1
|
Mollasalehi N, Francois-Moutal L, Porciani D, Burke DH, Khanna M. Aptamers Targeting Hallmark Proteins of Neurodegeneration. Nucleic Acid Ther 2022; 32:235-250. [PMID: 35452303 DOI: 10.1089/nat.2021.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Neurodegeneration is a progressive deterioration of neural structures leading to cognitive or motor impairment of the affected patient. There is still no effective therapy for any of the most common neurodegenerative diseases (NDs) such as Alzheimer's or Parkinson's disease. Although NDs exhibit distinct clinical characteristics, many are characterized by the accumulation of misfolded proteins or peptide fragments in the brain and/or spinal cord. The presence of similar inclusion bodies in patients with diverse NDs provides a rationale for developing therapies directed at overlapping disease mechanisms. A novel targeting strategy involves the use of aptamers for therapeutic development. Aptamers are short nucleic acid ligands able to recognize molecular targets with high specificity and high affinity. Despite the fact that several academic groups have shown that aptamers have the potential to be used in therapeutic and diagnostic applications, their clinical translation is still limited. In this study, we describe aptamers that have been developed against proteins relevant to NDs, including prion protein and amyloid beta (Aβ), cell surface receptors and other cytoplasmic proteins. This review also describes advances in the application of these aptamers in imaging, protein detection, and protein quantification, and it provides insights about their accelerated clinical use for disease diagnosis and therapy.
Collapse
Affiliation(s)
- Niloufar Mollasalehi
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA.,Center for Innovation in Brain Science, Tucson, Arizona, USA
| | - Liberty Francois-Moutal
- Center for Innovation in Brain Science, Tucson, Arizona, USA.,Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona, USA
| | - David Porciani
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri-Columbia, Columbia, Missouri, USA.,MU Bond Life Sciences Center, University of Missouri-Columbia, Columbia, Missouri, USA
| | - Donald H Burke
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri-Columbia, Columbia, Missouri, USA.,MU Bond Life Sciences Center, University of Missouri-Columbia, Columbia, Missouri, USA
| | - May Khanna
- Center for Innovation in Brain Science, Tucson, Arizona, USA.,Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona, USA
| |
Collapse
|
2
|
do Amaral MJ, Freire MHO, Almeida MS, Pinheiro AS, Cordeiro Y. Phase separation of the mammalian prion protein: physiological and pathological perspectives. J Neurochem 2022. [PMID: 35149997 DOI: 10.1111/jnc.15586] [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: 10/08/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/27/2022]
Abstract
Abnormal phase transitions have been implicated in the occurrence of proteinopathies. Disordered proteins with nucleic acid binding ability drive the formation of reversible micron-sized condensates capable of controlling nucleic acid processing/transport. This mechanism, achieved via liquid-liquid phase separation (LLPS), underlies the formation of long-studied membraneless organelles (e.g., nucleolus) and various transient condensates formed by driver proteins. The prion protein (PrP) is not a classical nucleic acid-binding protein. However, it binds nucleic acids with high affinity, undergoes nucleocytoplasmic shuttling, contains a long intrinsically disordered region rich in glycines and evenly spaced aromatic residues, among other biochemical/biophysical properties of bona fide drivers of phase transitions. Because of this, our group and others have characterized LLPS of recombinant PrP. In vitro phase separation of PrP is modulated by nucleic acid aptamers, and, depending on the aptamer conformation, the liquid droplets evolve to solid-like species. Herein we discuss recent studies and previous evidence supporting PrP phase transitions. We focus on the central role of LLPS related to PrP physiology and pathology, with a special emphasis on the interaction of PrP with different ligands, such as proteins and nucleic acids, which can play a role in prion disease pathogenesis. Finally, we comment on therapeutic strategies directed at the nonfunctional phase separation that could potentially tackle prion diseases or other protein misfolding disorders.
Collapse
Affiliation(s)
- Mariana J do Amaral
- Faculty of Pharmacy, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | | | - Anderson S Pinheiro
- Department of Biochemistry, Institute of Chemistry, Rio de Janeiro, RJ, Brazil
| | - Yraima Cordeiro
- Faculty of Pharmacy, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| |
Collapse
|
3
|
Murakami K, Izuo N, Bitan G. Aptamers targeting amyloidogenic proteins and their emerging role in neurodegenerative diseases. J Biol Chem 2022; 298:101478. [PMID: 34896392 PMCID: PMC8728582 DOI: 10.1016/j.jbc.2021.101478] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 01/08/2023] Open
Abstract
Aptamers are oligonucleotides selected from large pools of random sequences based on their affinity for bioactive molecules and are used in similar ways to antibodies. Aptamers provide several advantages over antibodies, including their small size, facile, large-scale chemical synthesis, high stability, and low immunogenicity. Amyloidogenic proteins, whose aggregation is relevant to neurodegenerative diseases, such as Alzheimer's, Parkinson's, and prion diseases, are among the most challenging targets for aptamer development due to their conformational instability and heterogeneity, the same characteristics that make drug development against amyloidogenic proteins difficult. Recently, chemical tethering of aptagens (equivalent to antigens) and advances in high-throughput sequencing-based analysis have been used to overcome some of these challenges. In addition, internalization technologies using fusion to cellular receptors and extracellular vesicles have facilitated central nervous system (CNS) aptamer delivery. In view of the development of these techniques and resources, here we review antiamyloid aptamers, highlighting preclinical application to CNS therapy.
Collapse
Affiliation(s)
- Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
| | - Naotaka Izuo
- Laboratory of Pharmaceutical Therapy and Neuropharmacology, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA.
| |
Collapse
|
4
|
Intrinsic disorder and phase transitions: Pieces in the puzzling role of the prion protein in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:1-43. [PMID: 34656326 DOI: 10.1016/bs.pmbts.2021.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
After four decades of prion protein research, the pressing questions in the literature remain similar to the common existential dilemmas. Who am I? Some structural characteristics of the cellular prion protein (PrPC) and scrapie PrP (PrPSc) remain unknown: there are no high-resolution atomic structures for either full-length endogenous human PrPC or isolated infectious PrPSc particles. Why am I here? It is not known why PrPC and PrPSc are found in specific cellular compartments such as the nucleus; while the physiological functions of PrPC are still being uncovered, the misfolding site remains obscure. Where am I going? The subcellular distribution of PrPC and PrPSc is wide (reported in 10 different locations in the cell). This complexity is further exacerbated by the eight different PrP fragments yielded from conserved proteolytic cleavages and by reversible post-translational modifications, such as glycosylation, phosphorylation, and ubiquitination. Moreover, about 55 pathological mutations and 16 polymorphisms on the PrP gene (PRNP) have been described. Prion diseases also share unique, challenging features: strain phenomenon (associated with the heterogeneity of PrPSc conformations) and the possible transmissibility between species, factors which contribute to PrP undruggability. However, two recent concepts in biochemistry-intrinsically disordered proteins and phase transitions-may shed light on the molecular basis of PrP's role in physiology and disease.
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Bouvier-Müller A, Ducongé F. Nucleic acid aptamers for neurodegenerative diseases. Biochimie 2017; 145:73-83. [PMID: 29104136 DOI: 10.1016/j.biochi.2017.10.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/31/2017] [Indexed: 02/07/2023]
Abstract
The increased incidence of neurodegenerative diseases represents a huge challenge for societies. These diseases are characterized by neuronal death and include several different pathologies, such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, Huntington's disease and transmissible spongiform encephalopathies. Most of these pathologies are often associated with the aggregation of misfolded proteins, such as amyloid-ß, tau, α-synuclein, huntingtin and prion proteins. However, the precise mechanisms that lead to neuronal dysfunction and death in these diseases remain poorly understood. Nucleic acid aptamers represent a new class of ligands that could be useful to better understand these diseases and develop better diagnosis and therapy. In this review, several of these aptamers are presented as well as their applications for neurodegenerative diseases.
Collapse
Affiliation(s)
- Alix Bouvier-Müller
- CEA, Fundamental Research Division (DRF), Institute of Biology François Jacob (Jacob), Molecular Imaging Research Center, 18 Route du Panorama, 92265 Fontenay-aux-Roses, France; Neurodegenerative Diseases Laboratory, CNRS CEA UMR 9199, Fontenay-aux-Roses, France; Paris-Saclay University, Paris-Sud University, Fontenay-aux-Roses, France
| | - Frédéric Ducongé
- CEA, Fundamental Research Division (DRF), Institute of Biology François Jacob (Jacob), Molecular Imaging Research Center, 18 Route du Panorama, 92265 Fontenay-aux-Roses, France; Neurodegenerative Diseases Laboratory, CNRS CEA UMR 9199, Fontenay-aux-Roses, France; Paris-Saclay University, Paris-Sud University, Fontenay-aux-Roses, France.
| |
Collapse
|
7
|
Unraveling Prion Protein Interactions with Aptamers and Other PrP-Binding Nucleic Acids. Int J Mol Sci 2017; 18:ijms18051023. [PMID: 28513534 PMCID: PMC5454936 DOI: 10.3390/ijms18051023] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/23/2017] [Accepted: 05/04/2017] [Indexed: 12/13/2022] Open
Abstract
Transmissible spongiform encephalopathies (TSEs) are a group of neurodegenerative disorders that affect humans and other mammals. The etiologic agents common to these diseases are misfolded conformations of the prion protein (PrP). The molecular mechanisms that trigger the structural conversion of the normal cellular PrP (PrPC) into the pathogenic conformer (PrPSc) are still poorly understood. It is proposed that a molecular cofactor would act as a catalyst, lowering the activation energy of the conversion process, therefore favoring the transition of PrPC to PrPSc. Several in vitro studies have described physical interactions between PrP and different classes of molecules, which might play a role in either PrP physiology or pathology. Among these molecules, nucleic acids (NAs) are highlighted as potential PrP molecular partners. In this context, the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) methodology has proven extremely valuable to investigate PrP–NA interactions, due to its ability to select small nucleic acids, also termed aptamers, that bind PrP with high affinity and specificity. Aptamers are single-stranded DNA or RNA oligonucleotides that can be folded into a wide range of structures (from harpins to G-quadruplexes). They are selected from a nucleic acid pool containing a large number (1014–1016) of random sequences of the same size (~20–100 bases). Aptamers stand out because of their potential ability to bind with different affinities to distinct conformations of the same protein target. Therefore, the identification of high-affinity and selective PrP ligands may aid the development of new therapies and diagnostic tools for TSEs. This review will focus on the selection of aptamers targeted against either full-length or truncated forms of PrP, discussing the implications that result from interactions of PrP with NAs, and their potential advances in the studies of prions. We will also provide a critical evaluation, assuming the advantages and drawbacks of the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) technique in the general field of amyloidogenic proteins.
Collapse
|
8
|
Qu J, Yu S, Zheng Y, Zheng Y, Yang H, Zhang J. Aptamer and its applications in neurodegenerative diseases. Cell Mol Life Sci 2017; 74:683-695. [PMID: 27563707 PMCID: PMC11107737 DOI: 10.1007/s00018-016-2345-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 01/17/2023]
Abstract
Aptamers are small single-stranded DNA or RNA oligonucleotide fragments or small peptides, which can bind to targets by high affinity and specificity. Because aptamers are specific, non-immunogenic and non-toxic, they are ideal materials for clinical applications. Neurodegenerative disorders are ravaging the lives of patients. Even though the mechanism of these diseases is still elusive, they are mainly characterized by the accumulation of misfolded proteins in the central nervous system. So it is essential to develop potential measures to slow down or prevent the onset of these diseases. With the advancements of the technologies, aptamers have opened up new areas in this research field. Aptamers could bind with these related target proteins to interrupt their accumulation, subsequently blocking or preventing the process of neurodegenerative diseases. This review presents recent advances in the aptamer generation and its merits and limitations, with emphasis on its applications in neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, transmissible spongiform encephalopathy, Huntington's disease and multiple sclerosis.
Collapse
Affiliation(s)
- Jing Qu
- Department of Neurobiology, Beijing Institute of Brain Disorders, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Beijing Center of Neural Regeneration and Repair, Beijing Key Laboratory of Brain Major Disorders-State Key Lab Incubation Base, Beijing Neuroscience Disciplines, Capital Medical University, Beijing, 100069, China
| | - Shuqing Yu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China National Clinical Research Center for Neurological Diseases, State Key Disciplinary of Neurosurgery Department, Capital Medical University, Beijing, 100050, China
| | - Yuan Zheng
- Department of Neurobiology, Beijing Institute of Brain Disorders, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Beijing Center of Neural Regeneration and Repair, Beijing Key Laboratory of Brain Major Disorders-State Key Lab Incubation Base, Beijing Neuroscience Disciplines, Capital Medical University, Beijing, 100069, China
| | - Yan Zheng
- Department of Neurobiology, Beijing Institute of Brain Disorders, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Beijing Center of Neural Regeneration and Repair, Beijing Key Laboratory of Brain Major Disorders-State Key Lab Incubation Base, Beijing Neuroscience Disciplines, Capital Medical University, Beijing, 100069, China
| | - Hui Yang
- Department of Neurobiology, Beijing Institute of Brain Disorders, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Beijing Center of Neural Regeneration and Repair, Beijing Key Laboratory of Brain Major Disorders-State Key Lab Incubation Base, Beijing Neuroscience Disciplines, Capital Medical University, Beijing, 100069, China
| | - Jianliang Zhang
- Department of Neurobiology, Beijing Institute of Brain Disorders, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Beijing Center of Neural Regeneration and Repair, Beijing Key Laboratory of Brain Major Disorders-State Key Lab Incubation Base, Beijing Neuroscience Disciplines, Capital Medical University, Beijing, 100069, China.
| |
Collapse
|
9
|
Boese AS, Majer A, Saba R, Booth SA. Small RNA drugs for prion disease: a new frontier. Expert Opin Drug Discov 2013; 8:1265-84. [DOI: 10.1517/17460441.2013.818976] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
10
|
Cirillo D, Agostini F, Klus P, Marchese D, Rodriguez S, Bolognesi B, Tartaglia GG. Neurodegenerative diseases: quantitative predictions of protein-RNA interactions. RNA (NEW YORK, N.Y.) 2013; 19:129-140. [PMID: 23264567 PMCID: PMC3543085 DOI: 10.1261/rna.034777.112] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 11/16/2012] [Indexed: 06/01/2023]
Abstract
Increasing evidence indicates that RNA plays an active role in a number of neurodegenerative diseases. We recently introduced a theoretical framework, catRAPID, to predict the binding ability of protein and RNA molecules. Here, we use catRAPID to investigate ribonucleoprotein interactions linked to inherited intellectual disability, amyotrophic lateral sclerosis, Creutzfeuld-Jakob, Alzheimer's, and Parkinson's diseases. We specifically focus on (1) RNA interactions with fragile X mental retardation protein FMRP; (2) protein sequestration caused by CGG repeats; (3) noncoding transcripts regulated by TAR DNA-binding protein 43 TDP-43; (4) autogenous regulation of TDP-43 and FMRP; (5) iron-mediated expression of amyloid precursor protein APP and α-synuclein; (6) interactions between prions and RNA aptamers. Our results are in striking agreement with experimental evidence and provide new insights in processes associated with neuronal function and misfunction.
Collapse
Affiliation(s)
- Davide Cirillo
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Federico Agostini
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Petr Klus
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Domenica Marchese
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Silvia Rodriguez
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Benedetta Bolognesi
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| |
Collapse
|
11
|
Cavaliere P, Pagano B, Granata V, Prigent S, Rezaei H, Giancola C, Zagari A. Cross-talk between prion protein and quadruplex-forming nucleic acids: a dynamic complex formation. Nucleic Acids Res 2012; 41:327-39. [PMID: 23104426 PMCID: PMC3592392 DOI: 10.1093/nar/gks970] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Prion protein (PrP) is involved in lethal neurodegenerative diseases, and many issues remain unclear about its physio-pathological role. Quadruplex-forming nucleic acids (NAs) have been found to specifically bind to both PrP cellular and pathological isoforms. To clarify the relevance of these interactions, thermodynamic, kinetic and structural studies have been performed, using isothermal titration calorimetry, surface plasmon resonance and circular dichroism methodologies. Three quadruplex-forming sequences, d(TGGGGT), r(GGAGGAGGAGGA), d(GGAGGAGGAGGA), and various forms of PrP were selected for this study. Our results showed that these quadruplexes exhibit a high affinity and specificity toward PrP, with KD values within the range 62÷630 nM, and a weaker affinity toward a PrP-β oligomer, which mimics the pathological isoform. We demonstrated that the NA quadruplex architecture is the structural determinant for the recognition by both PrP isoforms. Furthermore, we spotted both PrP N-terminal and C-terminal domains as the binding regions involved in the interaction with DNA/RNAs, using several PrP truncated forms. Interestingly, a reciprocally induced structure loss was observed upon PrP–NA interaction. Our results allowed to surmise a quadruplex unwinding-activity of PrP, that may have a feedback in vivo.
Collapse
Affiliation(s)
- Paola Cavaliere
- Dipartimento delle Scienze Biologiche, Università degli Studi di Napoli Federico II, Naples 80134, Italy
| | | | | | | | | | | | | |
Collapse
|
12
|
Marc D, Barbachou S, Soubieux D. The RNA-binding domain of influenzavirus non-structural protein-1 cooperatively binds to virus-specific RNA sequences in a structure-dependent manner. Nucleic Acids Res 2012; 41:434-49. [PMID: 23093596 PMCID: PMC3592425 DOI: 10.1093/nar/gks979] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Influenzavirus non-structural protein NS1 is involved in several steps of the virus replication cycle. It counteracts the interferon response, and also exhibits other activities towards viral and cellular RNAs. NS1 is known to bind non-specifically to double-stranded RNA (dsRNA) as well as to viral and cellular RNAs. We set out to search whether NS1 could preferentially bind sequence-specific RNA patterns, and performed an in vitro selection (SELEX) to isolate NS1-specific aptamers from a pool of 80-nucleotide(nt)-long RNAs. Among the 63 aptamers characterized, two families were found to harbour a sequence that is strictly conserved at the 5' terminus of all positive-strand RNAs of influenzaviruses A. We found a second virus-specific motif, a 9 nucleotide sequence located 15 nucleotides downstream from NS1's stop codon. In addition, a majority of aptamers had one or two symmetrically positioned copies of the 5'-GUAAC / 3'-CUUAG double-stranded motif, which closely resembles the canonical 5'-splice site. Through an in-depth analysis of the interaction combining fluorimetry and gel-shift assays, we showed that NS1's RNA-binding domain (RBD) specifically recognizes sequence patterns in a structure-dependent manner, resulting in an intimate interaction with high affinity (low nanomolar to subnanomolar K(D) values) that leads to oligomerization of the RBD on its RNA ligands.
Collapse
Affiliation(s)
- Daniel Marc
- Equipe BioVA, UMR1282 Infectiologie et Santé Publique, Institut National de la Recherche Agronomique, Nouzilly F-37380, France.
| | | | | |
Collapse
|
13
|
Mitkevich OV, Kochneva-Pervukhova NV, Surina ER, Benevolensky SV, Kushnirov VV, Ter-Avanesyan MD. DNA aptamers detecting generic amyloid epitopes. Prion 2012; 6:400-6. [PMID: 22874671 DOI: 10.4161/pri.20678] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Amyloids are fibrillar protein aggregates resulting from non-covalent autocatalytic polymerization of various structurally and functionally unrelated proteins. Previously we have selected DNA aptamers, which bind specifically to the in vitro assembled amyloid fibrils of the yeast prionogenic protein Sup35. Here we show that such DNA aptamers can be used to detect SDS-insoluble amyloid aggregates of the Sup35 protein, and of some other amyloidogenic proteins, including mouse PrP, formed in yeast cells. The obtained data suggest that these aggregates and the Sup35 amyloid fibrils assembled in vitro possess common conformational epitopes recognizable by aptamers. The described DNA aptamers may be used for detection of various amyloid aggregates in yeast and, presumably, other organisms.
Collapse
Affiliation(s)
- Olga V Mitkevich
- A.N. Bach Institute of Biochemistry, The Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | | |
Collapse
|
14
|
Zhang H, Han Y, Guo Y, Dong C. Porphyrin functionalized graphene nanosheets-based electrochemical aptasensor for label-free ATP detection. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm35379b] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
15
|
Pu Y, Zhu Z, Han D, Liu H, Liu J, Liao J, Zhang K, Tan W. Insulin-binding aptamer-conjugated graphene oxide for insulin detection. Analyst 2011; 136:4138-40. [PMID: 21874167 DOI: 10.1039/c1an15407a] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This paper describes a simple and sensitive aptamer/graphene oxide (GO) based assay for insulin detection. GO can protect DNA from nuclease cleavage, but aptamers can be detached from the GO surface by specific target binding. This exposes the aptamers to enzymatic cleavage and releases the target for a new cycle. Cycling of targets leads to significant signal amplification and low LOD.
Collapse
Affiliation(s)
- Ying Pu
- Xiangya Hospital, Central South University, P.O. Box 190. Changsha, Hunan 410008, China
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Wang P, Hatcher KL, Bartz JC, Chen SG, Skinner P, Richt J, Liu H, Sreevatsan S. Selection and characterization of DNA aptamers against PrP(Sc). Exp Biol Med (Maywood) 2011; 236:466-76. [PMID: 21444369 DOI: 10.1258/ebm.2011.010323] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transmissible spongiform encephalopathies (TSEs) are a group of zoonotic and fatal neurodegenerative disorders that affect humans and animals. The pathogenesis of TSEs involves a conformational conversion of the cellular prion protein (PrP) into abnormal isoforms. Currently, cellular and pathological forms of PrP are differentiated using specific antibody-based analyses that are resource intensive and not applicable to all species and strains. Thus, there is an urgent need for sensitive and efficient assays that can detect pathological forms of PrP. Using systematic evolution of ligands by exponential enrichment, we developed DNA aptamers that can differentiate normal and abnormal PrP isoforms. These aptamers represent the first reagents that can identify pathological isoforms of PrP across multiple host species. Second, they are able to distinguish different strains of prions. Third, they can be used to detect prions in peripheral blood cells, which are otherwise undetectable using conventional antibody-based detection methods. Thus, DNA aptamers offer promise for the development of presymptomatic screens of tissue, blood and other body fluids for prion contamination.
Collapse
Affiliation(s)
- Ping Wang
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Abstract
Aptamers are nucleic acid sequences synthesized through in vitro selection and amplification technique, possessing a broader range of applications in therapeutics, biosensing, diagnostics, and research. Aptamers offer a number of advantages over their antibodies counterpart, one of them is their ability to undergo chemical derivatization to increase their life in the body fluids and bioavailability in animals. Although aptamers were discovered in 1990s, they have become one of the most widely investigated molecules, with a huge number of publications in the last decade. This article presents an overview of the advancements that have been made in aptamers. We mainly focused on articles published since 2005.
Collapse
Affiliation(s)
- Muhammad Ali Syed
- Department of Biosciences, Comsats Institute of Information Technology, Islamabad, Pakistan.
| | | |
Collapse
|
18
|
Mashima T, Matsugami A, Nishikawa F, Nishikawa S, Katahira M. Unique quadruplex structure and interaction of an RNA aptamer against bovine prion protein. Nucleic Acids Res 2009; 37:6249-58. [PMID: 19666719 PMCID: PMC2764455 DOI: 10.1093/nar/gkp647] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
RNA aptamers against bovine prion protein (bPrP) were obtained, most of the obtained aptamers being found to contain the r(GGAGGAGGAGGA) (R12) sequence. Then, it was revealed that R12 binds to both bPrP and its β-isoform with high affinity. Here, we present the structure of R12. This is the first report on the structure of an RNA aptamer against prion protein. R12 forms an intramolecular parallel quadruplex. The quadruplex contains G:G:G:G tetrad and G(:A):G:G(:A):G hexad planes. Two quadruplexes form a dimer through intermolecular hexad–hexad stacking. Two lysine clusters of bPrP have been identified as binding sites for R12. The electrostatic interaction between the uniquely arranged phosphate groups of R12 and the lysine clusters is suggested to be responsible for the affinity of R12 to bPrP. The stacking interaction between the G:G:G:G tetrad planes and tryptophan residues may also contribute to the affinity. One R12 dimer molecule is supposed to simultaneously bind the two lysine clusters of one bPrP molecule, resulting in even higher affinity. The atomic coordinates of R12 would be useful for the development of R12 as a therapeutic agent against prion diseases and Alzheimer's disease.
Collapse
Affiliation(s)
- Tsukasa Mashima
- Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | | | | | | | | |
Collapse
|
19
|
Gilch S, Schätzl HM. Aptamers against prion proteins and prions. Cell Mol Life Sci 2009; 66:2445-55. [PMID: 19396399 PMCID: PMC11115877 DOI: 10.1007/s00018-009-0031-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 04/01/2009] [Accepted: 04/03/2009] [Indexed: 12/19/2022]
Abstract
Prion diseases are fatal neurodegenerative and infectious disorders of humans and animals, characterized by structural transition of the host-encoded cellular prion protein (PrP(c)) into the aberrantly folded pathologic isoform PrP(Sc). RNA, DNA or peptide aptamers are classes of molecules which can be selected from complex combinatorial libraries for high affinity and specific binding to prion proteins and which might therefore be useful in diagnosis and therapy of prion diseases. Nucleic acid aptamers, which can be chemically synthesized, stabilized and immobilized, appear more suitable for diagnostic purposes, allowing use of PrP(Sc) as selection target. Peptide aptamers facilitate appropriate intracellular expression, targeting and re-routing without losing their binding properties to PrP, a requirement for potential therapeutic gene transfer experiments in vivo. Elucidation of structural properties of peptide aptamers might be used as basis for rational drug design, providing another attractive application of peptide aptamers in the search for effective anti-prion strategies.
Collapse
Affiliation(s)
- Sabine Gilch
- Institute of Virology, Technische Universität München, Trogerstr. 30, 81675 Munich, Germany
| | - Hermann M. Schätzl
- Institute of Virology, Technische Universität München, Trogerstr. 30, 81675 Munich, Germany
| |
Collapse
|
20
|
Bibby DF, Gill AC, Kirby L, Farquhar CF, Bruce ME, Garson JA. Application of a novel in vitro selection technique to isolate and characterise high affinity DNA aptamers binding mammalian prion proteins. J Virol Methods 2008; 151:107-15. [PMID: 18433888 DOI: 10.1016/j.jviromet.2008.03.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 03/10/2008] [Indexed: 11/18/2022]
Abstract
Clinical diagnosis and research into transmissible spongiform encephalopathies are hampered by the lack of sufficiently sensitive and specific reagents able to adequately detect the normal cellular form of the prion protein, PrP(C), and the pathological isoform, PrP(Sc). In order to provide such reagents, we applied Systematic Evolution of Ligands by EXponential enrichment (SELEX) against a recombinant murine prion protein, to select single-stranded DNA ligands (aptamers) of high affinity. The SELEX protocol and subsequent aptamer characterisation employed protein immobilisation/partitioning using nickel-complexed magnetic particles and a novel SYBR Green-mediated quantitative real-time PCR technique. Following eight rounds of selection, the enriched aptamer pool was cloned and 24 clones sequenced. Seven of these were 'orphan' clones and the remainder were grouped into three separate T-rich families. All but four of the aptamer clones exhibited specific binding to the murine prion protein and the majority also bound to human and ovine prion proteins. Dissociation constants (K(d)) ranged from 18 to 79 nM. Flow cytometry with fluorescein-labelled aptamers confirmed that binding to cells was dependent on the expression of PrP(C). Preliminary studies also indicate that a trivalent aptamer pool is capable of binding the pathological isoform PrP(Sc) following guanidinium denaturation.
Collapse
Affiliation(s)
- David F Bibby
- Centre for Virology, Department of Infection, Windeyer Institute, University College London, London W1T 4JF, UK
| | | | | | | | | | | |
Collapse
|
21
|
Murakami K, Nishikawa F, Noda K, Yokoyama T, Nishikawa S. Anti-bovine prion protein RNA aptamer containing tandem GGA repeat interacts both with recombinant bovine prion protein and its beta isoform with high affinity. Prion 2008; 2:73-80. [PMID: 19098441 DOI: 10.4161/pri.2.2.7024] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In order to obtain RNA aptamers against bovine prion protein (bPrP), we carried out in vitro selection from RNA pools containing a 55-nucleotide randomized region to target recombinant bPrP. Most of obtained aptamers contained conserved GGA tandem repeats (GGA)(4) and aptamer #1 (apt #1) showed a high affinity for both bPrP and its beta isoform (bPrP-beta). The sequence of apt #1 suggested that it would have a G-quadruplex structure, which was confirmed using CD spectra in titration with KCl. A mutagenic study of this conserved region, and competitive assays, showed that the conserved (GGA)(4) sequence is important for specific binding to bPrP and bPrP-beta. Following 5'-biotinylation, aptamer #1 specifically detected PrP(c) in bovine brain homogenate in a Northwestern blotting assay. Protein deletion mutant analysis showed that the bPrP aptamer binds within 25-131 of the bPrP sequence. Interestingly, the minimized aptamer #1 (17 nt) showed greater binding to bPrP and bPrP-beta as compared to apt #1. This minimized form of aptamer #1 may therefore be useful in the detection of bPrP, diagnosis of prion disease, enrichment of bPr and ultimately in gaining a better understanding of prion diseases.
Collapse
Affiliation(s)
- Kazuyoshi Murakami
- Graduate School of Life and Environmental Science, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
| | | | | | | | | |
Collapse
|
22
|
Intriguing nucleic-acid-binding features of mammalian prion protein. Trends Biochem Sci 2008; 33:132-40. [DOI: 10.1016/j.tibs.2007.11.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Revised: 11/14/2007] [Accepted: 11/26/2007] [Indexed: 11/19/2022]
|
23
|
Ogasawara D, Hasegawa H, Kaneko K, Sode K, Ikebukuro K. Screening of DNA aptamer against mouse prion protein by competitive selection. Prion 2007; 1:248-54. [PMID: 19164908 DOI: 10.4161/pri.1.4.5803] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Prion disease is a neurodegenerative disorder, in which the normal prion protein (PrP) changes structurally into an abnormal form and accumulates in the brain. There is a great demand for the development of a viable approach to diagnosis and therapy. Not only has the ligand against PrP been used for diagnosis, but it has also become a promising tool for therapy, as an antibody. Aptamers are a novel type of ligand composed of nucleic acids. DNA aptamers in particular have many advantages over antibodies. Therefore, we tried to isolate the DNA aptamer for mouse PrP. We developed a competitive selection method and tried to screen the DNA aptamer with it. In the fourth round of selection, several clones of the aptamer with an affinity to PrP were enriched, and clone 4-9 showed the highest affinity of all. The investigation by aptamer blotting and Western blotting showed that clone 4-9 was specifically able to recognize both alpha-PrP and beta-PrP. Moreover, it was indicated that clone 4-9 could recognize the flexible region of the N-terminal domain of PrP. These characteristics suggest that clone 4-9 might be a useful tool in prion-disease diagnosis and research.
Collapse
Affiliation(s)
- Daisuke Ogasawara
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | | | | | | | | |
Collapse
|
24
|
Yang Y, Yang D, Schluesener HJ, Zhang Z. Advances in SELEX and application of aptamers in the central nervous system. ACTA ACUST UNITED AC 2007; 24:583-92. [PMID: 17681489 DOI: 10.1016/j.bioeng.2007.06.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Revised: 06/12/2007] [Accepted: 06/13/2007] [Indexed: 11/22/2022]
Abstract
SELEX (Systematic Evolution of Ligands by Exponential Enrichment) is a screening technique that involves the progressive selection of highly specific ligands by repeated rounds of partition and amplification from a large combinatorial nucleic acid library. The products of the selection are called aptamers, which are short single stranded DNA or RNA molecules, binding with high affinity, attributed to their specific three-dimensional shapes, to a large variety of targets, ranging from small molecules to complex mixtures. Various improvement of the original SELEX method described in 1990 have been obtained recently, such as capillary electrophoresis SELEX, Toggle-SELEX, Tailored-SELEX, Photo-SELEX, and others. These new variants greatly shorten time of selection and improve aptamer affinity and specificity. Such aptamers have great potential as detecting and/or diagnostic reagents. Furthermore, some aptamers specifically inhibit biological functions of targeted proteins, and are considered as potent therapeutic lead structures evaluated in preclinical disease models. Recently, one aptamer has been approved by Food and Drug Administration of US for treating age-related macular degeneration. This review presents recent advances in the field of SELEX with special emphasis on applications of aptamers as analytical, diagnostic and therapeutic tools in the central nervous system.
Collapse
Affiliation(s)
- Yan Yang
- Experimental Medical Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | | | | | | |
Collapse
|
25
|
King DJ, Safar JG, Legname G, Prusiner SB. Thioaptamer interactions with prion proteins: sequence-specific and non-specific binding sites. J Mol Biol 2007; 369:1001-14. [PMID: 17481659 DOI: 10.1016/j.jmb.2007.02.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Revised: 02/01/2007] [Accepted: 02/02/2007] [Indexed: 11/19/2022]
Abstract
Binding of nucleic acids to the prion protein (PrP) created a conundrum that required distinguishing between non-specific interactions and biologically important polynucleotides. In the process of developing selective ligands for PrP, we found using a single-stranded DNA thioaptamer library that the binding of thioaptamers to PrP occurs on at least two different sites on the protein. Selection against recombinant (rec) PrP of Syrian hamster (SHa) sequence 90-231 folded into an alpha-helical-rich conformation identified a 12-base consensus sequence within a series of 20 thioaptamers, all of which consist of 40 bases. Each thioaptamer was comprised of both normal and thio-dA modified bases. One thioaptamer designated 97 bound to recSHaPrP with affinity of 0.58(+/-0.1) nM; lower affinities for bovine (Bo), and human (Hu) were found, establishing that binding is dependent on the primary structure of PrP. High affinity binding of thioaptamer 97 to PrP was found to be mediated through the dodecyl sequence GACACAAGCCGA within the consensus region with five critical backbone modifications 5' to each dA residue. A control oligonucleotide with an equivalent number of phosphorothioates to thioaptamer 97 and a scrambled consensus sequence could not distinguish among the three PrP sequences. Control oligonucleotides bearing non-selected sequences bound to PrP at a sequence-independent DNA-binding site. In contrast, the high-affinity binding of thioaptamer 97 to PrP depends on (1) backbone modifications, (2) oligonucleotide sequence, and (3) PrP sequence.
Collapse
Affiliation(s)
- David J King
- Institute for Neurodegenerative Diseases, University of California San Francisco, CA 94143-0518, USA
| | | | | | | |
Collapse
|
26
|
Rich RL, Myszka DG. Survey of the year 2006 commercial optical biosensor literature. J Mol Recognit 2007; 20:300-66. [DOI: 10.1002/jmr.862] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|