Aptamers Overview: Selection, Features and Applications

Hernandez, Luiza I.; Machado, Isabel Cristina Kasper; Schäfer, Thomas; Hernandez, Frank J.

doi:10.2174/1568026615666150413153717

Cited by 33 publications

(22 citation statements)

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“…This process involves binding of random sequences to the target of interest, then separation of the bound sequences and amplification of the recovered aptamers by the polymerase chain reaction (PCR) [ 15 , 20 ]. Aptamers have been studied as bio- probes in diverse diagnostic and therapeutic applications as well as in the production of new drugs and improving drug delivery systems [ 21 ]. Additionally, several attempts have been carried out to isolate aptamers against targets involved in various diseases, such as cancer and viral infections [ 13 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Selection and targeting of EpCAM protein by ssDNA aptamer

et al. 2017

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Aptamers are molecules that reveal highly complex and refined molecular recognition properties. These molecules are capable of binding with high affinity and selectivity to targets, ranging from small molecules to whole living cells. Several aptamers have been selected for targeting cellular proteins and they have also used in developing therapeutics and diagnostic strategies. Epithelial cell adhesion molecule (EpCAM) is considered as a cancer stem cell (CSC) biomarker and one of the most promising targets for aptamer selection against CSCs. In this study, we have developed a ssDNA aptamer with high affinity and selectivity of targeting the EpCAM protein extracellular domain. The SELEX technique was applied and the resulted sequences were tested on EpCAM-positive human gastric cancer cell line, KATO III, and the EpCAM-negative mouse embryonic fibroblast, NIH/3T3 cells. Ep1 aptamer was successfully isolated and showed selective binding on EpCAM-positive KATO III cells when compared to EpCAM-negative NIH/3T3 cells, as observed by the flow cytometry and the confocal imaging results. Additionally, the binding of Ep1 to EpCAM protein was assessed using mobility shifting assay and aptamers-protein docking. Furthermore, the binding affinity of Ep1 was measured against EpCAM protein using EpCAM-immobilized on magnetic beads and showed apparent affinity of 118 nM. The results of this study could suggest that Ep1 aptamer can bind specifically to the cellular EpCAM protein, making it an attractive ligand for targeted drug delivery and as an imaging agent for the identification of cancer cells.

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Section: Introductionmentioning

confidence: 99%

Selection and targeting of EpCAM protein by ssDNA aptamer

et al. 2017

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“…Nucleic acid aptamers are single-stranded DNA or RNA molecules, generally 25 to 60 bases in length, identified from pools of random-sequence oligonucleotides (ONs) by an in vitro selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment) [1], introduced in the early 90s independently by the research groups of Gold and Szostak [2][3][4]. Thanks to their unique three-dimensional folding, aptamers can recognize a wide range of molecular targets including proteins, small molecules, ions, whole cells and even entire organisms, such as viruses or bacteria, with affinities, expressed in terms of dissociation constants (K d ), ranging from picomolar (pM) to micromolar (μM) [5][6][7]. Each ON aptamer can adopt a unique subset of 3D structures defined by the combination of base-pairing, π-π stacking, sugar puckering, as well as electrostatic, hydrogen bonding and noncanonical intra-molecular interactions.…”

Section: Description and Selection Of Nucleic Acid Aptamersmentioning

confidence: 99%

G-quadruplex-based aptamers against protein targets in therapy and diagnostics

Platella

Riccardi

Montesarchio

et al. 2017

Biochimica et Biophysica Acta (BBA) - General Subjects

135

116

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Nucleic acid aptamers are single-stranded DNA or RNA molecules identified to recognize with high affinity specific targets including proteins, small molecules, ions, whole cells and even entire organisms, such as viruses or bacteria. They can be identified from combinatorial libraries of DNA or RNA oligonucleotides by SELEX technology, an in vitro iterative selection procedure consisting of binding (capture), partitioning and amplification steps. Remarkably, many of the aptamers selected against biologically relevant protein targets are G-rich sequences that can fold into stable G-quadruplex (G4) structures. Aiming at disseminating novel inspiring ideas within the scientific community in the field of G4-structures, the emphasis of this review is placed on: 1) recent advancements in SELEX technology for the efficient and rapid identification of new candidate aptamers (introduction of microfluidic systems and next generation sequencing); 2) recurrence of G4 structures in aptamers selected by SELEX against biologically relevant protein targets; 3) discovery of several G4-forming motifs in important regulatory regions of the human or viral genome bound by endogenous proteins, which per se can result into potential aptamers; 4) an updated overview of G4-based aptamers with therapeutic potential and 5) a discussion on the most attractive G4-based aptamers for diagnostic applications. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.

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“…Despite the highly efficient signal amplification ability, most of the CRISPR-based sensors reported to date are employed in nucleic acid detection 38 - 43 . Nucleic acid aptamers obtained by in vitro selection methods 44 - 47 generalize CRISPR-based sensor application to a wide range of non-nucleic acid targets such as ions and small molecules; however, access to protein detection remains limited 48 - 50 .…”

Section: Introductionmentioning

confidence: 99%

An ultrasensitive hybridization chain reaction-amplified CRISPR-Cas12a aptasensor for extracellular vesicle surface protein quantification

Xing¹,

Lù²,

Huang³

et al. 2020

Theranostics

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Tumor-derived extracellular vesicle (TEV) protein biomarkers facilitate cancer diagnosis and prognostic evaluations. However, the lack of reliable and convenient quantitative methods for evaluating TEV proteins prevents their clinical application. Methods: Here, based on dual amplification of hybridization chain reaction (HCR) and CRISPR-Cas12a, we developed the apta-HCR-CRISPR assay for direct high-sensitivity detection of TEV proteins. The TEV protein-targeted aptamer was amplified by HCR to produce a long-repeated sequence comprising multiple CRISPR RNA (crRNA) targetable barcodes, and the signals were further amplified by CRISPR-Cas12a collateral cleavage activities, resulting in a fluorescence signal. Results: The established strategy was verified by detecting the TEV protein markers nucleolin and programmed death ligand 1 (PD-L1). Both achieved limit of detection (LOD) values as low as 10 2 particles/µL, which is at least 10 4 -fold more sensitive than aptamer-ELISA and 10 2 -fold more sensitive than apta-HCR-ELISA. We directly applied our assay to a clinical analysis of circulating TEVs from 50 µL of serum, revealing potential applications of nucleolin + TEVs for nasopharyngeal carcinoma cancer (NPC) diagnosis and PD-L1 + TEVs for therapeutic monitoring. Conclusion: The platform was simple and easy to operate, and this approach should be useful for the highly sensitive and versatile quantification of TEV proteins in clinical samples.

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Aptamers Overview: Selection, Features and Applications

Cited by 33 publications

References 0 publications

Selection and targeting of EpCAM protein by ssDNA aptamer

Selection and targeting of EpCAM protein by ssDNA aptamer

G-quadruplex-based aptamers against protein targets in therapy and diagnostics

An ultrasensitive hybridization chain reaction-amplified CRISPR-Cas12a aptasensor for extracellular vesicle surface protein quantification

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