1
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Anwar S, Mir F, Yokota T. Enhancing the Effectiveness of Oligonucleotide Therapeutics Using Cell-Penetrating Peptide Conjugation, Chemical Modification, and Carrier-Based Delivery Strategies. Pharmaceutics 2023; 15:pharmaceutics15041130. [PMID: 37111616 PMCID: PMC10140998 DOI: 10.3390/pharmaceutics15041130] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Oligonucleotide-based therapies are a promising approach for treating a wide range of hard-to-treat diseases, particularly genetic and rare diseases. These therapies involve the use of short synthetic sequences of DNA or RNA that can modulate gene expression or inhibit proteins through various mechanisms. Despite the potential of these therapies, a significant barrier to their widespread use is the difficulty in ensuring their uptake by target cells/tissues. Strategies to overcome this challenge include cell-penetrating peptide conjugation, chemical modification, nanoparticle formulation, and the use of endogenous vesicles, spherical nucleic acids, and smart material-based delivery vehicles. This article provides an overview of these strategies and their potential for the efficient delivery of oligonucleotide drugs, as well as the safety and toxicity considerations, regulatory requirements, and challenges in translating these therapies from the laboratory to the clinic.
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Affiliation(s)
- Saeed Anwar
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Farin Mir
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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2
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A nucleolin-activated polyvalent aptamer nanoprobe for the detection of cancer cells. Anal Bioanal Chem 2023; 415:2217-2226. [PMID: 36864310 DOI: 10.1007/s00216-023-04629-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023]
Abstract
Sensitive detection of cancer cells plays a critical role in early cancer diagnosis. Nucleolin, overexpressed on the surface of cancer cells, is regarded as a candidate biomarker for cancer diagnosis. Thus, cancer cells can be detected through the detection of membrane nucleolin. Herein, we designed a nucleolin-activated polyvalent aptamer nanoprobe (PAN) to detect cancer cells. In brief, a long single-stranded DNA with many repeated sequences was synthesized through rolling circle amplification (RCA). Then the RCA product acted as a scaffold chain to combine with multiple AS1411 sequences, which was doubly modified with fluorophore and quenching group, respectively. The fluorescence of PAN was initially quenched. Upon binding to target protein, the conformation of PAN changed, leading to the recovery of fluorescence. The fluorescence signal of cancer cells treated with PAN was much brighter compared with that of monovalent aptamer nanoprobes (MAN) at the same concentration. Furthermore, the binding affinity of PAN to B16 cells was proved to be 30 times higher than that of MAN by calculating the dissociation constants. The results indicated that PAN could specifically detect target cells, and this design concept has potential to become promising in cancer diagnosis.
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3
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Zhu Y, Hart GW. Dual-specificity RNA aptamers enable manipulation of target-specific O-GlcNAcylation and unveil functions of O-GlcNAc on β-catenin. Cell 2023; 186:428-445.e27. [PMID: 36626902 PMCID: PMC9868088 DOI: 10.1016/j.cell.2022.12.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 11/02/2022] [Accepted: 12/08/2022] [Indexed: 01/11/2023]
Abstract
O-GlcNAc is a dynamic post-translational modification (PTM) that regulates protein functions. In studying the regulatory roles of O-GlcNAc, a major roadblock is the inability to change O-GlcNAcylation on a single protein at a time. Herein, we developed a dual RNA-aptamer-based approach that simultaneously targeted O-GlcNAc transferase (OGT) and β-catenin, the key transcription factor of the Wnt signaling pathway, to selectively increase O-GlcNAcylation of the latter without affecting other OGT substrates. Using the OGT/β-catenin dual-specificity aptamers, we found that O-GlcNAcylation of β-catenin stabilizes the protein by inhibiting its interaction with β-TrCP. O-GlcNAc also increases β-catenin's interaction with EZH2, recruits EZH2 to promoters, and dramatically alters the transcriptome. Further, by coupling riboswitches or an inducible expression system to aptamers, we enabled inducible regulation of protein-specific O-GlcNAcylation. Together, our findings demonstrate the efficacy and versatility of dual-specificity aptamers for regulating O-GlcNAcylation on individual proteins.
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Affiliation(s)
- Yi Zhu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
| | - Gerald W Hart
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
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4
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Piasek AM, Musolf P, Sobiepanek A. Aptamer-based Advances in Skin Cancer Research. Curr Med Chem 2023; 30:953-973. [PMID: 35400317 DOI: 10.2174/0929867329666220408112735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 01/24/2022] [Accepted: 02/07/2022] [Indexed: 11/22/2022]
Abstract
Cancer diseases have been one of the biggest health threats for the last two decades. Approximately 9% of all diagnosed cancers are skin cancers, including melanoma and non-melanoma. In all cancer cases, early diagnosis is essential to achieve efficient treatment. New solutions and advanced techniques for rapid diagnosis are constantly being sought. Aptamers are single-stranded RNA or DNA synthetic sequences or peptides, which offer novel possibilities to this area of research by specifically binding selected molecules, the so-called cancer biomarkers. Nowadays, they are widely used as diagnostic probes in imaging and targeted therapy. In this review, we have summarized the recently made advances in diagnostics and treatment of skin cancers, which have been achieved by combining aptamers with basic or modern technologies.
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Affiliation(s)
- Adrianna Maria Piasek
- Laboratory of Biomolecular Interactions Studies, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Paulina Musolf
- Laboratory of Biomolecular Interactions Studies, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Anna Sobiepanek
- Laboratory of Biomolecular Interactions Studies, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
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5
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Shraim AS, Abdel Majeed BA, Al-Binni M, Hunaiti A. Therapeutic Potential of Aptamer-Protein Interactions. ACS Pharmacol Transl Sci 2022; 5:1211-1227. [PMID: 36524009 PMCID: PMC9745894 DOI: 10.1021/acsptsci.2c00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Indexed: 11/06/2022]
Abstract
Aptamers are single-stranded oligonucleotides (RNA or DNA) with a typical length between 25 and 100 nucleotides which fold into three-dimensional structures capable of binding to target molecules. Specific aptamers can be isolated against a large variety of targets through efficient and relatively cheap methods, and they demonstrate target-binding affinities that sometimes surpass those of antibodies. Consequently, interest in aptamers has surged over the past three decades, and their application has shown promise in advancing knowledge in target analysis, designing therapeutic interventions, and bioengineering. With emphasis on their therapeutic applications, aptamers are emerging as a new innovative class of therapeutic agents with promising biochemical and biological properties. Aptamers have the potential of providing a feasible alternative to antibody- and small-molecule-based therapeutics given their binding specificity, stability, low toxicity, and apparent non-immunogenicity. This Review examines the general properties of aptamers and aptamer-protein interactions that help to understand their binding characteristics and make them important therapeutic candidates.
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Affiliation(s)
- Ala’a S. Shraim
- Department
of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, 19328 Amman, Jordan
- Pharmacological
and Diagnostic Research Center (PDRC), Al-Ahliyya
Amman University, 19328 Amman, Jordan
| | - Bayan A. Abdel Majeed
- Department
of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, 19328 Amman, Jordan
- Pharmacological
and Diagnostic Research Center (PDRC), Al-Ahliyya
Amman University, 19328 Amman, Jordan
| | - Maysaa’
Adnan Al-Binni
- Department
of Clinical Laboratory Sciences, School of Science, The University of Jordan, 11942 Amman, Jordan
| | - Abdelrahim Hunaiti
- Department
of Clinical Laboratory Sciences, School of Science, The University of Jordan, 11942 Amman, Jordan
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6
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Lennon SR, Batey RT. Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches. J Mol Biol 2022; 434:167585. [PMID: 35427633 PMCID: PMC9474592 DOI: 10.1016/j.jmb.2022.167585] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022]
Abstract
Riboswitches are an outstanding example of genetic regulation mediated by RNA conformational switching. In these non-coding RNA elements, the occupancy status of a ligand-binding domain governs the mRNA's decision to form one of two mutually exclusive structures in the downstream expression platform. Temporal constraints upon the function of many riboswitches, requiring folding of complex architectures and conformational switching in a limited co-transcriptional timeframe, make them ideal model systems for studying these processes. In this review, we focus on the mechanism of ligand-directed conformational changes in one of the most widely distributed riboswitches in bacteria: the cobalamin family. We describe the architectural features of cobalamin riboswitches whose structures have been determined by x-ray crystallography, which suggest a direct physical role of cobalamin in effecting the regulatory switch. Next, we discuss a series of experimental approaches applied to several model cobalamin riboswitches that interrogate these structural models. As folding is central to riboswitch function, we consider the differences in folding landscapes experienced by RNAs that are produced in vitro and those that are allowed to fold co-transcriptionally. Finally, we highlight a set of studies that reveal the difficulties of studying cobalamin riboswitches outside the context of transcription and that co-transcriptional approaches are essential for developing a more accurate picture of their structure-function relationships in these switches. This understanding will be essential for future advancements in the use of small-molecule guided RNA switches in a range of applications such as biosensors, RNA imaging tools, and nucleic acid-based therapies.
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Affiliation(s)
- Shelby R Lennon
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA.
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7
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De Mey W, Esprit A, Thielemans K, Breckpot K, Franceschini L. RNA in Cancer Immunotherapy: Unlocking the Potential of the Immune System. Clin Cancer Res 2022; 28:3929-3939. [PMID: 35583609 PMCID: PMC9475240 DOI: 10.1158/1078-0432.ccr-21-3304] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/24/2022] [Accepted: 05/03/2022] [Indexed: 01/07/2023]
Abstract
Recent advances in the manufacturing, modification, purification, and cellular delivery of ribonucleic acid (RNA) have enabled the development of RNA-based therapeutics for a broad array of applications. The approval of two SARS-CoV-2-targeting mRNA-based vaccines has highlighted the advances of this technology. Offering rapid and straightforward manufacturing, clinical safety, and versatility, this paves the way for RNA therapeutics to expand into cancer immunotherapy. Together with ongoing trials on RNA cancer vaccination and cellular therapy, RNA therapeutics could be introduced into clinical practice, possibly stewarding future personalized approaches. In the present review, we discuss recent advances in RNA-based immuno-oncology together with an update on ongoing clinical applications and their current challenges.
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Affiliation(s)
- Wout De Mey
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Arthur Esprit
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kris Thielemans
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Karine Breckpot
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium.,Corresponding Author: Karine Breckpot, Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium. Phone: 32-2-477-45-66; E-mail:
| | - Lorenzo Franceschini
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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8
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Akbarian M, Bertassoni LE, Tayebi L. Biological aspects in controlling angiogenesis: current progress. Cell Mol Life Sci 2022; 79:349. [PMID: 35672585 PMCID: PMC10171722 DOI: 10.1007/s00018-022-04348-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 12/25/2022]
Abstract
All living beings continue their life by receiving energy and by excreting waste products. In animals, the arteries are the pathways of these transfers to the cells. Angiogenesis, the formation of the arteries by the development of pre-existed parental blood vessels, is a phenomenon that occurs naturally during puberty due to certain physiological processes such as menstruation, wound healing, or the adaptation of athletes' bodies during exercise. Nonetheless, the same life-giving process also occurs frequently in some patients and, conversely, occurs slowly in some physiological problems, such as cancer and diabetes, so inhibiting angiogenesis has been considered to be one of the important strategies to fight these diseases. Accordingly, in tissue engineering and regenerative medicine, the highly controlled process of angiogenesis is very important in tissue repairing. Excessive angiogenesis can promote tumor progression and lack of enough angiogensis can hinder tissue repair. Thereby, both excessive and deficient angiogenesis can be problematic, this review article introduces and describes the types of factors involved in controlling angiogenesis. Considering all of the existing strategies, we will try to lay out the latest knowledge that deals with stimulating/inhibiting the angiogenesis. At the end of the article, owing to the early-reviewed mechanical aspects that overshadow angiogenesis, the strategies of angiogenesis in tissue engineering will be discussed.
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Affiliation(s)
- Mohsen Akbarian
- Department of Chemistry, National Cheng Kung University, Tainan, 701, Taiwan
| | - Luiz E Bertassoni
- Division of Biomaterials and Biomechanics, Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, OR, USA
| | - Lobat Tayebi
- Marquette University School of Dentistry, Milwaukee, WI, 53233, USA.
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9
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Ozer I, Pitoc GA, Layzer JM, Moreno A, Olson LB, Layzer KD, Hucknall AM, Sullenger BA, Chilkoti A. PEG-Like Brush Polymer Conjugate of RNA Aptamer That Shows Reversible Anticoagulant Activity and Minimal Immune Response. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2107852. [PMID: 34994037 DOI: 10.1002/adma.202107852] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Ribonucleic acid (RNA) therapeutics are an emerging class of drugs. RNA aptamers are of significant therapeutic and clinical interest because their activity can be easily reversed in vivo-a useful feature that is difficult to achieve using other therapeutic modalities. Despite their therapeutic promise, RNA aptamers are limited by their poor blood circulation. The attachment of polyethylene glycol (PEG) to RNA aptamers addresses this limitation. However, an RNA aptamer-PEG conjugate that is a reversible anticoagulant fails in a clinical trial due to the reactivity of the conjugate with pre-existing PEG antibodies and has cast a pall over PEGylation of aptamers and other biologics, despite its long history of utility in drug delivery. Here, PEG antibody-reactivity of this RNA aptamer is eliminated by conjugating it to a next-generation PEG-like brush polymer-poly[(oligoethylene glycol) methyl ether methacrylate)] (POEGMA). The conjugate retained the drug's therapeutic action and the ability to be easily reversed. Importantly, this conjugate does not bind pre-existing PEG antibodies that are prevalent in humans and does not induce a humoral immune response against the polymer itself in mice. These findings suggest a path to rescuing the PEGylation of RNA therapeutics and vaccines from the deleterious side-effects of PEG.
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Affiliation(s)
- Imran Ozer
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - George A Pitoc
- Department of Surgery, Duke University Medical Center, Durham, NC, 27707, USA
| | - Juliana M Layzer
- Department of Surgery, Duke University Medical Center, Durham, NC, 27707, USA
- Duke Clinical and Translational Science Institute, Durham, NC, 27707, USA
| | - Angelo Moreno
- Department of Surgery, Duke University Medical Center, Durham, NC, 27707, USA
| | - Lyra B Olson
- Department of Surgery, Duke University Medical Center, Durham, NC, 27707, USA
| | - Kyle D Layzer
- Department of Surgery, Duke University Medical Center, Durham, NC, 27707, USA
| | - Angus M Hucknall
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Bruce A Sullenger
- Department of Surgery, Duke University Medical Center, Durham, NC, 27707, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
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10
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Jasuja R, Pencina KM, Peng L, Bhasin S. Accurate Measurement and Harmonized Reference Ranges for Total and Free Testosterone Levels. Endocrinol Metab Clin North Am 2022; 51:63-75. [PMID: 35216721 DOI: 10.1016/j.ecl.2021.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Diagnosing testosterone deficiency requires accurate and precise measurement of total testosterone levels by an accurate method, such as liquid chromatography-tandem mass spectrometry in a laboratory certified by an accuracy-based program (eg, Centers for Disease Control and Prevention's Hormone Standardization (HoST) Program), and, if needed, free testosterone level. Free testosterone level should ideally be measured by equilibrium dialysis method. Testosterone levels should be measured in 2 or more fasting samples obtained in the morning. Harmonized reference ranges for total testosterone can be applied to laboratories that certified by the HoST Program.
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Affiliation(s)
- Ravi Jasuja
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA
| | - Karol M Pencina
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA
| | - Liming Peng
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA
| | - Shalender Bhasin
- Research Program in Men's Health: Aging and Metabolism, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA.
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11
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Biosensors as diagnostic tools in clinical applications. Biochim Biophys Acta Rev Cancer 2022; 1877:188726. [DOI: 10.1016/j.bbcan.2022.188726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/18/2022] [Accepted: 03/25/2022] [Indexed: 11/19/2022]
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12
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Chen J, Zhao Y, Feng W. Selection and Characterization of DNA Aptamers Targeting hLCN6 Protein for Sperm Capture. Appl Biochem Biotechnol 2022; 194:2565-2580. [PMID: 35171466 DOI: 10.1007/s12010-022-03834-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2022] [Indexed: 11/25/2022]
Abstract
It is an urgent and difficult task to establish a simple and efficient method for identifying and isolating sperm cells from mixed stains in forensic science. In this project, we developed a DNA aptamer-based system for sperm separation and purification from mixed stain samples by targeting sperm surface proteins. Human lipocalin 6 (hLCN6) is an epididymal secreted protein that binds to the head and tail of sperm cells and associated with sperm maturation. Using systematic evolution of ligands by exponential enrichment (SELEX) technology, aptamers that bind with high affinity and specificity to hLCN6 were screened from a random single-stranded DNA (ssDNA) library using magnetic bead-bound hLCN6 as target. The enriched library was obtained after 15 SELEX rounds. Of hLCN6-binding aptamer variants, 19 were further classified into one of the four groups based on their N60 random sequence regions, wherein one representative from each group was characterized. Prediction analysis of the secondary structure suggested discrete features with typical loop and stem motifs. Binding capability of selected aptamers was investigated by quantitative PCR, and aptamer H2 was found to be the most specific aptamer to sperm cells. The dissociation constant (Kd) of H2 aptamer was calculated as 3.21 ± 0.75 nM. Furthermore, H2 aptamer-coupled magnetic beads can recognize and capture sperm cells, which establishes the foundation of an approach for rapidly isolating sperm cells from mixed stains based on nucleic acid-protein interaction.
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Affiliation(s)
- Jiong Chen
- Department of Forensic Biology, Henan University of Science and Technology, Kaiyuan Street 263, Luoyang, 471023, China.
| | - Yue Zhao
- CITIC Heavy Industries Co., Ltd, Luoyang, 471003, China
| | - Wei Feng
- Department of Forensic Biology, Henan University of Science and Technology, Kaiyuan Street 263, Luoyang, 471023, China
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13
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Roueinfar M, Templeton HN, Sheng JA, Hong KL. An Update of Nucleic Acids Aptamers Theranostic Integration with CRISPR/Cas Technology. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27031114. [PMID: 35164379 PMCID: PMC8839139 DOI: 10.3390/molecules27031114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/17/2022]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system is best known for its role in genomic editing. It has also demonstrated great potential in nucleic acid biosensing. However, the specificity limitation in CRISPR/Cas has created a hurdle for its advancement. More recently, nucleic acid aptamers known for their high affinity and specificity properties for their targets have been integrated into CRISPR/Cas systems. This review article gives a brief overview of the aptamer and CRISPR/Cas technology and provides an updated summary and discussion on how the two distinctive nucleic acid technologies are being integrated into modern diagnostic and therapeutic applications
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Affiliation(s)
- Mina Roueinfar
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.R.); (H.N.T.); (J.A.S.)
- Department of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Wilkes University, 84 W. South Street, Wilkes-Barre, PA 18766, USA
| | - Hayley N. Templeton
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.R.); (H.N.T.); (J.A.S.)
| | - Julietta A. Sheng
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.R.); (H.N.T.); (J.A.S.)
| | - Ka Lok Hong
- Department of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Wilkes University, 84 W. South Street, Wilkes-Barre, PA 18766, USA
- Department of Pharmaceutical Sciences, School of Pharmacy, Notre Dame of Maryland University, 4701 North Charles Street, Baltimore, MD 21210, USA
- Correspondence: ; Tel.: +1-410-532-5044
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14
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Samuelian JS, Gremminger TJ, Song Z, Poudyal RR, Li J, Zhou Y, Staller SA, Carballo JA, Roychowdhury-Saha M, Chen SJ, Burke DH, Heng X, Baum DA. An RNA aptamer that shifts the reduction potential of metabolic cofactors. Nat Chem Biol 2022; 18:1263-1269. [PMID: 36097297 PMCID: PMC9596375 DOI: 10.1038/s41589-022-01121-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 07/25/2022] [Indexed: 01/19/2023]
Abstract
The discovery of ribozymes has inspired exploration of RNA's potential to serve as primordial catalysts in a hypothesized RNA world. Modern oxidoreductase enzymes employ differential binding between reduced and oxidized forms of redox cofactors to alter cofactor reduction potential and enhance the enzyme's catalytic capabilities. The utility of differential affinity has been underexplored as a chemical strategy for RNA. Here we show an RNA aptamer that preferentially binds oxidized forms of flavin over reduced forms and markedly shifts flavin reduction potential by -40 mV, similar to shifts for oxidoreductases. Nuclear magnetic resonance structural analysis revealed π-π and donor atom-π interactions between the aptamer and flavin that cause unfavorable contacts with the electron-rich reduced form, suggesting a mechanism by which the local environment of the RNA-binding pocket drives the observed shift in cofactor reduction potential. It seems likely that primordial RNAs could have used similar strategies in RNA world metabolisms.
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Affiliation(s)
- John S. Samuelian
- grid.262962.b0000 0004 1936 9342Department of Chemistry, Saint Louis University, St. Louis, MO USA
| | - Thomas J. Gremminger
- grid.134936.a0000 0001 2162 3504Department of Biochemistry, University of Missouri, Columbia, MO USA ,Present Address: KCAS, LLC, Shawnee, KS USA
| | - Zhenwei Song
- grid.134936.a0000 0001 2162 3504Department of Biochemistry, University of Missouri, Columbia, MO USA
| | - Raghav R. Poudyal
- grid.134936.a0000 0001 2162 3504Department of Biochemistry, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Bond Life Sciences Center, University of Missouri, Columbia, MO USA ,grid.410513.20000 0000 8800 7493Present Address: Pfizer, Biomedicine Design, Cambridge, MA USA
| | - Jun Li
- grid.134936.a0000 0001 2162 3504Department of Physics, University of Missouri, Columbia, MO USA
| | - Yuanzhe Zhou
- grid.134936.a0000 0001 2162 3504Department of Physics, University of Missouri, Columbia, MO USA
| | - Seth A. Staller
- grid.134936.a0000 0001 2162 3504Department of Biochemistry, University of Missouri, Columbia, MO USA ,Present Address: Laronde, Inc., Cambridge, MA USA
| | - Johan A. Carballo
- grid.262962.b0000 0004 1936 9342Department of Chemistry, Saint Louis University, St. Louis, MO USA
| | - Manami Roychowdhury-Saha
- grid.411377.70000 0001 0790 959XDepartment of Chemistry, Indiana University, Bloomington, IN USA ,grid.505809.10000 0004 5998 7997Present Address: GRAIL, Menlo Park, CA USA
| | - Shi-Jie Chen
- grid.134936.a0000 0001 2162 3504Department of Biochemistry, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Department of Physics, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Institute for Data Science and Informatics, University of Missouri, Columbia, MO USA
| | - Donald H. Burke
- grid.134936.a0000 0001 2162 3504Department of Biochemistry, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Bond Life Sciences Center, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Department of Biological Engineering, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO USA
| | - Xiao Heng
- grid.134936.a0000 0001 2162 3504Department of Biochemistry, University of Missouri, Columbia, MO USA
| | - Dana A. Baum
- grid.262962.b0000 0004 1936 9342Department of Chemistry, Saint Louis University, St. Louis, MO USA
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15
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Ender A, Stadler PF, Mörl M, Findeiß S. RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing. Methods Mol Biol 2022; 2518:179-202. [PMID: 35666446 DOI: 10.1007/978-1-0716-2421-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Riboswitches are an attractive target for the directed design of RNA-based regulators by in silico prediction. These noncoding RNA elements consist of an aptamer platform for the highly selective ligand recognition and an expression platform which controls gene activity typically at the level of transcription or translation. In previous work, we could successfully apply RNA folding prediction to implement a new riboswitch mechanism regulating processing of a tRNA by RNase P. In this contribution, we present detailed information about our pipeline consisting of in silico design combined with the biochemical analysis for the verification of the implemented mechanism. Furthermore, we discuss the applicability of the presented biochemical in vivo and in vitro methods for the characterization of other artificial riboswitches.
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Affiliation(s)
- Anna Ender
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
- Max Planck Institute for Mathematics in the Science, Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
- Santa Fe Institute, Santa Fe, NM, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| | - Sven Findeiß
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany.
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16
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Slow Off-Rate Modified Aptamer (SOMAmer) Proteomic Analysis of Patient-Derived Malignant Glioma Identifies Distinct Cellular Proteomes. Int J Mol Sci 2021; 22:ijms22179566. [PMID: 34502484 PMCID: PMC8431317 DOI: 10.3390/ijms22179566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 02/04/2023] Open
Abstract
Malignant gliomas derive from brain glial cells and represent >75% of primary brain tumors. This includes anaplastic astrocytoma (grade III; AS), the most common and fatal glioblastoma multiforme (grade IV; GBM), and oligodendroglioma (ODG). We have generated patient-derived AS, GBM, and ODG cell models to study disease mechanisms and test patient-centered therapeutic strategies. We have used an aptamer-based high-throughput SOMAscan® 1.3K assay to determine the proteomic profiles of 1307 different analytes. SOMAscan® proteomes of AS and GBM self-organized into closely adjacent proteomes which were clearly distinct from ODG proteomes. GBM self-organized into four proteomic clusters of which SOMAscan® cluster 4 proteome predicted a highly inter-connected proteomic network. Several up- and down-regulated proteins relevant to glioma were successfully validated in GBM cell isolates across different SOMAscan® clusters and in corresponding GBM tissues. Slow off-rate modified aptamer proteomics is an attractive analytical tool for rapid proteomic stratification of different malignant gliomas and identified cluster-specific SOMAscan® signatures and functionalities in patient GBM cells.
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17
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Mollocana-Lara EC, Ni M, Agathos SN, Gonzales-Zubiate FA. The infinite possibilities of RNA therapeutics. J Ind Microbiol Biotechnol 2021; 48:6360324. [PMID: 34463324 PMCID: PMC8788720 DOI: 10.1093/jimb/kuab063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022]
Abstract
Although the study of ribonucleic acid (RNA) therapeutics started decades ago, for many years, this field of research was overshadowed by the growing interest in DNA-based therapies. Nowadays, the role of several types of RNA in cell regulation processes and the development of various diseases have been elucidated, and research in RNA therapeutics is back with force. This short literature review aims to present general aspects of many of the molecules currently used in RNA therapeutics, including in vitro transcribed mRNA (IVT mRNA), antisense oligonucleotides (ASOs), aptamers, small interfering RNAs (siRNAs), and microRNAs (miRNAs). In addition, we describe the state of the art of technologies applied for synthetic RNA manufacture and delivery. Likewise, we detail the RNA-based therapies approved by the FDA so far, as well as the ongoing clinical investigations. As a final point, we highlight the current and potential advantages of working on RNA-based therapeutics and how these could lead to a new era of accessible and personalized healthcare.
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Affiliation(s)
- Evelyn C Mollocana-Lara
- School of Biological Sciences and Engineering, Yachay Tech University, 100119, San Miguel de Urcuquí, Ecuador
| | - Ming Ni
- GenScript, Zhenjiang, Jiangsu Province, P.R. China
| | - Spiros N Agathos
- Bioengineering Laboratory, Earth and Life Institute, Catholic University of Louvain, Louvain-la-Neuve, Belgium
| | - Fernando A Gonzales-Zubiate
- School of Biological Sciences and Engineering, Yachay Tech University, 100119, San Miguel de Urcuquí, Ecuador
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18
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Frutiger A, Tanno A, Hwu S, Tiefenauer RF, Vörös J, Nakatsuka N. Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications. Chem Rev 2021; 121:8095-8160. [PMID: 34105942 DOI: 10.1021/acs.chemrev.1c00044] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.
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Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Alexander Tanno
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Stephanie Hwu
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Raphael F Tiefenauer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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Ziółkowski R, Jarczewska M, Górski Ł, Malinowska E. From Small Molecules Toward Whole Cells Detection: Application of Electrochemical Aptasensors in Modern Medical Diagnostics. SENSORS (BASEL, SWITZERLAND) 2021; 21:724. [PMID: 33494499 PMCID: PMC7866209 DOI: 10.3390/s21030724] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023]
Abstract
This paper focuses on the current state of art as well as on future trends in electrochemical aptasensors application in medical diagnostics. The origin of aptamers is presented along with the description of the process known as SELEX. This is followed by the description of the broad spectrum of aptamer-based sensors for the electrochemical detection of various diagnostically relevant analytes, including metal cations, abused drugs, neurotransmitters, cancer, cardiac and coagulation biomarkers, circulating tumor cells, and viruses. We described also possible future perspectives of aptasensors development. This concerns (i) the approaches to lowering the detection limit and improvement of the electrochemical aptasensors selectivity by application of the hybrid aptamer-antibody receptor layers and/or nanomaterials; and (ii) electrochemical aptasensors integration with more advanced microfluidic devices as user-friendly medical instruments for medical diagnostic of the future.
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Affiliation(s)
- Robert Ziółkowski
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (M.J.); (Ł.G.)
| | - Marta Jarczewska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (M.J.); (Ł.G.)
| | - Łukasz Górski
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (M.J.); (Ł.G.)
| | - Elżbieta Malinowska
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (M.J.); (Ł.G.)
- Center for Advanced Materials and Technologies, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
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20
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Subjakova V, Oravczova V, Hianik T. Polymer Nanoparticles and Nanomotors Modified by DNA/RNA Aptamers and Antibodies in Targeted Therapy of Cancer. Polymers (Basel) 2021; 13:341. [PMID: 33494545 PMCID: PMC7866063 DOI: 10.3390/polym13030341] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/14/2021] [Accepted: 01/16/2021] [Indexed: 12/14/2022] Open
Abstract
Polymer nanoparticles and nano/micromotors are novel nanostructures that are of increased interest especially in the diagnosis and therapy of cancer. These structures are modified by antibodies or nucleic acid aptamers and can recognize the cancer markers at the membrane of the cancer cells or in the intracellular side. They can serve as a cargo for targeted transport of drugs or nucleic acids in chemo- immuno- or gene therapy. The various mechanisms, such as enzyme, ultrasound, magnetic, electrical, or light, served as a driving force for nano/micromotors, allowing their transport into the cells. This review is focused on the recent achievements in the development of polymer nanoparticles and nano/micromotors modified by antibodies and nucleic acid aptamers. The methods of preparation of polymer nanoparticles, their structure and properties are provided together with those for synthesis and the application of nano/micromotors. The various mechanisms of the driving of nano/micromotors such as chemical, light, ultrasound, electric and magnetic fields are explained. The targeting drug delivery is based on the modification of nanostructures by receptors such as nucleic acid aptamers and antibodies. Special focus is therefore on the method of selection aptamers for recognition cancer markers as well as on the comparison of the properties of nucleic acid aptamers and antibodies. The methods of immobilization of aptamers at the nanoparticles and nano/micromotors are provided. Examples of applications of polymer nanoparticles and nano/micromotors in targeted delivery and in controlled drug release are presented. The future perspectives of biomimetic nanostructures in personalized nanomedicine are also discussed.
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Affiliation(s)
| | | | - Tibor Hianik
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska dolina F1, 842 48 Bratislava, Slovakia; (V.S.); (V.O.)
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21
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Vishwakarma A, Lal R, Ramya M. Aptamer-based approaches for the detection of waterborne pathogens. Int Microbiol 2021; 24:125-140. [PMID: 33404933 DOI: 10.1007/s10123-020-00154-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/13/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Waterborne ailments pose a serious threat to public health and are a huge economic burden. Lack of hygiene in drinking and recreational water is the chief source of microbial pathogens in developing countries. Poor water quality and sanitation account for more than 3.4 million deaths a year worldwide. This has urged authorities and researchers to explore different avenues of pathogen detection. There is a growing demand for rapid and reliable sensor technologies, in particular those that can detect in situ and perform in harsh conditions. Some of the major waterborne pathogens include Vibrio cholerae, Leptospira interrogans, Campylobacter jejuni, Shigella spp., enterotoxigenic Escherichia coli, Clostridium difficile, Cryptosporidium parvum, Entamoeba histolytica, and Hepatitis A virus. While conventional methods of pathogen detection like serodiagnosis and microbiological methods have been superseded by nucleic acid amplification methods, there is still potential for improvement. This review provides an insight into aptamers and their utility in the form of aptasensors. It discusses how aptamer-based approaches have emerged as a novel strategy and its advantages over more resource-intensive and complex biochemical approaches.
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Affiliation(s)
- Archana Vishwakarma
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India
| | - Roshni Lal
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India
| | - Mohandass Ramya
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India.
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22
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High bio-recognizing aptamer designing and optimization against human herpes virus-5. Eur J Pharm Sci 2020; 156:105572. [PMID: 32980430 DOI: 10.1016/j.ejps.2020.105572] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/20/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023]
Abstract
While the world is tackling one of the direst health emergencies, it has come to light that in the fight against viruses, preparedness is everything. A disease with the initial symptoms of the common flu has the capacity to disrupt the life of 7.8 billion people and thus no infection and especially no virus can be ignored. Hence, we have designed the high bio-recognizing DNA aptamer for diagnosis and therapeutics role against glycoprotein-B (gB) of Human Herpes Virus-5 (HHV-5). HHV-5 is linked with epidemiological and asymptomatic diseases leading to high mortality. Herein, we report potent aptamer (5'CTCGCTTACCCCTGGGTGTGCGGG3') which has high specificity to gB with energy score -523.28 kJ/mol, more than reference aptamer L19 (-363.50 kJ/mol). The stable binding of aptamer with gB was confirmed with atomic fluctuations 0.1 to 1.8 Å through anisotropic network analysis. Aptamer formed stem-loop conformation (-1.0 kcal/mol) by stochastic simulation and found stable with physicochemical properties. Importantly, aptamer was found biologically significant with consisting of putative transcription factors in its vicinity (SP1, GATA1, AP2, NF1) and also possesses homology with exonic sequence of SGSH gene which indicated regulatory role in blockade of viruses. Inaddition, we also proposed plausible mechanism of action of aptamer as antiviral therapeutics.
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23
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Lamont RF, Richardson LS, Boniface JJ, Cobo T, Exner MM, Christensen IB, Forslund SK, Gaba A, Helmer H, Jørgensen JS, Khan RN, McElrath TF, Petro K, Rasmussen M, Singh R, Tribe RM, Vink JS, Vinter CA, Zhong N, Menon R. Commentary on a combined approach to the problem of developing biomarkers for the prediction of spontaneous preterm labor that leads to preterm birth. Placenta 2020; 98:13-23. [PMID: 33039027 DOI: 10.1016/j.placenta.2020.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/16/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Globally, preterm birth has replaced congenital malformation as the major cause of perinatal mortality and morbidity. The reduced rate of congenital malformation was not achieved through a single biophysical or biochemical marker at a specific gestational age, but rather through a combination of clinical, biophysical and biochemical markers at different gestational ages. Since the aetiology of spontaneous preterm birth is also multifactorial, it is unlikely that a single biomarker test, at a specific gestational age will emerge as the definitive predictive test. METHODS The Biomarkers Group of PREBIC, comprising clinicians, basic scientists and other experts in the field, with a particular interest in preterm birth have produced this commentary with short, medium and long-term aims: i) to alert clinicians to the advances that are being made in the prediction of spontaneous preterm birth; ii) to encourage clinicians and scientists to continue their efforts in this field, and not to be disheartened or nihilistic because of a perceived lack of progress and iii) to enable development of novel interventions that can reduce the mortality and morbidity associated with preterm birth. RESULTS Using language that we hope is clear to practising clinicians, we have identified 11 Sections in which there exists the potential, feasibility and capability of technologies for candidate biomarkers in the prediction of spontaneous preterm birth and how current limitations to this research might be circumvented. DISCUSSION The combination of biophysical, biochemical, immunological, microbiological, fetal cell, exosomal, or cell free RNA at different gestational ages, integrated as part of a multivariable predictor model may be necessary to advance our attempts to predict sPTL and PTB. This will require systems biological data using "omics" data and artificial intelligence/machine learning to manage the data appropriately. The ultimate goal is to reduce the mortality and morbidity associated with preterm birth.
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Affiliation(s)
- R F Lamont
- Research Unit of Gynaecology and Obstetrics, Department of Gynaecology and Obstetrics, Odense University Hospital, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark; Division of Surgery, Northwick Park Institute for Medical Research Campus, University College London, London, UK.
| | - L S Richardson
- Dept of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Dept. Electrical and Computer Engineering Texas A&M University, College Station, TX, USA
| | - J J Boniface
- Sera Prognostics, Inc., 2749 East Parleys Way, Suite 200, Salt Lake City, UT, 84109, USA
| | - T Cobo
- BCNatal - Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecología, Obstetrícia I Neonatología, Fetal i+D Fetal Medicine Research Center, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona. Barcelona. Spain, Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | - M M Exner
- Hologic, Inc., 10210 Genetic Center Dr, San Diego, CA, 92121, USA
| | | | - S K Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin and the Max-Delbrück Center, Berlin, Germany
| | - A Gaba
- Department of Obstetrics and Maternal-fetal Medicine, Vienna Medical University, Austria
| | - H Helmer
- Department of Obstetrics and Maternal-fetal Medicine, Vienna Medical University, Austria
| | - J S Jørgensen
- Research Unit of Gynaecology and Obstetrics, Department of Gynaecology and Obstetrics, Odense University Hospital, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark; Centre for Innovative Medical Technologies (CIMT), Odense University Hospital, Kløvervænget 8, 5000, Odense C, Denmark; Odense Patient Data Explorative Network (OPEN), Odense University Hospital/University of Southern Denmark, J. B. Winsløws Vej 9 a, 3. Floor, 5000, Odense C, Denmark
| | - R N Khan
- Division of Medical Science and Graduate Entry Medicine, School of Medicine, University of Nottingham, Room 4115, Medical School, Royal Derby Hospital Centre, Derby, DE22 3DT, UK
| | | | - K Petro
- Hologic, Inc., 10210 Genetic Center Dr, San Diego, CA, 92121, USA
| | - M Rasmussen
- MIRVIE Inc., 820 Dubuque Ave., South San Francisco, CA, 94080, USA
| | - R Singh
- ARCEDI Biotech ApS, Aarhus, Denmark
| | - R M Tribe
- Dept. of Women and Children's Health, School of Life Course Sciences, King's College London, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - J S Vink
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA
| | - C A Vinter
- Research Unit of Gynaecology and Obstetrics, Department of Gynaecology and Obstetrics, Odense University Hospital, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - N Zhong
- New York State Institute for Basic Research in Developmental Disabilities, 105 Forest Hill Road, Staten Island, NY, 10314, USA
| | - R Menon
- Dept of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Dept. Electrical and Computer Engineering Texas A&M University, College Station, TX, USA.
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Debiais M, Lelievre A, Smietana M, Müller S. Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors. Nucleic Acids Res 2020; 48:3400-3422. [PMID: 32112111 PMCID: PMC7144939 DOI: 10.1093/nar/gkaa132] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 12/16/2022] Open
Abstract
In analogy to split-protein systems, which rely on the appropriate fragmentation of protein domains, split aptamers made of two or more short nucleic acid strands have emerged as novel tools in biosensor set-ups. The concept relies on dissecting an aptamer into a series of two or more independent fragments, able to assemble in the presence of a specific target. The stability of the assembled structure can further be enhanced by functionalities that upon folding would lead to covalent end-joining of the fragments. To date, only a few aptamers have been split successfully, and application of split aptamers in biosensing approaches remains as promising as it is challenging. Further improving the stability of split aptamer target complexes and with that the sensitivity as well as efficient working modes are important tasks. Here we review functional nucleic acid assemblies that are derived from aptamers and ribozymes/DNAzymes. We focus on the thrombin, the adenosine/ATP and the cocaine split aptamers as the three most studied DNA split systems and on split DNAzyme assemblies. Furthermore, we extend the subject into split light up RNA aptamers used as mimics of the green fluorescent protein (GFP), and split ribozymes.
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Affiliation(s)
- Mégane Debiais
- Institut des Biomolécules Max Mousseron, University of Montpellier, CNRS, ENCSM, Montpellier, France
| | - Amandine Lelievre
- University Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, University of Montpellier, CNRS, ENCSM, Montpellier, France
| | - Sabine Müller
- University Greifswald, Institute for Biochemistry, Greifswald, Germany
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Tsypin M, Asmellash S, Meyer K, Touchet B, Roder H. Extending the information content of the MALDI analysis of biological fluids via multi-million shot analysis. PLoS One 2019; 14:e0226012. [PMID: 31815946 PMCID: PMC6901224 DOI: 10.1371/journal.pone.0226012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 11/18/2019] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Reliable measurements of the protein content of biological fluids like serum or plasma can provide valuable input for the development of personalized medicine tests. Standard MALDI analysis typically only shows high abundance proteins, which limits its utility for test development. It also exhibits reproducibility issues with respect to quantitative measurements. In this paper we show how the sensitivity of MALDI profiling of intact proteins in unfractionated human serum can be substantially increased by exposing a sample to many more laser shots than are commonly used. Analytical reproducibility is also improved. METHODS To assess what is theoretically achievable we utilized spectra from the same samples obtained over many years and combined them to generate MALDI spectral averages of up to 100,000,000 shots for a single sample, and up to 8,000,000 shots for a set of 40 different serum samples. Spectral attributes, such as number of peaks and spectral noise of such averaged spectra were investigated together with analytical reproducibility as a function of the number of shots. We confirmed that results were similar on MALDI instruments from different manufacturers. RESULTS We observed an expected decrease of noise, roughly proportional to the square root of the number of shots, over the whole investigated range of the number of shots (5 orders of magnitude), resulting in an increase in the number of reliably detected peaks. The reproducibility of the amplitude of these peaks, measured by CV and concordance analysis also improves with very similar dependence on shot number, reaching median CVs below 2% for shot numbers > 4 million. Measures of analytical information content and association with biological processes increase with increasing number of shots. CONCLUSIONS We demonstrate that substantially increasing the number of laser shots in a MALDI-TOF analysis leads to more informative and reliable data on the protein content of unfractionated serum. This approach has already been used in the development of clinical tests in oncology.
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Affiliation(s)
- Maxim Tsypin
- Biodesix Inc., Boulder, Colorado, United States of America
| | | | - Krista Meyer
- Biodesix Inc., Boulder, Colorado, United States of America
| | | | - Heinrich Roder
- Biodesix Inc., Boulder, Colorado, United States of America
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26
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Ponce AT, Hong KL. A Mini-Review: Clinical Development and Potential of Aptamers for Thrombotic Events Treatment and Monitoring. Biomedicines 2019; 7:biomedicines7030055. [PMID: 31357413 PMCID: PMC6784064 DOI: 10.3390/biomedicines7030055] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/21/2019] [Accepted: 07/24/2019] [Indexed: 01/01/2023] Open
Abstract
The unique opportunity for aptamer uses in thrombotic events has sparked a considerable amount of research in the area. The short half-lives of unmodified aptamers in vivo remain one of the major challenges in therapeutic aptamers. Much of the incremental successful therapeutic aptamer stories were due to modifications in the aptamer bases. This mini-review briefly summarizes the successes and challenges in the clinical development of aptamers for thrombotic events, and highlights some of the most recent developments in using aptamers for anticoagulation monitoring.
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Affiliation(s)
- Alex T Ponce
- Department of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Wilkes University, 84 W. South Street, Wilkes-Barre, PA 18766, USA
| | - Ka Lok Hong
- Department of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Wilkes University, 84 W. South Street, Wilkes-Barre, PA 18766, USA.
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Ali MH, Elsherbiny ME, Emara M. Updates on Aptamer Research. Int J Mol Sci 2019; 20:E2511. [PMID: 31117311 PMCID: PMC6566374 DOI: 10.3390/ijms20102511] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023] Open
Abstract
For many years, different probing techniques have mainly relied on antibodies for molecular recognition. However, with the discovery of aptamers, this has changed. The science community is currently considering using aptamers in molecular targeting studies because of the many potential advantages they have over traditional antibodies. Some of these possible advantages are their specificity, higher binding affinity, better target discrimination, minimized batch-to-batch variation, and reduced side effects. Overall, these characteristics of aptamers have attracted scholars to use them as molecular probes in place of antibodies, with some aptamer-based targeting products being now available in the market. The present review is aimed at discussing the potential of aptamers as probes in molecular biology and in super-resolution microscopy.
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Affiliation(s)
- Mohamed H Ali
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
- current address: Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
| | - Marwa E Elsherbiny
- Department of Pharmacology and Toxicology, Ahram Canadian University, 6th of October City, Giza 12566, Egypt.
| | - Marwan Emara
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
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28
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Heck C, Michaeli Y, Bald I, Ebenstein Y. Analytical epigenetics: single-molecule optical detection of DNA and histone modifications. Curr Opin Biotechnol 2018; 55:151-158. [PMID: 30326408 DOI: 10.1016/j.copbio.2018.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/12/2018] [Accepted: 09/16/2018] [Indexed: 12/13/2022]
Abstract
The field of epigenetics describes the relationship between genotype and phenotype, by regulating gene expression without changing the canonical base sequence of DNA. It deals with molecular genomic information that is encoded by a rich repertoire of chemical modifications and molecular interactions. This regulation involves DNA, RNA and proteins that are enzymatically tagged with small molecular groups that alter their physical and chemical properties. It is now clear that epigenetic alterations are involved in development and disease, and thus, are the focus of intensive research. The ability to record epigenetic changes and quantify them in rare medical samples is critical for next generation diagnostics. Optical detection offers the ultimate single-molecule sensitivity and the potential for spectral multiplexing. Here we review recent progress in ultrasensitive optical detection of DNA and histone modifications.
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Affiliation(s)
- Christian Heck
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel; Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Yael Michaeli
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ilko Bald
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Str. 11, 12489 Berlin, Germany.
| | - Yuval Ebenstein
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.
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29
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Pereira RL, Nascimento IC, Santos AP, Ogusuku IEY, Lameu C, Mayer G, Ulrich H. Aptamers: novelty tools for cancer biology. Oncotarget 2018; 9:26934-26953. [PMID: 29928493 PMCID: PMC6003562 DOI: 10.18632/oncotarget.25260] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/22/2018] [Indexed: 02/07/2023] Open
Abstract
Although the term ‘cancer’ was still over two thousand years away of being coined, the first known cases of the disease date back to about 3000BC, in ancient Egypt. Five thousand years later, still lacking a cure, it has become one of the leading causes of death, killing over half a dozen million people yearly. So far, monoclonal antibodies are the most successful immune-therapy tools when it comes to fighting cancer. The number of clinical trials that use them has been increasing steadily during the past few years, especially since the Food and Drug Administration greenlit the use of the first immune-checkpoint blockade antibodies. However, albeit successful, this approach does come with the cost of auto-inflammatory toxicity. Taking this into account, the development of new therapeutic reagents with low toxicity becomes evident, particularly ones acting in tandem with the tools currently at our disposal. Ever since its discovery in the early nineties, aptamer technology has been used for a wide range of diagnostic and therapeutic applications. With similar properties to those of monoclonal antibodies, such as high-specificity of recognition and high-affinity binding, and the advantages of being developed using in vitro selection procedures, aptamers quickly became convenient building blocks for the generation of multifunctional constructs. In this review, we discuss the steps involved in the in vitro selection process that leads to functional aptamers - known as Systematic Evolution of Ligands by Exponential Enrichment - as well as the most recent applications of this technology in diagnostic and treatment of oncological illnesses. Moreover, we also suggest ways to improve such use.
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Affiliation(s)
- Ricardo L Pereira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Isis C Nascimento
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Ana P Santos
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Isabella E Y Ogusuku
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Claudiana Lameu
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Günter Mayer
- Chemical Biology and Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53121, Bonn, Germany.,Center of Aptamer Research and Development (CARD), University of Bonn, 53121, Bonn, Germany
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
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30
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McAllister TE, Yeh TL, Abboud MI, Leung IKH, Hookway ES, King ONF, Bhushan B, Williams ST, Hopkinson RJ, Münzel M, Loik ND, Chowdhury R, Oppermann U, Claridge TDW, Goto Y, Suga H, Schofield CJ, Kawamura A. Non-competitive cyclic peptides for targeting enzyme-substrate complexes. Chem Sci 2018; 9:4569-4578. [PMID: 29899950 PMCID: PMC5969509 DOI: 10.1039/c8sc00286j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/23/2018] [Indexed: 01/19/2023] Open
Abstract
Affinity reagents are of central importance for selectively identifying proteins and investigating their interactions. We report on the development and use of cyclic peptides, identified by mRNA display-based RaPID methodology, that are selective for, and tight binders of, the human hypoxia inducible factor prolyl hydroxylases (PHDs) - enzymes crucial in hypoxia sensing. Biophysical analyses reveal the cyclic peptides to bind in a distinct site, away from the enzyme active site pocket, enabling conservation of substrate binding and catalysis. A biotinylated cyclic peptide captures not only the PHDs, but also their primary substrate hypoxia inducible factor HIF1-α. Our work highlights the potential for tight, non-active site binding cyclic peptides to act as promising affinity reagents for studying protein-protein interactions.
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Affiliation(s)
- T E McAllister
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - T-L Yeh
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - M I Abboud
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - I K H Leung
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- School of Chemical Sciences , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand
| | - E S Hookway
- Botnar Research Centre , NIHR Oxford Biomedical Research Unit , University of Oxford , Windmill Road , Oxford , OX3 7LD , UK
| | - O N F King
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - B Bhushan
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- Division of Cardiovascular Medicine , Radcliffe Department of Medicine , University of Oxford , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
| | - S T Williams
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - R J Hopkinson
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - M Münzel
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - N D Loik
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
| | - R Chowdhury
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - U Oppermann
- Botnar Research Centre , NIHR Oxford Biomedical Research Unit , University of Oxford , Windmill Road , Oxford , OX3 7LD , UK
| | - T D W Claridge
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Y Goto
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
| | - H Suga
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
- JST , CREST , The University of Tokyo , Tokyo 113-0033 , Japan
| | - C J Schofield
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - A Kawamura
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- Division of Cardiovascular Medicine , Radcliffe Department of Medicine , University of Oxford , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
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31
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Electrochemical Aptasensors for Food and Environmental Safeguarding: A Review. BIOSENSORS-BASEL 2018; 8:bios8020028. [PMID: 29570679 PMCID: PMC6022872 DOI: 10.3390/bios8020028] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/09/2018] [Accepted: 03/20/2018] [Indexed: 12/21/2022]
Abstract
Food and environmental monitoring is one of the most important aspects of dealing with recent threats to human well-being and ecosystems. In this framework, electrochemical aptamer-based sensors are resilient due to their ability to resolve food and environmental contamination. An aptamer-based sensor is a compact analytical device combining an aptamer as the bio-sensing element integrated on the transducer surface. Aptamers display many advantages as biorecognition elements in sensor development when compared to affinity-based (antibodies) sensors. Aptasensors are small, chemically unchanging, and inexpensive. Moreover, they offer extraordinary elasticity and expediency in the design of their assemblies, which has led to innovative sensors that show tremendous sensitivity and selectivity. This review will emphasize recent food and environmental safeguarding using aptasensors; there are good prospects for their performance as a supplement to classical techniques.
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32
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MacPherson IS, Temme JS, Krauss IJ. DNA display of folded RNA libraries enabling RNA-SELEX without reverse transcription. Chem Commun (Camb) 2018; 53:2878-2881. [PMID: 28220154 DOI: 10.1039/c6cc09991b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A method for the physical attachment of folded RNA libraries to their encoding DNA is presented as a way to circumvent the reverse transcription step during systematic evolution of RNA ligands by exponential enrichment (RNA-SELEX). A DNA library is modified with one isodC base to stall T7 polymerase and a 5' "capture strand" which anneals to the nascent RNA transcript. This method is validated in a selection of RNA aptamers against human α-thrombin with dissociation constants in the low nanomolar range. This method will be useful in the discovery of RNA aptamers and ribozymes containing base modifications that make them resistant to accurate reverse transcription.
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Affiliation(s)
- I S MacPherson
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawai'i at Manoa, 651 Ilalo St., Biosciences Building, Suite 325, Honolulu, Hawaii 96813-5525, USA. and Department of Chemistry, Brandeis University, 415 South St. MS 015, Waltham, MA 02454-9110, USA.
| | - J S Temme
- Department of Chemistry, Brandeis University, 415 South St. MS 015, Waltham, MA 02454-9110, USA.
| | - I J Krauss
- Department of Chemistry, Brandeis University, 415 South St. MS 015, Waltham, MA 02454-9110, USA.
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33
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Abstract
RNA-binding proteins (RBPs) are typically thought of as proteins that bind RNA through one or multiple globular RNA-binding domains (RBDs) and change the fate or function of the bound RNAs. Several hundred such RBPs have been discovered and investigated over the years. Recent proteome-wide studies have more than doubled the number of proteins implicated in RNA binding and uncovered hundreds of additional RBPs lacking conventional RBDs. In this Review, we discuss these new RBPs and the emerging understanding of their unexpected modes of RNA binding, which can be mediated by intrinsically disordered regions, protein-protein interaction interfaces and enzymatic cores, among others. We also discuss the RNA targets and molecular and cellular functions of the new RBPs, as well as the possibility that some RBPs may be regulated by RNA rather than regulate RNA.
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34
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Chiron C, Tompkins TA, Burguière P. Flow cytometry: a versatile technology for specific quantification and viability assessment of micro-organisms in multistrain probiotic products. J Appl Microbiol 2018; 124:572-584. [PMID: 29236340 DOI: 10.1111/jam.13666] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/29/2017] [Accepted: 10/18/2017] [Indexed: 01/21/2023]
Abstract
AIMS Classical microbiology techniques are the gold standard for probiotic enumeration. However, these techniques are limited by parameters of time, specificity and incapacity to detect viable but nonculturable (VBNC) micro-organisms and nonviable cells. The aim of the study was to evaluate flow cytometry as a novel method for the specific quantification of viable and nonviable probiotics in multistrain products. METHODS AND RESULTS Custom polyclonal antibodies were produced against five probiotic strains from different species (Bifidobacterium bifidum R0071, Bifidobacterium longum ssp. infantis R0033, Bifidobacterium longum ssp. longum R0175, Lactobacillus helveticus R0052 and Lactobacillus rhamnosus R0011). Evaluation of specificity confirmed that all antibodies were specific at least at the subspecies level. A flow cytometry method combining specific antibodies and viability assessment with SYTO® 24 and propidium iodide was applied to quantify these strains in three commercial products. Analyses were conducted on two flow cytometry instruments by two operators and compared with classical microbiology using selective media. Results indicated that flow cytometry provides higher cell counts than classical microbiology (P < 0·05) in 73% of cases highlighting the possible presence of VBNC. Equivalent performances (repeatability and reproducibility) were obtained for both methods. CONCLUSIONS This study showed that flow cytometry methods can be applied to probiotic enumeration and viability assessment. Combination with polyclonal antibodies can achieve sufficient specificity to differentiate closely related strains. SIGNIFICANCE AND IMPACT OF THE STUDY Flow cytometry provides absolute and specific quantification of viable and nonviable probiotic strains in a very short time (<2 h) compared with classical techniques (>48 h), bringing efficient tools for research and development and quality control.
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Affiliation(s)
- C Chiron
- Lallemand Health Solutions Inc., Montreal, QC, Canada
| | - T A Tompkins
- Lallemand Health Solutions Inc., Montreal, QC, Canada
| | - P Burguière
- Lallemand Health Solutions Inc., Montreal, QC, Canada
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35
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Krusemark CJ, Tilmans NP, Brown PO, Harbury PB. Directed Chemical Evolution with an Outsized Genetic Code. PLoS One 2016; 11:e0154765. [PMID: 27508294 PMCID: PMC4980042 DOI: 10.1371/journal.pone.0154765] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/15/2016] [Indexed: 12/02/2022] Open
Abstract
The first demonstration that macromolecules could be evolved in a test tube was reported twenty-five years ago. That breakthrough meant that billions of years of chance discovery and refinement could be compressed into a few weeks, and provided a powerful tool that now dominates all aspects of protein engineering. A challenge has been to extend this scientific advance into synthetic chemical space: to enable the directed evolution of abiotic molecules. The problem has been tackled in many ways. These include expanding the natural genetic code to include unnatural amino acids, engineering polyketide and polypeptide synthases to produce novel products, and tagging combinatorial chemistry libraries with DNA. Importantly, there is still no small-molecule analog of directed protein evolution, i.e. a substantiated approach for optimizing complex (≥ 10^9 diversity) populations of synthetic small molecules over successive generations. We present a key advance towards this goal: a tool for genetically-programmed synthesis of small-molecule libraries from large chemical alphabets. The approach accommodates alphabets that are one to two orders of magnitude larger than any in Nature, and facilitates evolution within the chemical spaces they create. This is critical for small molecules, which are built up from numerous and highly varied chemical fragments. We report a proof-of-concept chemical evolution experiment utilizing an outsized genetic code, and demonstrate that fitness traits can be passed from an initial small-molecule population through to the great-grandchildren of that population. The results establish the practical feasibility of engineering synthetic small molecules through accelerated evolution.
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Affiliation(s)
- Casey J. Krusemark
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America
| | - Nicolas P. Tilmans
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Patrick O. Brown
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Pehr B. Harbury
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
- * E-mail:
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36
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The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions. Pflugers Arch 2016; 468:1029-40. [PMID: 27165283 PMCID: PMC4893068 DOI: 10.1007/s00424-016-1819-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/29/2016] [Accepted: 04/01/2016] [Indexed: 02/06/2023]
Abstract
Post-transcriptional regulation of gene expression plays a critical role in almost all cellular processes. Regulation occurs mostly by RNA-binding proteins (RBPs) that recognise RNA elements and form ribonucleoproteins (RNPs) to control RNA metabolism from synthesis to decay. Recently, the repertoire of RBPs was significantly expanded owing to methodological advances such as RNA interactome capture. The newly identified RNA binders are involved in diverse biological processes and belong to a broad spectrum of protein families, many of them exhibiting enzymatic activities. This suggests the existence of an extensive crosstalk between RNA biology and other, in principle unrelated, cell functions such as intermediary metabolism. Unexpectedly, hundreds of new RBPs do not contain identifiable RNA-binding domains (RBDs), raising the question of how they interact with RNA. Despite the many functions that have been attributed to RNA, our understanding of RNPs is still mostly governed by a rather protein-centric view, leading to the idea that proteins have evolved to bind to and regulate RNA and not vice versa. However, RNPs formed by an RNA-driven interaction mechanism (RNA-determined RNPs) are abundant and offer an alternative explanation for the surprising lack of classical RBDs in many RNA-interacting proteins. Moreover, RNAs can act as scaffolds to orchestrate and organise protein networks and directly control their activity, suggesting that nucleic acids might play an important regulatory role in many cellular processes, including metabolism.
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37
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Abstract
Hundreds of distinct chemical modifications to DNA and histone amino acids have been described. Regulation exerted by these so-called epigenetic marks is vital to normal development, stability of cell identity through mitosis, and nongenetic transmission of traits between generations through meiosis. Loss of this regulation contributes to many diseases. Evidence indicates epigenetic marks function in combinations, whereby a given modification has distinct effects on local genome control, depending on which additional modifications are locally present. This review summarizes emerging methods for assessing combinatorial epigenomic states, as well as challenges and opportunities for their refinement.
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Affiliation(s)
- Paul D. Soloway
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, United States
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38
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Mozioglu E, Gokmen O, Tamerler C, Kocagoz ZT, Akgoz M. Selection of Nucleic Acid Aptamers Specific for Mycobacterium tuberculosis. Appl Biochem Biotechnol 2015; 178:849-64. [PMID: 26541162 DOI: 10.1007/s12010-015-1913-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/26/2015] [Indexed: 12/14/2022]
Abstract
Tuberculosis (TB) remains to be a major global health problem, with about 9 million new cases and 1.4 million deaths in 2011. For the control of tuberculosis as well as other infectious diseases, WHO recommended "ASSURED" (Affordable, Sensitive, Specific, User-friendly, Rapid and robust, Equipment-free, and Deliverable to the end user) diagnostic tools that can easily be maintained and used in developing countries. Aptamers are promising tools for developing point-of-care diagnostic assays for TB. In this study, ssDNA aptamers that recognize Mycobacterium tuberculosis H37Ra were selected by systematic evolution of ligands by exponential enrichment (SELEX). For this purpose, two different selection protocols, ultrafiltration and centrifugation, were applied. A total of 21 TB specific aptamers were selected. These aptamers exhibited "G-rich" regions on the 3' terminus of the aptamers, including a motif of "TGGGG," "GTGG," or "CTGG." Binding capability of selected aptamers were investigated by quantitative PCR and Mtb36 DNA aptamer was found the most specific aptamer to M. tuberculosis H37Ra. The dissociation constant (K d) of Mtb36 aptamer was calculated as 5.09 ± 1.43 nM in 95% confidence interval. Relative binding ratio of Mtb36 aptamer to M. tuberculosis H37Ra over Mycobacterium bovis and Escherichia coli was also determined about 4 times and 70 times more, respectively. Mtb36 aptamer is highly selective for M. tuberculosis, and it can be used in an aptamer-based biosensor for the detection of M. tuberculosis.
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Affiliation(s)
- Erkan Mozioglu
- Molecular Biology-Biotechnology & Genetics Research Center, Istanbul Technical University, Istanbul, Turkey. .,Bioanalysis Laboratory, TÜBİTAK UME (National Metrology Institute), Kocaeli, Turkey.
| | - Ozgur Gokmen
- Chemistry Department, Gebze Institute of Technology, Kocaeli, Turkey.
| | - Candan Tamerler
- Molecular Biology-Biotechnology & Genetics Research Center, Istanbul Technical University, Istanbul, Turkey. .,Mechanical Engineering and Bioengineering Research Center, University of Kansas, Lawrence, KS, USA.
| | - Zuhtu Tanil Kocagoz
- Department of Microbiology and Clinical Microbiology, Acıbadem University, Istanbul, Turkey. .,Trends in Innovative Biotechnology Organization, Istanbul, Turkey.
| | - Muslum Akgoz
- Bioanalysis Laboratory, TÜBİTAK UME (National Metrology Institute), Kocaeli, Turkey.
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39
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McKeague M, McConnell EM, Cruz-Toledo J, Bernard ED, Pach A, Mastronardi E, Zhang X, Beking M, Francis T, Giamberardino A, Cabecinha A, Ruscito A, Aranda-Rodriguez R, Dumontier M, DeRosa MC. Analysis of In Vitro Aptamer Selection Parameters. J Mol Evol 2015; 81:150-61. [PMID: 26530075 DOI: 10.1007/s00239-015-9708-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
Nucleic acid aptamers are novel molecular recognition tools that offer many advantages compared to their antibody and peptide-based counterparts. However, challenges associated with in vitro selection, characterization, and validation have limited their wide-spread use in the fields of diagnostics and therapeutics. Here, we extracted detailed information about aptamer selection experiments housed in the Aptamer Base, spanning over two decades, to perform the first parameter analysis of conditions used to identify and isolate aptamers de novo. We used information from 492 published SELEX experiments and studied the relationships between the nucleic acid library, target choice, selection methods, experimental conditions, and the affinity of the resulting aptamer candidates. Our findings highlight that the choice of target and selection template made the largest and most significant impact on the success of a de novo aptamer selection. Our results further emphasize the need for improved documentation and more thorough experimentation of SELEX criteria to determine their correlation with SELEX success.
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Affiliation(s)
- Maureen McKeague
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Erin M McConnell
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Jose Cruz-Toledo
- Biology Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Elyse D Bernard
- Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture, Ottawa, ON, K1A 0K9, Canada
| | - Amanda Pach
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Emily Mastronardi
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Xueru Zhang
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Michael Beking
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Tariq Francis
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Amanda Giamberardino
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Ashley Cabecinha
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Annamaria Ruscito
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Rocio Aranda-Rodriguez
- Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture, Ottawa, ON, K1A 0K9, Canada
| | - Michel Dumontier
- Biology Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada. .,Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
| | - Maria C DeRosa
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
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40
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Gilboa-Geffen A, Hamar P, Le MTN, Wheeler LA, Trifonova R, Petrocca F, Wittrup A, Lieberman J. Gene Knockdown by EpCAM Aptamer-siRNA Chimeras Suppresses Epithelial Breast Cancers and Their Tumor-Initiating Cells. Mol Cancer Ther 2015; 14:2279-91. [PMID: 26264278 DOI: 10.1158/1535-7163.mct-15-0201-t] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 08/03/2015] [Indexed: 11/16/2022]
Abstract
Effective therapeutic strategies for in vivo siRNA delivery to knockdown genes in cells outside the liver are needed to harness RNA interference for treating cancer. EpCAM is a tumor-associated antigen highly expressed on common epithelial cancers and their tumor-initiating cells (TIC, also known as cancer stem cells). Here, we show that aptamer-siRNA chimeras (AsiC, an EpCAM aptamer linked to an siRNA sense strand and annealed to the siRNA antisense strand) are selectively taken up and knock down gene expression in EpCAM(+) cancer cells in vitro and in human cancer biopsy tissues. PLK1 EpCAM-AsiCs inhibit colony and mammosphere formation (in vitro TIC assays) and tumor initiation by EpCAM(+) luminal and basal-A triple-negative breast cancer (TNBC) cell lines, but not EpCAM(-) mesenchymal basal-B TNBCs, in nude mice. Subcutaneously administered EpCAM-AsiCs concentrate in EpCAM(+) Her2(+) and TNBC tumors and suppress their growth. Thus, EpCAM-AsiCs provide an attractive approach for treating epithelial cancer.
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MESH Headings
- Animals
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/metabolism
- Aptamers, Nucleotide/administration & dosage
- Aptamers, Nucleotide/genetics
- Aptamers, Nucleotide/metabolism
- Base Sequence
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carcinogenesis/metabolism
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Epithelial Cell Adhesion Molecule
- Female
- Gene Expression
- Gene Knockdown Techniques
- Humans
- Mice, Nude
- Neoplasm Transplantation
- Neoplasms, Glandular and Epithelial/metabolism
- Neoplasms, Glandular and Epithelial/pathology
- Neoplastic Stem Cells/physiology
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA Interference
- RNA, Small Interfering/administration & dosage
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Tumor Burden
- Polo-Like Kinase 1
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Affiliation(s)
- Adi Gilboa-Geffen
- Cellular and Molecular Medicine Program, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Peter Hamar
- Cellular and Molecular Medicine Program, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts. Institute of Pathophysiology, Semmelweis University, Budapest, Hungary
| | - Minh T N Le
- Cellular and Molecular Medicine Program, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Lee Adam Wheeler
- Cellular and Molecular Medicine Program, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Radiana Trifonova
- Cellular and Molecular Medicine Program, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Fabio Petrocca
- Cellular and Molecular Medicine Program, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Anders Wittrup
- Cellular and Molecular Medicine Program, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Judy Lieberman
- Cellular and Molecular Medicine Program, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts.
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Isolation of Foreign Material-Free Endothelial Progenitor Cells Using CD31 Aptamer and Therapeutic Application for Ischemic Injury. PLoS One 2015; 10:e0131785. [PMID: 26148001 PMCID: PMC4493074 DOI: 10.1371/journal.pone.0131785] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/05/2015] [Indexed: 01/09/2023] Open
Abstract
Endothelial progenitor cells (EPCs) can be isolated from human bone marrow or peripheral blood and reportedly contribute to neovascularization. Aptamers are 40-120-mer nucleotides that bind to a specific target molecule, as antibodies do. To utilize apatmers for isolation of EPCs, in the present study, we successfully generated aptamers that recognize human CD31, an endothelial cell marker. CD31 aptamers bound to human umbilical cord blood-derived EPCs and showed specific interaction with human CD31, but not with mouse CD31. However, CD31 aptamers showed non-specific interaction with CD31-negative 293FT cells and addition of polyanionic competitor dextran sulfate eliminated non-specific interaction without affecting cell viability. From the mixture of EPCs and 293FT cells, CD31 aptamers successfully isolated EPCs with 97.6% purity and 94.2% yield, comparable to those from antibody isolation. In addition, isolated EPCs were decoupled from CD31 aptamers with a brief treatment of high concentration dextran sulfate. EPCs isolated with CD31 aptamers and subsequently decoupled from CD31 aptamers were functional and enhanced the restoration of blood flow when transplanted into a murine hindlimb ischemia model. In this study, we demonstrated isolation of foreign material-free EPCs, which can be utilized as a universal protocol in preparation of cells for therapeutic transplantation.
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42
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Ming X, Laing B. Bioconjugates for targeted delivery of therapeutic oligonucleotides. Adv Drug Deliv Rev 2015; 87:81-9. [PMID: 25689735 DOI: 10.1016/j.addr.2015.02.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/04/2015] [Accepted: 02/06/2015] [Indexed: 01/05/2023]
Abstract
Bioconjugates have been used to deliver therapeutic oligonucleotides to their pharmacological targets in diseased cells. Molecular-scale conjugates can be prepared by directly linking targeting ligands with oligonucleotides and the resultant conjugates can selectively bind to cell surface receptors in target cells in diseased tissues. Besides targeted delivery, additional functionality can be incorporated in the conjugates by utilization of carrier molecules, and these larger conjugates are called carrier-associated conjugates. Both molecular and carrier-associated conjugates have achieved initial successes in clinical trials for treating liver diseases; therefore, currently the greater challenge is to deliver oligonucleotides to extrahepatic tissues such as tumors. This review will provide an update on the application of oligonucleotide conjugates for targeted delivery during the last decade. By identifying key elements for successful delivery, it is suggested that oligonucleotide conjugates with intermediate size, cell targeting ability, and endosomal release functionality are superior systems to advance oligonucleotides to achieve their full therapeutic potentials.
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Affiliation(s)
- Xin Ming
- Division of Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Brian Laing
- Division of Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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43
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Evaluating the dual target binding capabilities of immobilized aptamers using flow cytometry. Biointerphases 2015; 10:019015. [PMID: 25787142 DOI: 10.1116/1.4915107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In the current study, the authors quantify the binding activity of particle-immobilized DNA aptamers to their nucleotide and non-nucleotide targets. For the purposes of this work, DNA and vascular endothelial growth factor (VEGF) binding analysis was carried out for VEGF-binding aptamers and compared to that of an ampicillin-binding aptamer as well as a non-aptamer DNA probe. Binding analysis followed incubation of one target type, coincubation of both DNA and VEGF targets, and serial incubations of each target type. Moreover, recovery of aptamer binding activity following displacement of the DNA target from aptamer:DNA duplexes was also explored. Flow cytometry served as the quantitative tool to directly monitor binding events of both the DNA target and protein target to the various aptamer and non-aptamer functionalized particles. The current work demonstrates how processing steps such as annealing and binding history of particle-immobilized aptamers can affect subsequent binding activity. To this end, the authors demonstrate the ability to fully recover DNA target binding activity capabilities and to partially recover protein target binding activity.
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44
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Bradbury A, Plückthun A. Reproducibility: Standardize antibodies used in research. Nature 2015; 518:27-9. [PMID: 25652980 DOI: 10.1038/518027a] [Citation(s) in RCA: 461] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Andrew Bradbury
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
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45
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46
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Citartan M, Gopinath SC, Chen Y, Lakshmipriya T, Tang TH. Monitoring recombinant human erythropoietin abuse among athletes. Biosens Bioelectron 2015; 63:86-98. [DOI: 10.1016/j.bios.2014.06.068] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 06/02/2014] [Accepted: 06/27/2014] [Indexed: 11/16/2022]
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47
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Emahi I, Mulvihill IM, Baum DA. Pyrroloquinoline quinone maintains redox activity when bound to a DNA aptamer. RSC Adv 2015. [DOI: 10.1039/c4ra11052h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Newly identified DNA aptamers for PQQ provide an environment in which PQQ is still accessible for redox chemistry.
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Affiliation(s)
- Ismaila Emahi
- Saint Louis University
- Department of Chemistry
- St. Louis
- USA 63103
| | | | - Dana A. Baum
- Saint Louis University
- Department of Chemistry
- St. Louis
- USA 63103
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48
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Hartley D, Blumenthal T, Carrillo M, DiPaolo G, Esralew L, Gardiner K, Granholm AC, Iqbal K, Krams M, Lemere C, Lott I, Mobley W, Ness S, Nixon R, Potter H, Reeves R, Sabbagh M, Silverman W, Tycko B, Whitten M, Wisniewski T. Down syndrome and Alzheimer's disease: Common pathways, common goals. Alzheimers Dement 2014; 11:700-9. [PMID: 25510383 DOI: 10.1016/j.jalz.2014.10.007] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 08/26/2014] [Accepted: 10/02/2014] [Indexed: 12/17/2022]
Abstract
In the United States, estimates indicate there are between 250,000 and 400,000 individuals with Down syndrome (DS), and nearly all will develop Alzheimer's disease (AD) pathology starting in their 30s. With the current lifespan being 55 to 60 years, approximately 70% will develop dementia, and if their life expectancy continues to increase, the number of individuals developing AD will concomitantly increase. Pathogenic and mechanistic links between DS and Alzheimer's prompted the Alzheimer's Association to partner with the Linda Crnic Institute for Down Syndrome and the Global Down Syndrome Foundation at a workshop of AD and DS experts to discuss similarities and differences, challenges, and future directions for this field. The workshop articulated a set of research priorities: (1) target identification and drug development, (2) clinical and pathological staging, (3) cognitive assessment and clinical trials, and (4) partnerships and collaborations with the ultimate goal to deliver effective disease-modifying treatments.
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Affiliation(s)
- Dean Hartley
- Medical and Scientific Relations, Alzheimer's Association, Chicago, IL, USA.
| | - Thomas Blumenthal
- Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, CO, USA; Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Maria Carrillo
- Medical and Scientific Relations, Alzheimer's Association, Chicago, IL, USA
| | - Gilbert DiPaolo
- Department of Pathology and Cell Biology, Columbia University Medical Center and The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, New York, NY, USA
| | - Lucille Esralew
- Department of Behavioral Health, Trinitas Regional Medical Center, Elizabeth, NJ, USA
| | - Katheleen Gardiner
- Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, CO, USA; Department of Pediatrics, University of Colorado, Denver, CO, USA
| | - Ann-Charlotte Granholm
- Department of Neuroscience and the Center on Aging, Medical University of South Carolina, Columbia, SC, USA
| | - Khalid Iqbal
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, New York, NY, USA
| | | | - Cynthia Lemere
- Department of Neurology and the Anne Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ira Lott
- Department of Pediatrics, University of California, Irvine, CA, USA
| | - William Mobley
- Department of Neurosciences, University of California, San Diego, CA, USA
| | - Seth Ness
- Janssen Research & Development, Raritan, NJ, USA
| | - Ralph Nixon
- Department of Psychiatry and Cell Biology, New York University, Langone Medical Center, New York, NY, USA
| | - Huntington Potter
- Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, CO, USA; Department of Neurology, University of Colorado, Denver, CO, USA
| | - Roger Reeves
- Department of Physiology, McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marwan Sabbagh
- Banner Sun Health Research Institute, Banner Health, Sun City, AZ, USA
| | - Wayne Silverman
- Department of Behavioral Psychology, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Benjamin Tycko
- Department of Pathology and Cell Biology, Columbia University Medical Center and The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, New York, NY, USA
| | | | - Thomas Wisniewski
- Department of Neurology, Pathology, and Psychiatry, New York University, Langone Medical Center, New York, NY, USA
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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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50
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Brosius J. The persistent contributions of RNA to eukaryotic gen(om)e architecture and cellular function. Cold Spring Harb Perspect Biol 2014; 6:a016089. [PMID: 25081515 DOI: 10.1101/cshperspect.a016089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Currently, the best scenario for earliest forms of life is based on RNA molecules as they have the proven ability to catalyze enzymatic reactions and harbor genetic information. Evolutionary principles valid today become apparent in such models already. Furthermore, many features of eukaryotic genome architecture might have their origins in an RNA or RNA/protein (RNP) world, including the onset of a further transition, when DNA replaced RNA as the genetic bookkeeper of the cell. Chromosome maintenance, splicing, and regulatory function via RNA may be deeply rooted in the RNA/RNP worlds. Mostly in eukaryotes, conversion from RNA to DNA is still ongoing, which greatly impacts the plasticity of extant genomes. Raw material for novel genes encoding protein or RNA, or parts of genes including regulatory elements that selection can act on, continues to enter the evolutionary lottery.
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Affiliation(s)
- Jürgen Brosius
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
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