. [PMID: 26514597 DOI: 10.1016/j.biotechadv.2015.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/13/2015] [Accepted: 10/22/2015] [Indexed: 11/19/2022]
Abstract
Synthetic biology, in close concert with systems biology, is revolutionizing the field of metabolic engineering by providing novel tools and technologies to rationally, in a standardized way, reroute metabolism with a view to optimally converting renewable resources into a broad range of bio-products, bio-materials and bio-energy. Increasingly, these novel synthetic biology tools are exploiting the extensive programmable nature of RNA, vis-à-vis DNA- and protein-based devices, to rationally design standardized, composable, and orthogonal parts, which can be scaled and tuned promptly and at will. This review gives an extensive overview of the recently developed parts and tools for i) modulating gene expression ii) building genetic circuits iii) detecting molecules, iv) reporting cellular processes and v) building RNA nanostructures. These parts and tools are becoming necessary armamentarium for contemporary metabolic engineering. Furthermore, the design criteria, technological challenges, and recent metabolic engineering success stories of the use of RNA devices are highlighted. Finally, the future trends in transforming metabolism through RNA engineering are critically evaluated and summarized.
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Affiliation(s)
- Gert Peters
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Pieter Coussement
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jo Maertens
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jeroen Lammertyn
- BIOSYST-MeBioS, KU Leuven, Willem de Croylaan 42, 3001 Louvain, Belgium
| | - Marjan De Mey
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
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213
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Jiang HP, Zhu JX, Peng C, Gao J, Zheng F, Xiao YX, Feng YQ, Yuan BF. Facile one-pot synthesis of a aptamer-based organic-silica hybrid monolithic capillary column by "thiol-ene" click chemistry for detection of enantiomers of chemotherapeutic anthracyclines. Analyst 2015; 139:4940-6. [PMID: 25072056 DOI: 10.1039/c4an00767k] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the current study, we developed a facile strategy for the one-pot synthesis of an aptamer-based organic-silica hybrid monolithic capillary column. A 5'-SH-modified aptamer, specifically targeting doxorubicin, was covalently modified in the hybrid silica monolithic column by a sol-gel method combined with "thiol-ene" click reaction. The prepared monolithic column had good stability and permeability, large specific surface, and showed excellent selectivity towards chemotherapeutic anthracyclines of doxorubicin and epirubicin. In addition, the enantiomers of doxorubicin and epirubicin can be easily separated by aptamer-based affinity monolithic capillary liquid chromatography. Furthermore, doxorubicin and epirubicin spiked in serum and urine were also successfully determined, which suggested that the complex biological matrix had a negligible effect on the detection of doxorubicin and epirubicin. Finally, we quantified the concentration of epirubicin in the serum of breast cancer patients treated with epirubicin by intravenous injection. The developed analytical method is cost-effective and rapid, and biological samples can be directly analyzed without any tedious sample pretreatment, which is extremely useful for monitoring medicines in serum and urine for pharmacokinetic studies.
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Affiliation(s)
- Han-Peng Jiang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China.
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214
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Hoinka J, Dao P, Przytycka TM. AptaGUI-A Graphical User Interface for the Efficient Analysis of HT-SELEX Data. MOLECULAR THERAPY-NUCLEIC ACIDS 2015; 4:e257. [PMID: 26461977 PMCID: PMC4881754 DOI: 10.1038/mtna.2015.26] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/03/2015] [Indexed: 12/04/2022]
Affiliation(s)
- Jan Hoinka
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | - Phuong Dao
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | - Teresa M Przytycka
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
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215
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Novel delivery approaches for cancer therapeutics. J Control Release 2015; 219:248-268. [PMID: 26456750 DOI: 10.1016/j.jconrel.2015.09.067] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/09/2015] [Accepted: 09/30/2015] [Indexed: 02/07/2023]
Abstract
Currently, a majority of cancer treatment strategies are based on the removal of tumor mass mainly by surgery. Chemical and physical treatments such as chemo- and radiotherapies have also made a major contribution in inhibiting rapid growth of malignant cells. Furthermore, these approaches are often combined to enhance therapeutic indices. It is widely known that surgery, chemo- and radiotherapy also inhibit normal cells growth. In addition, these treatment modalities are associated with severe side effects and high toxicity which in turn lead to low quality of life. This review encompasses novel strategies for more effective chemotherapeutic delivery aiming to generate better prognosis. Currently, cancer treatment is a highly dynamic field and significant advances are being made in the development of novel cancer treatment strategies. In contrast to conventional cancer therapeutics, novel approaches such as ligand or receptor based targeting, triggered release, intracellular drug targeting, gene delivery, cancer stem cell therapy, magnetic drug targeting and ultrasound-mediated drug delivery, have added new modalities for cancer treatment. These approaches have led to selective detection of malignant cells leading to their eradication with minimal side effects. Lowering multi-drug resistance and involving influx transportation in targeted drug delivery to cancer cells can also contribute significantly in the therapeutic interventions in cancer.
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216
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Li P, Zhou L, Yu Y, Yang M, Ni S, Wei S, Qin Q. Characterization of DNA aptamers generated against the soft-shelled turtle iridovirus with antiviral effects. BMC Vet Res 2015; 11:245. [PMID: 26419355 PMCID: PMC4588899 DOI: 10.1186/s12917-015-0559-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/22/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Soft-shelled turtle iridovirus (STIV) causes severe systemic disease in farmed soft-shelled turtles (Trionyx sinensis). More efficient methods of controlling and detecting STIV infections are urgently needed. METHODS In this study, we generated eight single-stranded DNA (ssDNA) aptamers against STIV using systematic evolution of ligands by exponential enrichment (SELEX). RESULTS The aptamers formed representative stem-loop secondary structures. Electrophoretic mobility shift assays and fluorescent localization showed that the selected aptamers had high binding affinity for STIV. Aptamer QA-36 had the highest calculated binding affinity (K d ) of 53.8 nM. Flow cytometry and fluorescence microscopy of cell-aptamer interactions demonstrated that QA-12 was able to recognize both STIV-infected cells and tissues with a high level of specificity. Moreover, the selected aptamers inhibited STIV infection in vitro and in vivo, with aptamer QA-36 demonstrating the greatest protective effect against STIV and inhibiting STIV infection in a dose-dependent manner. DISCUSSION We generated DNA aptamers that bound STIV with a high level of specificity, providing an alternative means for investigating STIV pathogenesis, drug development, and medical therapies for STIV infection. CONCLUSIONS These DNA aptamers may thus be suitable antiviral candidates for the control of STIV infections.
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Affiliation(s)
- Pengfei Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Lingli Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Yepin Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Min Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Songwei Ni
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Shina Wei
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.
| | - Qiwei Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China. .,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.
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217
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Barfod A, Singh B, Johanson U, Riesbeck K, Kjellbom P. In vitro selection of RNA aptamers directed against protein E: a Haemophilus influenzae adhesin. Mol Biotechnol 2015; 56:714-25. [PMID: 24682699 DOI: 10.1007/s12033-014-9749-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein E (PE) of Haemophilus influenzae is a highly conserved ubiquitous surface protein involved in adhesion to and activation of epithelial cells. The host proteins-vitronectin, laminin, and plasminogen are major targets for PE-dependent interactions with the host. To identify novel inhibitory molecules of PE, we used an in vitro selection method based on systematic evolution of ligands by exponential enrichment known as SELEX in order to select 2'F-modified RNA aptamers that specifically bind to PE. Fourteen selection cycles were performed with decreasing concentrations of PE. Sequencing of clones from the 14th selection round revealed the presence of semiconserved sequence motifs in loop regions of the RNA aptamers. Among these, three aptamers showed the highest affinity to PE in electrophoretic mobility shift assays and in dot blots. These three aptamers also inhibited the interaction of PE with vitronectin as revealed by ELISA. Moreover, pre-treatment of H. influenzae with the aptamers significantly inhibited binding of vitronectin to the bacterial surface. Biacore experiments indicated that one of the aptamers had a higher binding affinity for PE as compared to the other aptamers. Our results show that it is possible to select RNA inhibitors against bacterial adhesins using SELEX in order to inhibit interactions with target proteins.
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Affiliation(s)
- Anders Barfod
- Department of Biochemistry and Structural Biology, CMPS, Lund University, Box 124, 221 00, Lund, Sweden,
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218
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Chen L, Zeng X, Ferhan AR, Chi Y, Kim DH, Chen G. Signal-on electrochemiluminescent aptasensors based on target controlled permeable films. Chem Commun (Camb) 2015; 51:1035-8. [PMID: 25434590 DOI: 10.1039/c4cc07699k] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel permeability gate-based electrochemiluminescent (ECL) aptasensor has been constructed by utilizing target-responsive polyelectrolyte-aptamer film deposited on the solid-state ECL electrode to control the rate of diffusion of a coreactant that triggers the ECL.
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Affiliation(s)
- Lichan Chen
- MOE Key Laboratory of Analysis and Detection Technology for Food Safety, and College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China.
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219
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Cheng L, Zhang J, Lin Y, Wang Q, Zhang X, Ding Y, Cui H, Fan H. An electrochemical molecular recognition-based aptasensor for multiple protein detection. Anal Biochem 2015; 491:31-6. [PMID: 26344894 DOI: 10.1016/j.ab.2015.08.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 08/19/2015] [Accepted: 08/19/2015] [Indexed: 02/05/2023]
Abstract
This article reports a simple electrochemical approach for the detection of multiple proteins (thrombin and lysozyme) using Dabcyl-labeled aptamer modified metal nanoparticles (DLAPs). DLAPs were immobilized on β-cyclodextrins (β-CDs) modified electrode by means of host-guest self-assembly. During the time of detection, the aptamers' structure will change due to the specific binding with corresponding proteins that forced DLAPs far away from the electrode that had been modified by β-CDs. Thus, the capture of target proteins onto DLAPs was translated via the electrochemical current signal offered by metal nanoparticles. Linearity of the aptasensor for quantitative measurements was demonstrated. Determinations of proteins in human real serum samples were also performed to demonstrate detection in real clinical samples.
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Affiliation(s)
- Lin Cheng
- Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, People's Republic of China
| | - Jie Zhang
- Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, People's Republic of China
| | - Yan Lin
- Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, People's Republic of China
| | - Qiong Wang
- Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, People's Republic of China
| | - XiuXiu Zhang
- Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, People's Republic of China
| | - YanHua Ding
- Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, People's Republic of China
| | - Hanfeng Cui
- Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, People's Republic of China.
| | - Hao Fan
- Department of Pharmacy, JiangXi University of Traditional Chinese Medicine, JiangXi 330004, People's Republic of China.
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220
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Li P, Wei S, Zhou L, Yang M, Yu Y, Wei J, Jiang G, Qin Q. Selection and characterization of novel DNA aptamers specifically recognized by Singapore grouper iridovirus-infected fish cells. J Gen Virol 2015; 96:3348-3359. [PMID: 26310792 DOI: 10.1099/jgv.0.000270] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Singapore grouper iridovirus (SGIV) is a major viral pathogen of grouper aquaculture, and has caused heavy economic losses in China and South-east Asia. In this study, we generated four ssDNA aptamers against SGIV-infected grouper spleen (GS) cells using SELEX (systematic evolution of ligands by exponential enrichment) technology. Four aptamers exhibited high affinity to SGIV-infected GS cells, in particular the Q2 aptamer. Q2 had a binding affinity of 12.09 nM, the highest of the four aptamers. These aptamers also recognized SGIV-infected tissues with high levels of specificity. Protease treatment and flow cytometry analysis of SGIV-infected cells revealed that the target molecules of the Q3, Q4 and Q5 aptamers were trypsin-sensitive proteins, whilst the target molecules of Q2 might be membrane lipids or surface proteins that were not trypsin-sensitive. The generated aptamers appeared to inhibit SGIV infection in vitro. Aptamer Q2 conferred the highest levels of protection against SGIV and was able to inhibit SGIV infection in a dose-dependent manner. In addition, Q2 was efficiently internalized by SGIV-infected GS cells and localized at the viral assembly sites. Our results demonstrated that the four novel aptamers we generated were specific for SGIV-infected cells and could potentially be applied as rapid molecular diagnostic test reagents or therapeutic drugs targeting SGIV.
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Affiliation(s)
- Pengfei Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, PR China
| | - Shina Wei
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Lingli Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, PR China
| | - Min Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Yepin Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, PR China
| | - Jingguang Wei
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Guohua Jiang
- Analytical and Testing Center, Beijing Normal University, Xinjiekouwai Street, Beijing 100875, PR China
| | - Qiwei Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, PR China
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221
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Kun Á, Szathmáry E. Fitness Landscapes of Functional RNAs. Life (Basel) 2015; 5:1497-517. [PMID: 26308059 PMCID: PMC4598650 DOI: 10.3390/life5031497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/26/2015] [Accepted: 08/03/2015] [Indexed: 11/16/2022] Open
Abstract
The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world.
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Affiliation(s)
- Ádám Kun
- Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049 Munich/Pullach, Germany.
- MTA-ELTE-MTMT Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
| | - Eörs Szathmáry
- Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049 Munich/Pullach, Germany.
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
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222
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Abstract
Biological specimens are intrinsically three dimensional; however, because of the obscuring effects of light scatter, imaging deep into a tissue volume is problematic. Although efforts to eliminate the scatter by "clearing" the tissue have been ongoing for over a century, there have been a large number of recent innovations. This Review introduces the physical basis for light scatter in tissue, describes the mechanisms underlying various clearing techniques, and discusses several of the major advances in light microscopy for imaging cleared tissue.
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Affiliation(s)
- Douglas S Richardson
- Harvard Center for Biological Imaging, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Jeff W Lichtman
- Harvard Center for Biological Imaging, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
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223
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Acquah C, Danquah MK, Yon JLS, Sidhu A, Ongkudon CM. A review on immobilised aptamers for high throughput biomolecular detection and screening. Anal Chim Acta 2015; 888:10-8. [PMID: 26320953 DOI: 10.1016/j.aca.2015.05.050] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 05/20/2015] [Accepted: 05/22/2015] [Indexed: 02/07/2023]
Abstract
The discovery of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assay has led to the generation of aptamers from libraries of nucleic acids. Concomitantly, aptamer-target recognition and its potential biomedical applications have become a major research endeavour. Aptamers possess unique properties that make them superior biological receptors to antibodies with a plethora of target molecules. Some specific areas of opportunities explored for aptamer-target interactions include biochemical analysis, cell signalling and targeting, biomolecular purification processes, pathogen detection and, clinical diagnosis and therapy. Most of these potential applications rely on the effective immobilisation of aptamers on support systems to probe target species. Hence, recent research focus is geared towards immobilising aptamers as oligosorbents for biodetection and bioscreening. This article seeks to review advances in immobilised aptameric binding with associated successful milestones and respective limitations. A proposal for high throughput bioscreening using continuous polymeric adsorbents is also presented.
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Affiliation(s)
- Caleb Acquah
- Curtin Sarawak Research Institute, Curtin University, Sarawak, 98009, Malaysia; Department of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia
| | - Michael K Danquah
- Department of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia.
| | - John L S Yon
- Department of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia
| | - Amandeep Sidhu
- Curtin Sarawak Research Institute, Curtin University, Sarawak, 98009, Malaysia; Faculty of Health Sciences, Curtin University, Perth, 6109, Australia
| | - Clarence M Ongkudon
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia
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224
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Wang C, Kim J, Zhu Y, Yang J, Lee GH, Lee S, Yu J, Pei R, Liu G, Nuckolls C, Hone J, Lin Q. An aptameric graphene nanosensor for label-free detection of small-molecule biomarkers. Biosens Bioelectron 2015; 71:222-229. [PMID: 25912678 DOI: 10.1016/j.bios.2015.04.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 03/27/2015] [Accepted: 04/10/2015] [Indexed: 11/18/2022]
Abstract
This paper presents an aptameric graphene nanosensor for detection of small-molecule biomarkers. To address difficulties in direct detection of small molecules associated with their low molecular weight and electrical charge, we incorporate an aptamer-based competitive affinity assay in a graphene field effect transistor (FET), and demonstrate the utility of the nanosensor with dehydroepiandrosterone sulfate (DHEA-S), a small-molecule steroid hormone, as the target analyte. In the competitive affinity assay, DHEA-S specifically binds to aptamer molecules pre-hybridized to their complementary DNA anchor molecules immobilized on the graphene surface. This results in the competitive release of the strongly charged aptamer from the DNA anchor and hence a change in electrical properties of the graphene, which can be measured to achieve the detection of DHEA-S. We present experimental data on the label-free, specific and quantitative detection of DHEA-S at clinically appropriate concentrations with an estimated detection limit of 44.7 nM, and analyze the trend observed in the experiments using molecular binding kinetics theory. These results demonstrate the potential of our nanosensor in the detection of DHEA-S and other small molecules in biomedical applications.
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Affiliation(s)
- Cheng Wang
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA; Department of Microelectronic Engineering, Nankai University, Tianjin 300071, China
| | - Jinho Kim
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Yibo Zhu
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Jaeyoung Yang
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Gwan-Hyoung Lee
- Department of Materials Science and Engineering, Yonsei University, Seoul 120749, Republic of Korea
| | - Sunwoo Lee
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Jaeeun Yu
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Renjun Pei
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, Jiangsu 215123, China
| | - Guohua Liu
- Department of Microelectronic Engineering, Nankai University, Tianjin 300071, China
| | - Colin Nuckolls
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - James Hone
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA.
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225
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Lao YH, Phua KKL, Leong KW. Aptamer nanomedicine for cancer therapeutics: barriers and potential for translation. ACS NANO 2015; 9:2235-54. [PMID: 25731717 DOI: 10.1021/nn507494p] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Aptamer nanomedicine, including therapeutic aptamers and aptamer nanocomplexes, is beginning to fulfill its potential in both clinical trials and preclinical studies. Especially in oncology, aptamer nanomedicine may perform better than conventional or antibody-based chemotherapeutics due to specificity compared to the former and stability compared to the latter. Many proof-of-concept studies on applying aptamers to drug delivery, gene therapy, and cancer imaging have shown promising efficacy and impressive safety in vivo toward translation. Yet, there remains ample room for improvement and critical barriers to be addressed. In this review, we will first introduce the recent progress in clinical trials of aptamer nanomedicine, followed by a discussion of the barriers at the design and in vivo application stages. We will then highlight recent advances and engineering strategies proposed to tackle these barriers. Aptamer cancer nanomedicine has the potential to address one of the most important healthcare issues of the society.
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Affiliation(s)
- Yeh-Hsing Lao
- †Department of Biomedical Engineering, Columbia University, New York 10027, New York, United States
| | | | - Kam W Leong
- †Department of Biomedical Engineering, Columbia University, New York 10027, New York, United States
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226
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Slavkovic S, Altunisik M, Reinstein O, Johnson PE. Structure-affinity relationship of the cocaine-binding aptamer with quinine derivatives. Bioorg Med Chem 2015; 23:2593-7. [PMID: 25858454 DOI: 10.1016/j.bmc.2015.02.052] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/19/2015] [Accepted: 02/26/2015] [Indexed: 10/23/2022]
Abstract
In addition to binding its target molecule, cocaine, the cocaine-binding aptamer tightly binds the alkaloid quinine. In order to understand better how the cocaine-binding aptamer interacts with quinine we have used isothermal titration calorimetry-based binding experiments to study the interaction of the cocaine-binding aptamer to a series of structural analogs of quinine. As a basis for comparison we also investigated the binding of the cocaine-binding aptamer to a set of cocaine metabolites. The bicyclic aromatic ring on quinine is essential for tight affinity by the cocaine-binding aptamer with 6-methoxyquinoline alone being sufficient for tight binding while the aliphatic portion of quinine, quinuclidine, does not show detectable binding. Compounds with three fused aromatic rings are not bound by the aptamer. Having a methoxy group at the 6-position of the bicyclic ring is important for binding as substituting it with a hydrogen, an alcohol or an amino group all result in lower binding affinity. For all ligands that bind, association is driven by a negative enthalpy compensated by unfavorable binding entropy.
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Affiliation(s)
- Sladjana Slavkovic
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, Ontario M3J 1P3, Canada
| | - Merve Altunisik
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, Ontario M3J 1P3, Canada
| | - Oren Reinstein
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, Ontario M3J 1P3, Canada
| | - Philip E Johnson
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, Ontario M3J 1P3, Canada.
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227
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He X, Chen J, Yie SM, Ye SR, Dong DD, Li K. Using a sequence of estrogen response elements as a DNA aptamer for estrogen receptors in vitro. Nucleic Acid Ther 2015; 25:152-61. [PMID: 25734367 DOI: 10.1089/nat.2014.0521] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Estrogen receptors (ERs) are overexpressed in approximately 70% of breast cancer cases, and they play an important role in tumorigenesis. ERs are strong predictive factors for measuring responses to hormonal therapies. Aptamers are short and single stranded oligonucleotides that are able to recognize target molecules with high affinity. In the present study, we selected and synthesized an oligonucleotide, which has a similar sequence to estrogen response element in the Xenopus Vitellogenin A2 gene. The synthesized oligonucleotide was evaluated by using immunostaining of paraffin-embedded breast cancer tissues and treating MCF-7 human mammary carcinoma cell line in vitro. We found that the synthesized oligonucleotide had a high binding affinity to ER similar to estradiol. Using a specific anti-ER antibody as a standard control, we showed that the synthesized oligonucleotide specifically recognized and immunostained tumor cells of breast cancer without cross-reaction with normal tissues. The overall agreement of ER detection between the anti-ER antibody and the ER aptamer was 97.1% (kappa value=0.943; 95% CI=0.879-1.006; p<0.002). Similar to tamoxifen or fulvestrant, the oligonucleotide also had an inhibitory effect on cell proliferation of MCF-7 cell line in a dose- and time-dependent fashion but had no cytotoxic effect on human normal mammary epithelial cells. Therefore, the synthesized oligonucleotide may be used as an aptamer for immunostaining of paraffin-embedded tissue sections for breast cancer diagnosis, as well as a potential ER antagonist in the treatment of breast cancer.
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Affiliation(s)
- Xu He
- 1Core Laboratory, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Jie Chen
- 1Core Laboratory, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Shang-mian Yie
- 1Core Laboratory, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China.,2Research and Development Center, Sichuan HeLi Bio-pharmaceutical Co. Ltd., Sichuan HeBang Group, Chengdu, Sichuan, China
| | - Shang-rong Ye
- 2Research and Development Center, Sichuan HeLi Bio-pharmaceutical Co. Ltd., Sichuan HeBang Group, Chengdu, Sichuan, China
| | - Dan-Dan Dong
- 3Department of Pathology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Ke Li
- 3Department of Pathology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
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228
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Qin M, Chen Z, Luo Q, Wen Y, Zhang N, Jiang H, Yang H. Two-quartet G-quadruplexes formed by DNA sequences containing four contiguous GG runs. J Phys Chem B 2015; 119:3706-13. [PMID: 25689673 DOI: 10.1021/jp512914t] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The DNA sequence containing four contiguous GG runs (G2NxG2NyG2NzG2, G2 sequence) has the potential to form a two-quartet G-quadruplex. However, the prevalence, structure, and function of G2 sequences have not been well-studied. Here, bioinformatics analysis reveals the abundance of G2 sequences in the human genome and their enrichment in promoter regions. The density of G2 sequences in the genome and promoters is much higher than that of the G3 sequence (G3NxG3NyG3NzG3). Experiments show that the conformations and thermal stabilities of the two-quartet G-quadruplexes of G2 sequences are highly sensitive to the length and composition of the loops. Among the two-quartet G-quadruplexes, the parallel G-quadruplex with a loop length of 1 and the antiparallel G-quadruplex with a loop length of 3 show high thermal stabilities. Additionally, the stable parallel G-quadruplexes are stacked into intermolecular higher-order structures. This work determines the prevalence of G2 sequences in the human genome and demonstrates that the G-quadruplex structures for certain loop lengths and compositions may be stable in vivo. Thus, more attention should be paid to the structure and function of the two-quartet G-quadruplex.
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Affiliation(s)
- Mingyan Qin
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China
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229
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Pu Y, Liu Z, Lu Y, Yuan P, Liu J, Yu B, Wang G, Yang C, Liu H, Tan W. Using DNA aptamer probe for immunostaining of cancer frozen tissues. Anal Chem 2015; 87:1919-24. [PMID: 25536018 PMCID: PMC4318623 DOI: 10.1021/ac504175h] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 12/23/2014] [Indexed: 01/09/2023]
Abstract
Tissue immunostaining is critically important in clinical applications, and antibodies have been used extensively as the molecular probes. Recently, aptamer, as a new class of probes, have attracted much attention for their potential clinical and research value. Epithelial cell adhesion molecule (EpCAM) is a specific biomarker which is overexpressed in many cancers of epithelial origin. Here, a DNA-based EpCAM aptamer SYL3C is reported as a probe for the immunostaining of frozen and paraffin-embedded sections of colorectal cancer tissues. Commercialized EpCAM antibodies were also used as a standard control. EpCAM aptamer SYL3C specifically recognized and immunostained cancer nests of colorectal tumor sections, but it neither reacted with background cells within tumor sites nor exhibited cross-reaction to the benign lesions or inflammation of colorectal tissues. No cross-linking to EpCAM-negative malignant tumor sections occurred. Compared with standard antibody staining, our EpCAM aptamer SYL3C protocol is simpler to implement with a shorter reaction time. Moreover, SYL3C can specifically bind with either frozen or paraffin-embedded tissue sections. Since the histopathology of frozen tissue is closer to that of fresh tissue and since frozen sections can be produced more quickly than paraffin-embedded sections, SYL3C immunostaining of frozen sections is a quick protocol that is easy to implement.
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Affiliation(s)
- Ying Pu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhenxu Liu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yi Lu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Peng Yuan
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jun Liu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Bo Yu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Guodong Wang
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Chaoyong
James Yang
- State Key
Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory
for Chemical Biology of Fujian Province, Key Laboratory of Analytical
Chemistry, and Department of Chemical Biology, College of Chemistry
and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Huixia Liu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Weihong Tan
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, and Collaborative Research Center of Molecular Engineering
for Theranostics, Hunan University, Changsha, Hunan 410082, China
- Department of Chemistry and Physiology
and Functional Genomics, Center for Research at the Bio/Nano Interface,
Shands Cancer Center, University of Florida, Gainesville, Florida 32611-7200, United States
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230
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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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231
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de Araujo FF, Nagarkatti R, Gupta C, Marino AP, Debrabant A. Aptamer-based detection of disease biomarkers in mouse models for chagas drug discovery. PLoS Negl Trop Dis 2015; 9:e3451. [PMID: 25569299 PMCID: PMC4287562 DOI: 10.1371/journal.pntd.0003451] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/26/2014] [Indexed: 12/31/2022] Open
Abstract
Drug discovery initiatives, aimed at Chagas treatment, have been hampered by the lack of standardized drug screening protocols and the absence of simple pre-clinical assays to evaluate treatment efficacy in animal models. In this study, we used a simple Enzyme Linked Aptamer (ELA) assay to detect T. cruzi biomarker in blood and validate murine drug discovery models of Chagas disease. In two mice models, Apt-29 ELA assay demonstrated that biomarker levels were significantly higher in the infected group compared to the control group, and upon Benznidazole treatment, their levels reduced. However, biomarker levels in the infected treated group did not reduce to those seen in the non-infected treated group, with 100% of the mice above the assay cutoff, suggesting that parasitemia was reduced but cure was not achieved. The ELA assay was capable of detecting circulating biomarkers in mice infected with various strains of T. cruzi parasites. Our results showed that the ELA assay could detect residual parasitemia in treated mice by providing an overall picture of the infection in the host. They suggest that the ELA assay can be used in drug discovery applications to assess treatment efficacy in-vivo.
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Affiliation(s)
- Fernanda Fortes de Araujo
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Rana Nagarkatti
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Charu Gupta
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Ana Paula Marino
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alain Debrabant
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail:
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232
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Liu Z, Zhao H, He L, Yao Y, Zhou Y, Wu J, Liu J, Ding J. Aptamer density dependent cellular uptake of lipid-capped polymer nanoparticles for polyvalent targeted delivery of vinorelbine to cancer cells. RSC Adv 2015. [DOI: 10.1039/c4ra16371k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
In this work, MUC1 aptamer (designated S2.2) modified and vinorelbine (VRL) loaded lipid-polymer hybrid nanoparticles (Apt-VRL-NPs) were prepared.
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Affiliation(s)
- Zhenbao Liu
- School of Pharmaceutical Sciences
- Central South University
- Changsha 410013
- People's Republic of China
| | - Huanzhe Zhao
- School of Pharmaceutical Sciences
- Central South University
- Changsha 410013
- People's Republic of China
| | - Lingyun He
- School of Pharmaceutical Sciences
- Central South University
- Changsha 410013
- People's Republic of China
| | - Yao Yao
- School of Pharmaceutical Sciences
- Central South University
- Changsha 410013
- People's Republic of China
| | - Yanbin Zhou
- School of Pharmaceutical Sciences
- Central South University
- Changsha 410013
- People's Republic of China
| | - Jianping Wu
- School of Pharmaceutical Sciences
- Central South University
- Changsha 410013
- People's Republic of China
| | - Juewen Liu
- School of Pharmaceutical Sciences
- Central South University
- Changsha 410013
- People's Republic of China
- Department of Chemistry
| | - Jinsong Ding
- School of Pharmaceutical Sciences
- Central South University
- Changsha 410013
- People's Republic of China
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233
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Abstract
Growth factors (GFs) are major regulatory proteins that can govern cell fate, migration, and organization. Numerous aspects of the cell milieu can modulate cell responses to GFs, and GF regulation is often achieved by the native extracellular matrix (ECM). For example, the ECM can sequester GFs and thereby control GF bioavailability. In addition, GFs can exert distinct effects depending on whether they are sequestered in solution, at two-dimensional interfaces, or within three-dimensional matrices. Understanding how the context of GF sequestering impacts cell function in the native ECM can instruct the design of soluble or insoluble GF sequestering moieties, which can then be used in a variety of bioengineering applications. This Feature Article provides an overview of the natural mechanisms of GF sequestering in the cell milieu, and reviews the recent bioengineering approaches that have sequestered GFs to modulate cell function. Results to date demonstrate that the cell response to GF sequestering depends on the affinity of the sequestering interaction, the spatial proximity of sequestering in relation to cells, the source of the GF (supplemented or endogenous), and the phase of the sequestering moiety (soluble or insoluble). We highlight the importance of context for the future design of biomaterials that can leverage endogenous molecules in the cell milieu and mitigate the need for supplemented factors.
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Affiliation(s)
- David G. Belair
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI USA
| | - Ngoc Nhi Le
- Department of Material Science, University of Wisconsin, Madison, WI USA
| | - William L. Murphy
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI USA
- Department of Material Science, University of Wisconsin, Madison, WI USA
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234
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Microfluidic platform towards point-of-care diagnostics in infectious diseases. J Chromatogr A 2014; 1377:13-26. [PMID: 25544727 DOI: 10.1016/j.chroma.2014.12.041] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/06/2014] [Accepted: 12/09/2014] [Indexed: 01/09/2023]
Abstract
Rapid and timely diagnosis of infectious diseases is a critical determinant of clinical outcomes and general public health. For the detection of various pathogens, microfluidics-based platforms offer many advantages, including speed, cost, portability, high throughput, and automation. This review provides an overview of the recent advances in microfluidic technologies for point-of-care (POC) diagnostics for infectious diseases. The key aspects of such technologies for the development of a fully integrated POC platform are introduced, including sample preparation, on-chip nucleic acid analysis and immunoassay, and system integration/automation. The current challenges to practical implementation of this technology are discussed together with future perspectives.
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235
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Noncoding oligonucleotides: the belle of the ball in gene therapy. ADVANCES IN GENETICS 2014; 89:153-177. [PMID: 25620011 DOI: 10.1016/bs.adgen.2014.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Gene therapy carries the promise of cures for many diseases based on manipulating the expression of a person's genes toward the therapeutic goal. The relevance of noncoding oligonucleotides to human disease is attracting widespread attention. Noncoding oligonucleotides are not only involved in gene regulation, but can also be modified into therapeutic tools. There are many strategies that leverage noncoding oligonucleotides for gene therapy, including small interfering RNAs, antisense oligonucleotides, aptamers, ribozymes, decoys, and bacteriophage phi 29 RNAs. In this chapter, we will provide a broad, comprehensive overview of gene therapies that use noncoding oligonucleotides for disease treatment. The mechanism and development of each therapeutic will be described, with a particular focus on its clinical development. Finally, we will discuss the challenges associated with developing nucleic acid therapeutics and the prospects for future success.
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236
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London GM, Mayosi BM, Khati M. Isolation and characterization of 2'-F-RNA aptamers against whole HIV-1 subtype C envelope pseudovirus. Biochem Biophys Res Commun 2014; 456:428-33. [PMID: 25482445 DOI: 10.1016/j.bbrc.2014.11.101] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 11/26/2014] [Indexed: 10/24/2022]
Abstract
Aptamers, which are artificial nucleic acid ligands akin to antibodies in function, represent a new class of molecules that can prevent HIV infection. In this study, we isolated RNA aptamers against whole HV-1CAP45 enveloped pseudotyped virus, with a view to target surface molecules that facilitate infection, such as the envelope protein, in their native form. HIV-1CAP45 belongs to subtype C viruses endemic in Sub-Saharan Africa and responsible for the majority of the global HIV-1 infections. After nine rounds of the systematic evolution of ligands by exponential enrichment (SELEX) method, we isolated twenty-three aptamer clones that inhibited infection of target cells by HIV-1CAP45 with 50% inhibitory concentration (IC50) values of 0.1-50 nM. Four of these aptamers called CSIR1.1, CSIR1.4, CSIR1.5 and CSIR1.6 bound to gp120 with affinity constant (KD) values between 16.9 and 195 nM and one aptamer called CSIR1.2 bound gp41. Interestingly, one aptamer called CSIR1.3 that did not bind gp120 or gp41 also inhibited infection of the target cells by HIV-1CAP45 with IC50 of less than 5 nM. Taken together, these data show that the aptamers inhibit infection of HIV-1CAP45 by binding to gp120 or gp41, or other viral surface molecules necessary for infection. The results argue in favour of using these aptamers as analytical tools to further probe HIV-1 entry, and their future development as HIV-1 entry inhibitors.
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Affiliation(s)
- Grace M London
- Emerging Health Technologies Department, Biosciences Unit, CSIR, Pretoria, South Africa
| | - Bongani M Mayosi
- Department of Medicine, Groote Schuur Hospital and University of Cape Town, Cape Town, South Africa
| | - Makobetsa Khati
- Emerging Health Technologies Department, Biosciences Unit, CSIR, Pretoria, South Africa; Department of Medicine, Groote Schuur Hospital and University of Cape Town, Cape Town, South Africa.
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237
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Kong RM, Ding L, Wang Z, You J, Qu F. A novel aptamer-functionalized MoS2 nanosheet fluorescent biosensor for sensitive detection of prostate specific antigen. Anal Bioanal Chem 2014; 407:369-77. [PMID: 25366976 DOI: 10.1007/s00216-014-8267-9] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 09/16/2014] [Accepted: 10/09/2014] [Indexed: 02/04/2023]
Abstract
Prostate specific antigen (PSA) is a significant and the most widely used biomarker for the early diagnosis of prostate cancer and its subsequent treatment. A MoS2 nanosheet is a two-dimensional (2D) layered nanomaterial analogous to graphene. However, a MoS2 nanosheet has a higher fluorescence-quenching ability than graphene when applied to a dye-labeled single-stranded DNA probe. In this work, we propose a novel aptamer-functionalized MoS2 nanosheet fluorescent biosensor that detects PSA. The binding of the aptamer to the target PSA induces a rigid aptamer structure which makes the integration with the MoS2 nanosheet very weak. This results in the release of the aptamer probe from the nanosheet surface and restores the quenched fluorescence. This approach has the advantage of simple design and rapid detection of PSA. The biosensor has the merits of high sensitivity and high selectivity with a detection limit for the PSA of 0.2 ng/mL. The biosensor was also successfully applied to the detection of PSA in human serum samples with satisfactory results. The foregoing indicates its promising application to real-life biological samples.
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Affiliation(s)
- Rong-Mei Kong
- The Key Laboratory of Life-Organic Analysis, College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong, 273165, China
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238
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Lian Y, He F, Wang H, Tong F. A new aptamer/graphene interdigitated gold electrode piezoelectric sensor for rapid and specific detection of Staphylococcus aureus. Biosens Bioelectron 2014; 65:314-9. [PMID: 25461175 DOI: 10.1016/j.bios.2014.10.017] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 08/26/2014] [Accepted: 10/07/2014] [Indexed: 11/30/2022]
Abstract
A novel aptamer/graphene interdigitated gold electrode piezoelectric sensor was developed for the rapid and specific detection of Staphylococcus aureus (S. aureus) by employing S. aureus aptamer as a biological recognition element. 4-Mercaptobenzene-diazonium tetrafluoroborate (MBDT) salt was used as a molecular cross-linking agent to chemically bind graphene to interdigital gold electrodes (IDE) that are connected to a series electrode piezoelectric quartz crystal (SPQC). S. aureus aptamers were assembly immobilized onto graphene via the π-π stacking of DNA bases. Due to the specific binding between S. aureus and aptamer, when S. aureus is present, the DNA bases interacted with the aptamer, thereby dropping the aptamer from the surface of the graphene. The electric parameters of the electrode surface was changed and resulted in the change of oscillator frequency of the SPQC. This detection was completed within 60min. The constructed sensor demonstrated a linear relationship between resonance frequency shifts with bacterial concentrations ranging from 4.1×10(1)-4.1×10(5)cfu/mL with a detection limit of 41cfu/mL. The developed strategy can detect S. aureus rapidly and specifically for clinical diagnosis and food testing.
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Affiliation(s)
- Yan Lian
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Fengjiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Huan Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Feifei Tong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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239
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Romanucci V, Gaglione M, Messere A, Potenza N, Zarrelli A, Noppen S, Liekens S, Balzarini J, Di Fabio G. Hairpin oligonucleotides forming G-quadruplexes: new aptamers with anti-HIV activity. Eur J Med Chem 2014; 89:51-8. [PMID: 25462225 DOI: 10.1016/j.ejmech.2014.10.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 09/20/2014] [Accepted: 10/12/2014] [Indexed: 12/31/2022]
Abstract
We describe the facile syntheses of new modified oligonucleotides based on d(TG3AG) that form bimolecular G-quadruplexes and possess a HEG loop as an inversion of polarity site 3'-3' or 5'-5' and aromatic residues conjugated to the 5'-end through phosphodiester bonds. The conjugated hairpin G-quadruplexes exhibited parallel orientation, high thermal stability, elevated resistance in human serum and high or moderate anti-HIV-1 activity with low cytotoxicity. Further, these molecules showed significant binding to HIV envelope glycoproteins gp120, gp41 and HSA, as revealed by SPR assays. As a result, these conjugated hairpins represent the first active anti-HIV-1 bimolecular G-quadruplexes based on the d(TG3AG) sequence.
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Affiliation(s)
- Valeria Romanucci
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126 Napoli, Italy
| | - Maria Gaglione
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università̀ di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Anna Messere
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università̀ di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Nicoletta Potenza
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università̀ di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Armando Zarrelli
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126 Napoli, Italy
| | - Sam Noppen
- Rega Institute for Medical Research, KU Leuven, 10 Minderbroedersstraat, B-3000 Leuven, Belgium
| | - Sandra Liekens
- Rega Institute for Medical Research, KU Leuven, 10 Minderbroedersstraat, B-3000 Leuven, Belgium
| | - Jan Balzarini
- Rega Institute for Medical Research, KU Leuven, 10 Minderbroedersstraat, B-3000 Leuven, Belgium
| | - Giovanni Di Fabio
- Department of Chemical Sciences, University of Napoli 'Federico II', Via Cintia 4, I-80126 Napoli, Italy.
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240
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Goodwin AP, Nakatsuka MA, Mattrey RF. Stimulus-responsive ultrasound contrast agents for clinical imaging: motivations, demonstrations, and future directions. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:111-23. [PMID: 25195785 DOI: 10.1002/wnan.1285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/23/2014] [Accepted: 07/06/2014] [Indexed: 12/17/2022]
Abstract
Microbubble ultrasound contrast agents allow imaging of the vasculature with excellent resolution and signal-to-noise ratios. Contrast in microbubbles derives from their interaction with an ultrasound wave to generate signal at harmonic frequencies of the stimulating pulse; subtracting the elastic echo caused by the surrounding tissue can enhance the specificity of these harmonic signals significantly. The nonlinear acoustic emission is caused by pressure-driven microbubble size fluctuations, which in both theoretical descriptions and empirical measurements was found to depend on the mechanical properties of the shell that encapsulates the microbubble as well as stabilizes it against the surrounding aqueous environment. Thus biochemically induced switching between a rigid 'off' state and a flexible 'on' state provides a mechanism for sensing chemical markers for disease. In our research, we coupled DNA oligonucleotides to a stabilizing lipid monolayer to modulate stiffness of the shell and thereby induce stimulus-responsive behavior. In initial proof-of-principle studies, it was found that signal modulation came primarily from DNA crosslinks preventing the microbubble size oscillations rather than merely damping the signal. Next, these microbubbles were redesigned to include an aptamer sequence in the crosslinking strand, which not only allowed the sensing of the clotting enzyme thrombin but also provided a general strategy for sensing other soluble biomarkers in the bloodstream. Finally, the thrombin-sensitive microbubbles were validated in a rabbit model, presenting the first example of an ultrasound contrast agent that could differentiate between active and inactive clots for the diagnosis of deep venous thrombosis.
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Affiliation(s)
- Andrew P Goodwin
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
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241
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Dawidczyk CM, Russell LM, Searson PC. Nanomedicines for cancer therapy: state-of-the-art and limitations to pre-clinical studies that hinder future developments. Front Chem 2014; 2:69. [PMID: 25202689 PMCID: PMC4142601 DOI: 10.3389/fchem.2014.00069] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/05/2014] [Indexed: 01/31/2023] Open
Abstract
The ability to efficiently deliver a drug or gene to a tumor site is dependent on a wide range of factors including circulation time, interactions with the mononuclear phagocyte system, extravasation from circulation at the tumor site, targeting strategy, release from the delivery vehicle, and uptake in cancer cells. Nanotechnology provides the possibility of creating delivery systems where the design constraints are decoupled, allowing new approaches for reducing the unwanted side effects of systemic delivery, increasing tumor accumulation, and improving efficacy. The physico-chemical properties of nanoparticle-based delivery platforms introduce additional complexity associated with pharmacokinetics, tumor accumulation, and biodistribution. To assess the impact of nanoparticle-based delivery systems, we first review the design strategies and pharmacokinetics of FDA-approved nanomedicines. Next we review nanomedicines under development, summarizing the range of nanoparticle platforms, strategies for targeting, and pharmacokinetics. We show how the lack of uniformity in preclinical trials prevents systematic comparison and hence limits advances in the field.
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Affiliation(s)
- Charlene M Dawidczyk
- Institute for Nanobiotechnology, Johns Hopkins University Baltimore, MD, USA ; Johns Hopkins Center of Cancer Nanotechnology Excellence, Johns Hopkins University Baltimore, MD, USA ; Department of Materials Science and Engineering, Johns Hopkins University Baltimore, MD, USA
| | - Luisa M Russell
- Institute for Nanobiotechnology, Johns Hopkins University Baltimore, MD, USA ; Johns Hopkins Center of Cancer Nanotechnology Excellence, Johns Hopkins University Baltimore, MD, USA ; Department of Materials Science and Engineering, Johns Hopkins University Baltimore, MD, USA
| | - Peter C Searson
- Institute for Nanobiotechnology, Johns Hopkins University Baltimore, MD, USA ; Johns Hopkins Center of Cancer Nanotechnology Excellence, Johns Hopkins University Baltimore, MD, USA ; Department of Materials Science and Engineering, Johns Hopkins University Baltimore, MD, USA
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242
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Ye F, Zheng Y, Wang X, Tan X, Zhang T, Xin W, Wang J, Huang Y, Fan Q, Wang J. Recognition of Bungarus multicinctus venom by a DNA aptamer against β-bungarotoxin. PLoS One 2014; 9:e105404. [PMID: 25144237 PMCID: PMC4140777 DOI: 10.1371/journal.pone.0105404] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/21/2014] [Indexed: 01/03/2023] Open
Abstract
Antibody-based technology is the main method for diagnosis and treatment of snake bite envenoming currently. However, the development of an antibody, polyclonal or monoclonal, is a complicated and costly procedure. Aptamers are single stranded oligonucleotides that recognize specific targets such as proteins and have shown great potential over the years as diagnostic and therapeutic agents. In contrast to antibodies, aptamers can be selected in vitro without immunization of animals, and synthesized chemically with extreme accuracy, low cost and high degree of purity. In this study we firstly report on the identification of DNA aptamers that bind to β-bungarotoxin (β-BuTx), a neurotoxin from the venom of Bungarus multicinctus. A plate-SELEX method was used for the selection of β-BuTx specific aptamers. After 10 rounds of selection, four aptamer candidates were obtained, with the dissociation constant ranged from 65.9 nM to 995 nM measured by fluorescence spectroscopy. Competitive binding assays using both the fluorescently labeled and unlabeled aptamers revealed that the four aptamers bound to the same binding site of β-BuTx. The best binder, βB-1, bound specifically to β-BuTx, but not to BSA, casein or α-Bungarotoxin. Moreover, electrophoretic mobility shift assay and enzyme-linked aptamer assay demonstrated that βB-1 could discriminate B. multicinctus venom from other snake venoms tested. The results suggest that aptamer βB-1 can serve as a useful tool for the design and development of drugs and diagnostic tests for β-BuTx poisoning and B. multicinctus bites.
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Affiliation(s)
- Fengping Ye
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Ying Zheng
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Xi Wang
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Xiaolong Tan
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Tao Zhang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
| | - Wenwen Xin
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
| | - Jie Wang
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Yong Huang
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Quanshui Fan
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
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243
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Abstract
The demand for rapid and accurate diagnosis of plant diseases has risen in the last decade. On-site diagnosis of single or multiple pathogens using portable devices is the first step in this endeavour. Despite extensive attempts to develop portable devices for pathogen detection, current technologies are still restricted to detecting known pathogens with limited detection accuracy. Developing new detection techniques for rapid and accurate detection of multiple plant pathogens and their associated variants is essential. Recent single DNA sequencing technologies are a promising new avenue for developing future portable devices for plant pathogen detection. In this review, we detail the current progress in portable devices and technologies used for detecting plant pathogens, the current position of emerging sequencing technologies for analysis of plant genomics, and the future of portable devices for rapid pathogen diagnosis.
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Affiliation(s)
- Amir Sanati Nezhad
- McGill University and Genome Quebec Innovation Centre, Department of Biomedical Engineering, McGill University, Montreal, Quebec, Canada.
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244
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Zeng Z, Tung CH, Zu Y. A cancer cell-activatable aptamer-reporter system for one-step assay of circulating tumor cells. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e184. [PMID: 25118170 PMCID: PMC4221596 DOI: 10.1038/mtna.2014.36] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/30/2014] [Indexed: 01/22/2023]
Abstract
The current antibody-mediated numeration assays of circulating tumor cells (CTCs) require multiple steps and are time-consuming. To overcome these technical limitations, a cancer cell-activatable aptamer-reporter was formulated by conjugating a biomarker-specific aptamer sequence with paired fluorochrome-quencher molecules. In contrast to the antibody probes, the intact aptamer-reporter was optically silent in the absence of cells of interest. However, when used in an assay, the aptamer selectively targeted cancer cells through interaction with a specific surface biomarker, which triggered internalization of the aptamer-reporter and, subsequently, into cell lysosomes. Rapid lysosomal degradation of the aptamer-reporter resulted in separation of the paired fluorochrome-quencher molecules. The released fluorochrome emitted bright fluorescent signals exclusively within the targeted cancer cells, with no background noise in the assay. Thus, the assays could be completed in a single step within minutes. By using this one-step assay, CTCs in whole blood and marrow aspirate samples of patients with lymphoma tumors were selectively highlighted and rapidly detected with no off-target signals from background blood cells. The development of the cancer cell-activatable aptamer-reporter system allows for the possibility of a simple and robust point-of-care test for CTC detection, which is currently unavailable.
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Affiliation(s)
- Zihua Zeng
- Department of Pathology and Genomic Medicine and Cancer Pathology Laboratory, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Ching-Hsuan Tung
- Department of Translational Imaging, Houston Methodist Research Institute, Houston, Texas, USA
| | - Youli Zu
- Department of Pathology and Genomic Medicine and Cancer Pathology Laboratory, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
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245
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Kruspe S, Mittelberger F, Szameit K, Hahn U. Aptamers as drug delivery vehicles. ChemMedChem 2014; 9:1998-2011. [PMID: 25130604 DOI: 10.1002/cmdc.201402163] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/02/2014] [Indexed: 01/22/2023]
Abstract
The benefits of directed and selective therapy for systemic treatment are reasons for increased interest in exploiting aptamers for cell-specific drug delivery. Nucleic acid based pharmaceuticals represent an interesting and novel tool to counter human diseases. Combining inhibitory potential and cargo transfer upon internalization, nanocarriers as well as various therapeutics including siRNAs, chemotherapeutics, photosensitizers, or proteins can be imported via these synthetic nucleic acids. However, widespread clinical application is still hampered by obstacles that must be overcome. In this review, we give an overview of applications and recent advances in aptamer-mediated drug delivery. We also introduce prominent selection methods as well as useful approaches in choice of drug and conjugation method. We discuss the challenges that need to be considered and present strategies that have been applied to achieve intracellular delivery of effectors transported by readily internalized aptamers.
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Affiliation(s)
- Sven Kruspe
- Institut für Biochemie und Molekularbiologie, Universität Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg (Germany)
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246
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Belyaeva TA, Nicol C, Cesur O, Travé G, Blair GE, Stonehouse NJ. An RNA Aptamer Targets the PDZ-Binding Motif of the HPV16 E6 Oncoprotein. Cancers (Basel) 2014; 6:1553-69. [PMID: 25062098 PMCID: PMC4190555 DOI: 10.3390/cancers6031553] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 06/23/2014] [Accepted: 07/03/2014] [Indexed: 01/01/2023] Open
Abstract
Human papillomavirus 16 (HPV16) is a high-risk DNA tumour virus which is the primary causative agent of cervical cancer. Cell transformation arises from deregulated expression of the E6 and E7 oncogenes. E6 has been shown to bind a number of cellular proteins, including p53 and proteins containing a PDZ domain. This study reports the first RNA aptamers to E6. These have been employed as molecular tools to further investigate E6-p53 and E6-PDZ interactions. This study is focussed on two aptamers (termed F2 and F4) which induced apoptosis in cells derived from an HPV16-transformed cervical carcinoma. The molecules were able to inhibit the interaction between E6 and PDZ1 from Magi1, with F2 being the most effective inhibitor. Neither of the aptamers inhibited E6-p53 interaction or p53 degradation. This study shows the specificity of this approach and highlights the potential benefits of the E6 aptamers as potential therapeutic or diagnostic agents in the future.
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Affiliation(s)
- Tamara A Belyaeva
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Clare Nicol
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Ozlem Cesur
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Gilles Travé
- UMR 7242 CNRS-Université de Strasbourg, Ecole Supérieure de Biotechnologie, Boulevard Sébastien Brant, Illkirch 67412, France.
| | - George Eric Blair
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Nicola J Stonehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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247
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Zeng Z, Parekh P, Li Z, Shi ZZ, Tung CH, Zu Y. Specific and sensitive tumor imaging using biostable oligonucleotide aptamer probes. Am J Cancer Res 2014; 4:945-52. [PMID: 25057318 PMCID: PMC4107294 DOI: 10.7150/thno.9246] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/29/2014] [Indexed: 12/20/2022] Open
Abstract
Although several imaging modalities are widely used for tumor imaging, none are tumor type-specific. Different types of cancer exhibit differential therapeutic responses, thus necessitating development of an imaging modality able to detect various tumor types with high specificity. To illustrate this point, CD30-specific oligonucleotide aptamer in vivo imaging probes were conjugated to the near-infrared IRD800CW reporter. Mice bearing xenografted CD30-positive or control CD30-negative lymphoma tumors on contralateral sides of the same mouse were developed. Following a systemic administration of aptamer probes, whole body imaging of tumor-bearing mice was performed. Imaging signal from tumor sites was analyzed and imaging specificity confirmed by tissue immunostaining. The in vivo biodistribution of aptamer probes was also evaluated. Whole body scans revealed that the RNA-based aptamer probes selectively highlighted CD30-expressing lymphoma tumors immediately after systemic administration, but did not react with control tumors in the same mouse. The resultant imaging signal lasted up to 1 hr and the aptamer probes were rapidly eliminated from the body through urinary and lower intestinal tracts. For more sensitive imaging, biostable CD30-specific ssDNA-based aptamer probes were also generated. Systemic administration of these probes also selectively highlighted the CD30-positive lymphoma tumors, with imaging signal detected 4-5 folds higher than that derived from control tumors in the same animal, and lasted for up to 24hr. This study demonstrates that oligonucleotide aptamer probes can provide tumor type-specific imaging with high sensitivity and a long-lasting signal, indicating their potential for clinical applications.
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248
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Wang K, Liao J, Yang X, Zhao M, Chen M, Yao W, Tan W, Lan X. A label-free aptasensor for highly sensitive detection of ATP and thrombin based on metal-enhanced PicoGreen fluorescence. Biosens Bioelectron 2014; 63:172-177. [PMID: 25086329 DOI: 10.1016/j.bios.2014.07.022] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/27/2014] [Accepted: 07/08/2014] [Indexed: 11/29/2022]
Abstract
A label-free fluorescence aptasensor for highly selective and sensitive detection of ATP and thrombin was developed by using PicoGreen (PG) as signal molecule and surface-bound metal-enhanced fluorescence (MEF) substrates (silver island films, SIFs) as signal enhancers. On binding with ATP or thrombin, aptamers undergo structure switching, leading to a reduction of fluorescence intensity of PG. Chang of fluorescence intensity can be magnified by SIFs. The limit of detection for ATP and thrombin is 1.3 nM and 0.073 nM, respectively. The fluorescence quenching efficiency is linear in the logarithmic scale with ATP concentration range from 10 nM to 100 μM (R(2)=0.995) and thrombin concentration range from 0.1 nM to 100 nM (R(2)=0.997). The coefficients of variation of the intra-assay reproducibility and inter-assay reproducibility for ATP (10 μM) assay are 3.8% and 5.2%, respectively. In addition, the aptasensor is stable and can be reliably used for ATP measurement in biological samples. Overall, the aptasensor can be a useful and cost effective tool for the specific detection of ATP, thrombin and potentially other biomolecules in biological samples.
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Affiliation(s)
- Kaiyu Wang
- Institute of Laboratory Medicine, Fuzhou General Hospital of Nanjing Military Command, Fuzhou 350025, PR China; Department of Laboratory Medicine, Dongfang Hospital, Xiamen University, Fuzhou 350025, PR China; Department of Laboratory Medicine, Fuzong Clinical College, Fujian Medical University, Fuzhou 350025, PR China
| | - Jian Liao
- Institute of Laboratory Medicine, Fuzhou General Hospital of Nanjing Military Command, Fuzhou 350025, PR China; Department of Laboratory Medicine, Dongfang Hospital, Xiamen University, Fuzhou 350025, PR China
| | - Xiangyue Yang
- Institute of Laboratory Medicine, Fuzhou General Hospital of Nanjing Military Command, Fuzhou 350025, PR China; Department of Laboratory Medicine, Dongfang Hospital, Xiamen University, Fuzhou 350025, PR China
| | - Meng Zhao
- Institute of Laboratory Medicine, Fuzhou General Hospital of Nanjing Military Command, Fuzhou 350025, PR China; Department of Laboratory Medicine, Dongfang Hospital, Xiamen University, Fuzhou 350025, PR China
| | - Min Chen
- Institute of Laboratory Medicine, Fuzhou General Hospital of Nanjing Military Command, Fuzhou 350025, PR China; Department of Laboratory Medicine, Dongfang Hospital, Xiamen University, Fuzhou 350025, PR China
| | - Weirong Yao
- Department of Laboratory Medicine, Fuzong Clinical College, Fujian Medical University, Fuzhou 350025, PR China
| | - Weihong Tan
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Shands Cancer Center, University of Florida, Gainesville, Florida 32611, United States; Plant Pathology Lab, North Florida Research and Education Center, University of Florida, Quincy, Florida 32351, United States; Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, PR China.
| | - Xiaopeng Lan
- Institute of Laboratory Medicine, Fuzhou General Hospital of Nanjing Military Command, Fuzhou 350025, PR China; Department of Laboratory Medicine, Dongfang Hospital, Xiamen University, Fuzhou 350025, PR China; Department of Laboratory Medicine, Fuzong Clinical College, Fujian Medical University, Fuzhou 350025, PR China.
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249
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Zhu J, Huang H, Dong S, Ge L, Zhang Y. Progress in aptamer-mediated drug delivery vehicles for cancer targeting and its implications in addressing chemotherapeutic challenges. Theranostics 2014; 4:931-44. [PMID: 25057317 PMCID: PMC4107293 DOI: 10.7150/thno.9663] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 06/23/2014] [Indexed: 12/28/2022] Open
Abstract
Aptamers are novel oligonucleotides with flexible three-dimensional configurations that recognize and bind to their cognate targets, including tumor surface receptors, in a high-affinity and highly specific manner. Because of their unique intrinsic properties, a variety of aptamer-mediated nanovehicles have been developed to directionally transport anti-cancer drugs to tumor sites to minimize systemic cytotoxicity and to enhance permeation by these tumoricidal agents. Despite advances in the selection and synthesis of aptamers and in the conjugation and self-assembly of nanotechnologies, current chemotherapy and drug delivery systems face great challenges. These challenges are due to the limitations of aptamers and vehicles and because of complicated tumor mechanisms, including heterogeneity, anti-cancer drug resistance, and hypoxia-induced aberrances. In this review, we will summarize current approaches utilizing tumor surface hallmarks and aptamers and their roles and mechanisms in therapeutic nanovehicles targeting tumors. Delivery forms include nanoparticles, nanotubes, nanogels, aptamer-drug conjugates, and novel molecular trains. Moreover, the obstacles posed by the aforementioned issues will be highlighted, and possible solutions will be acknowledged. Furthermore, future perspectives will be presented, including cutting-edge integration with RNA interference nanotechnology and personalized chemotherapy, which will facilitate innovative approaches to aptamer-based therapeutics.
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250
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Rastädter D, Biswas M, Burghardt I. Molecular Dynamics Study of the Controlled Destabilization of an RNA Hairpin Structure by a Covalently Attached Azobenzene Switch. J Phys Chem B 2014; 118:8478-88. [DOI: 10.1021/jp501399k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dominique Rastädter
- Institute
of Physical and
Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse
7, 60438 Frankfurt
am Main, Germany
| | - Mithun Biswas
- Institute
of Physical and
Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse
7, 60438 Frankfurt
am Main, Germany
| | - Irene Burghardt
- Institute
of Physical and
Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse
7, 60438 Frankfurt
am Main, Germany
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