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Open AccessArticle

Assessment of Aptamer as a Potential Drug Targeted Delivery for Retinal Angiogenesis Inhibition

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David Moreira

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Jéssica Lopes-Nunes

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Fátima Milhano Santos

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Maria Paula Cabral Campello

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Maria Cristina Oliveira

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António Paulo

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Cândida Tomaz

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Carla Cruz

Pharmaceuticals 2023, 16(5), 751; https://doi.org/10.3390/ph16050751 - 16 May 2023

Viewed by 442

Abstract

AT11-L0 is an aptamer derivative of AS1411 composed of G-rich sequences that can adopt a G-quadruplex (G4) structure and target nucleolin (NCL), a protein that acts as a co-receptor for several growth factors. Hence, this study aimed to characterize the AT11-L0 G4 structure [...] Read more.

AT11-L0 is an aptamer derivative of AS1411 composed of G-rich sequences that can adopt a G-quadruplex (G4) structure and target nucleolin (NCL), a protein that acts as a co-receptor for several growth factors. Hence, this study aimed to characterize the AT11-L0 G4 structure and its interaction with several ligands for NCL targeting and to evaluate their capacity to inhibit angiogenesis using an in vitro model. The AT11-L0 aptamer was then used to functionalize drug-associated liposomes to increase the bioavailability of the aptamer-based drug in the formulation. Biophysical studies, such as nuclear magnetic resonance, circular dichroism, and fluorescence titrations, were performed to characterize the liposomes functionalized with the AT11-L0 aptamer. Finally, these liposome formulations with the encapsulated drugs were tested on the human umbilical vein endothelial cell (HUVEC) model to assess their antiangiogenic capacity. The results showed that the AT11-L0 aptamer–ligand complexes are highly stable, presenting melting temperatures from 45 °C to 60 °C, allowing for efficient targeting of NCL with a K_D in the order of nM. The aptamer-functionalized liposomes loaded with ligands C₈ and dexamethasone did not show cytotoxic effects in HUVEC cells compared with the free ligands and AT11-L0, as assessed by cell viability assays. AT11-L0 aptamer-functionalized liposomes encapsulating C₈ and dexamethasone did not present a significant reduction in the angiogenic process when compared with the free ligands. In addition, AT11-L0 did not show anti-angiogenic effects at the concentrations tested. However, C₈ shows potential as an angiogenesis inhibitor, which should be further developed and optimized in future experiments. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Open AccessArticle

Dose-Dependent Von Willebrand Factor Inhibition by Aptamer BB-031 Correlates with Thrombolysis in a Microfluidic Model of Arterial Occlusion

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Pharmaceuticals 2022, 15(12), 1450; https://doi.org/10.3390/ph15121450 - 22 Nov 2022

Viewed by 930

Abstract

Von Willebrand Factor (VWF) plays a critical role in thrombus formation, stabilization, and propagation. Previous studies have demonstrated that targeted inhibition of VWF induces thrombolysis when administered in vivo in animal models of ischemic stroke. The study objective was to quantify dose-dependent inhibition [...] Read more.

Von Willebrand Factor (VWF) plays a critical role in thrombus formation, stabilization, and propagation. Previous studies have demonstrated that targeted inhibition of VWF induces thrombolysis when administered in vivo in animal models of ischemic stroke. The study objective was to quantify dose-dependent inhibition of VWF-platelet function and its relationship with thrombolysis using BB-031, an aptamer that binds VWF and inhibits its function. VWF:Ac, VWF:RCo, T-TAS, and ristocetin-induced impedance aggregometry were used to assess BB-031-mediated inhibition of VWF. Reductions in original thrombus surface area and new deposition during administration of treatment were measured in a microfluidic model of arterial thrombolysis. Rotational thromboelastometry was used to assess changes in hemostasis. BB-031 induced maximal inhibition at the highest dose (3384 nM) in VWF:Ac, and demonstrated dose-dependent responses in all other assays. BB-031, but not vehicle, induced recanalization in the microfluidic model. Maximal lytic efficacy in the microfluidic model was seen at 1692 nM and not 3384 nM BB-031 when assessed by surface area. Minor changes in ROTEM parameters were seen at 3384 nM BB-031. Targeted VWF inhibition by BB-031 results in clinically measurable impairment of VWF function, and specifically VWF-GPIb function as measured by VWF:Ac. BB-031 also induced thrombolysis as measured in a microfluidic model of occlusion and reperfusion. Moderate correlation between inhibition and lysis was observed. Additional studies are required to further examine off-target effects of BB-031 at high doses, however, these are expected to be above the range of clinical targeted dosing. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Open AccessArticle

Imaging of Clear Cell Renal Carcinoma with Immune Checkpoint Targeting Aptamer-Based Probe

Pharmaceuticals 2022, 15(6), 697; https://doi.org/10.3390/ph15060697 - 01 Jun 2022

Cited by 4 | Viewed by 1585

Abstract

Immune checkpoint targeting immunotherapy has revolutionized the treatment of certain cancers in the recent years. Determination of the status of immune checkpoint expression in particular cancers may assist decision making. Here, we describe the development of a single-stranded aptamer-based molecular probe specifically recognizing [...] Read more.

Immune checkpoint targeting immunotherapy has revolutionized the treatment of certain cancers in the recent years. Determination of the status of immune checkpoint expression in particular cancers may assist decision making. Here, we describe the development of a single-stranded aptamer-based molecular probe specifically recognizing human PD-L1. Target engaging aptamers are selected by iterative enrichment from a random ssDNA pool and the binding is characterized biochemically. Specificity and dose dependence is demonstrated in vitro in the cell culture using human kidney tumor cells (786-0), human melanoma cells (WM115 and WM266.4) and human glioblastoma LN18 cancer cells. The utility of the probe in vivo is demonstrated using two mouse tumor models, where we show that the probe exhibits excellent potential in imaging. We postulate that further development of the probe may allow universal imaging of different types of tumors depending on their PD-L1 status, which may find utility in cancer diagnosis. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Open AccessArticle

Aptamer–Gemcitabine Conjugates with Enzymatically Cleavable Linker for Targeted Delivery and Intracellular Drug Release in Cancer Cells

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Pharmaceuticals 2022, 15(5), 558; https://doi.org/10.3390/ph15050558 - 30 Apr 2022

Cited by 3 | Viewed by 1896

Abstract

Gemcitabine is a chemotherapeutic used clinically to treat a variety of cancers. However, because it lacks tumor cell specificity, gemcitabine may cause off-target cytotoxicity and adversely impact patients. To impart cancer cell specificity to gemcitabine and improve its therapeutic efficacy, we synthesized a [...] Read more.

Gemcitabine is a chemotherapeutic used clinically to treat a variety of cancers. However, because it lacks tumor cell specificity, gemcitabine may cause off-target cytotoxicity and adversely impact patients. To impart cancer cell specificity to gemcitabine and improve its therapeutic efficacy, we synthesized a unique aptamer–drug conjugate that carries a high gemcitabine payload (three molecules) via a dendrimer structure and enzymatically cleavable linkers for controlled intracellular drug release. First, linker–gemcitabinedendrimer–linker–gemcitabine products were produced, which had significantly lower cytotoxicity than an equimolar amount of free drug. Biochemical analysis revealed that lysosomal cathepsin B protease rapidly cleaved the dendritic linkers and released the conjugated gemcitabine as a free drug. Subsequently, the dendrimer–linker–gemcitabine was coupled with a cell-specific aptamer to form aptamer–gemcitabine conjugates. Functional assays confirmed that, under aptamer guidance, aptamer–gemcitabine conjugates were selectively bound to and then internalized by triple-negative breast cancer cells. Cellular therapy studies indicated that the aptamer–gemcitabine conjugates potentiated cytotoxic activity to targeted cancer cells but did not affect off-target control cells. Our study demonstrates a novel approach to aptamer-mediated targeted drug delivery that combines a high drug payload and an enzymatically controlled drug release switch to achieve higher therapeutic efficacy and fewer off-target effects relative to free-drug chemotherapy. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Open AccessArticle

T908 Polymeric Micelles Improved the Uptake of Sgc8-c Aptamer Probe in Tumor-Bearing Mice: A Co-Association Study between the Probe and Preformed Nanostructures

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Pharmaceuticals 2022, 15(1), 15; https://doi.org/10.3390/ph15010015 - 23 Dec 2021

Cited by 6 | Viewed by 2175

Abstract

Aptamers are oligonucleotides that have the characteristic of recognizing a target with high affinity and specificity. Based on our previous studies, the aptamer probe Sgc8-c-Alexa647 is a promising tool for molecular imaging of PTK7, which is an interesting biomarker in cancer. In order [...] Read more.

Aptamers are oligonucleotides that have the characteristic of recognizing a target with high affinity and specificity. Based on our previous studies, the aptamer probe Sgc8-c-Alexa647 is a promising tool for molecular imaging of PTK7, which is an interesting biomarker in cancer. In order to improve the delivery of this probe as well as create a novel drug delivery nanosystem targeted to the PTK7 receptor, we evaluate the co-association between the probe and preformed nanostructures. In this work, preformed pegylated liposomes (PPL) and linear and branched pristine polymeric micelles (PMs), based on PEO–PPO–PEO triblock copolymers were used: poloxamer F127^® and poloxamines T1307^® and T908^®. For it, Sgc8-c-Alexa647 and its co-association with the different nanostructures was exhaustively analyzed. DLS analysis showed nanometric sizes, and TEM and AFM showed notable differences between free- and co-associated probe. Likewise, all nanosystems were evaluated on A20 lymphoma cell line overexpressing PTK7, and the confocal microscopy images showed distinctness in cellular uptake. Finally, the biodistribution in BALB/c mice bearing lymphoma-tumor and pharmacokinetic study revealed an encouraging profile for T908-probe. All data obtained from this work suggested that PMs and, more specifically T908 ones, are good candidates to improve the pharmacokinetics and the tumor uptake of aptamer-based probes. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Open AccessArticle

A Comprehensive Analysis of the Thrombin Binding Aptamer Containing Functionalized Pyrrolo-2’-deoxycytidines

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Weronika Kotkowiak

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Zofia Jahnz-Wechmann

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Anna Pasternak

Pharmaceuticals 2021, 14(12), 1326; https://doi.org/10.3390/ph14121326 - 18 Dec 2021

Cited by 3 | Viewed by 1583

Abstract

Aptamers constitute an answer for the growing need for targeted therapy development. One of the most well-known representatives of this group of compounds is thrombin binding aptamers (TBA) targeted towards thrombin. The TBA inhibitory activity is determined by its spatial arrangement, which consists [...] Read more.

Aptamers constitute an answer for the growing need for targeted therapy development. One of the most well-known representatives of this group of compounds is thrombin binding aptamers (TBA) targeted towards thrombin. The TBA inhibitory activity is determined by its spatial arrangement, which consists of two G-tetrads linked by two shorter TT loops and one longer TGT loop and folds into a unimolecular, antiparallel G-quadruplex structure. Interesting properties of the aptamer can be further improved via the introduction of a number of chemical modifications. Herein, a comprehensive analysis of the influence of pyrrolo-2’-deoxycytidine (Py-dC) and its derivatives on TBA physicochemical and biological properties has been presented. The studies have shown that the presence of modified residues at the T7 position of the TGT loop has only minor effects on TBA thermodynamic stability without affecting its folding topology. All analyzed oligomers exhibit anticoagulant properties, but only aptamer modified with a decyl derivative of Py-dC was able to inhibit thrombin activity more efficiently than unmodified, parental compounds. Importantly, the same compound also possessed the potential to effectively restrain HeLa cell line growth. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Open AccessArticle

DNA Aptamers against Vaccinia-Related Kinase (VRK) 1 Block Proliferation in MCF7 Breast Cancer Cells

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Rebeca Carrión-Marchante

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Valerio Frezza

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Ana Salgado-Figueroa

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M. Isabel Pérez-Morgado

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M. Elena Martín

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Víctor M. González

Pharmaceuticals 2021, 14(5), 473; https://doi.org/10.3390/ph14050473 - 17 May 2021

Cited by 4 | Viewed by 1880

Abstract

Vaccinia-related kinase (VRK) 1 is a serin/threonine kinase that plays an important role in DNA damage response (DDR), phosphorylating some proteins involved in this process such as 53BP1, NBS1 or H2AX, and in the cell cycle progression. In addition, VRK1 is overexpressed in [...] Read more.

Vaccinia-related kinase (VRK) 1 is a serin/threonine kinase that plays an important role in DNA damage response (DDR), phosphorylating some proteins involved in this process such as 53BP1, NBS1 or H2AX, and in the cell cycle progression. In addition, VRK1 is overexpressed in many cancer types and its correlation with poor prognosis has been determined, showing VRK1 as a new therapeutic target in oncology. Using in vitro selection, high-affinity DNA aptamers to VRK1 were selected from a library of ssDNA. Selection was monitored using the enzyme-linked oligonucleotide assay (ELONA), and the selected aptamer population was cloned and sequenced. Three aptamers were selected and characterized. These aptamers recognized the protein kinase VRK1 with an affinity in the nanomolar range and showed a high sensibility. Moreover, the treatment of the MCF7 breast cell line with these aptamers resulted in a decrease in cyclin D1 levels, and an inhibition of cell cycle progression by G1 phase arrest, which induced apoptosis in cells. These results suggest that these aptamers are specific inhibitors of VRK1 that might be developed as potential drugs for the treatment of cancer. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Open AccessArticle

Improving Breast Cancer Treatment Specificity Using Aptamers Obtained by 3D Cell-SELEX

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Pharmaceuticals 2021, 14(4), 349; https://doi.org/10.3390/ph14040349 - 09 Apr 2021

Cited by 13 | Viewed by 2353

Abstract

Three-dimensional spheroids of non-malignant MCF10A and malignant SKBR3 breast cells were used for subsequent 3D Cell-SELEX to generate aptamers for specific binding and treatment of breast cancer cells. Using 3D Cell-SELEX combined with Next-Generation Sequencing and bioinformatics, ten abundant aptamer families with specific [...] Read more.

Three-dimensional spheroids of non-malignant MCF10A and malignant SKBR3 breast cells were used for subsequent 3D Cell-SELEX to generate aptamers for specific binding and treatment of breast cancer cells. Using 3D Cell-SELEX combined with Next-Generation Sequencing and bioinformatics, ten abundant aptamer families with specific structures were identified that selectively bind to SKBR3, and not to MCF10A cells. Multivalent aptamer polymers were synthesized by co-polymerization and analyzed for binding performance as well as therapeutic efficacy. Binding performance was determined by confocal fluorescence imaging and revealed specific binding and efficient internalization of aptamer polymers into SKBR3 spheroids. For therapeutic purposes, DNA sequences that intercalate the cytotoxic drug doxorubicin were co-polymerized into the aptamer polymers. Viability tests show that the drug-loaded polymers are specific and effective in killing SKBR3 breast cancer cells. Thus, the 3D-selected aptamers enhanced the specificity of doxorubicin against malignant over non-malignant breast cells. The innovative modular DNA aptamer platform based on 3D Cell SELEX and polymer multivalency holds great promise for diagnostics and treatment of breast cancer. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Open AccessCommunication

Remyelination-Promoting DNA Aptamer Conjugate Myaptavin-3064 Binds to Adult Oligodendrocytes In Vitro

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Mahboubeh Fereidan-Esfahani

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Pharmaceuticals 2020, 13(11), 403; https://doi.org/10.3390/ph13110403 - 19 Nov 2020

Cited by 2 | Viewed by 1700

Abstract

We previously applied Systematic Evolution of Ligands by EXponential enrichment (SELEX) technology to identify myelin-specific DNA aptamers, using crude mouse central nervous system myelin as bait. This selection identified a 40-nucleotide aptamer (LJM-3064). Multiple biotinylated LJM-3064 molecules were conjugated to a streptavidin core [...] Read more.

We previously applied Systematic Evolution of Ligands by EXponential enrichment (SELEX) technology to identify myelin-specific DNA aptamers, using crude mouse central nervous system myelin as bait. This selection identified a 40-nucleotide aptamer (LJM-3064). Multiple biotinylated LJM-3064 molecules were conjugated to a streptavidin core to mimic a multimeric immunoglobulin M (IgM) antibody, generating 3064-BS-streptavidin (Myaptavin-3064). We previously showed that Myaptavin-3064 induces remyelination in the Theiler’s murine encephalomyelitis virus (TMEV) model of chronic spinal cord demyelination. While details of target binding and the mechanism of action remain unclear, we hypothesized that Myaptavin-3064 induces remyelination by binding to oligodendrocytes (OLs). We now report the results of binding assays using the human oligodendroglioma (HOG) cell line, applying both flow cytometry and immunocytochemistry (IC) to assay aptamer conjugate binding to cells. IC assays were applied to compare aptamer conjugate binding to primary embryonic mouse mixed cortical cultures and primary adult rat mixed glial cultures. We show that Myaptavin-3064 binds to HOG cells, with increased binding upon differentiation. In contrast, a negative control aptamer conjugate, 3060-BS, which did not promote central nervous system (CNS) remyelination, does not bind to HOG cells. Myaptavin-3064 did not bind to lung (L2) or kidney (BHK) cell lines. Total internal reflection fluorescence (TIRF) imaging indicates that Myaptavin-3064 binds at the cell membrane of live cells. In addition to HOG cells, Myaptavin-3064 binds to adult rat OLs, but not to embryonic mouse mixed cortical cultures. These data support the hypothesis that Myaptavin-3064 binds to a surface molecule on both rodent and human OLs in a manner that triggers a remyelination signal pathway. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Review

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Open AccessReview

Recent Advances in Electrochemical Aptasensors for Detection of Biomarkers

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Marjan Majdinasab

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Jean Louis Marty

Pharmaceuticals 2022, 15(8), 995; https://doi.org/10.3390/ph15080995 - 12 Aug 2022

Cited by 6 | Viewed by 1412

Abstract

The early diagnosis of diseases is of great importance for the effective treatment of patients. Biomarkers are one of the most promising medical approaches in the diagnosis of diseases and their progress and facilitate reaching this goal. Among the many methods developed in [...] Read more.

The early diagnosis of diseases is of great importance for the effective treatment of patients. Biomarkers are one of the most promising medical approaches in the diagnosis of diseases and their progress and facilitate reaching this goal. Among the many methods developed in the detection of biomarkers, aptamer-based biosensors (aptasensors) have shown great promise. Aptamers are promising diagnostic molecules with high sensitivity and selectivity, low-cost synthesis, easy modification, low toxicity, and high stability. Electrochemical aptasensors with high sensitivity and accuracy have attracted considerable attention in the field of biomarker detection. In this review, we will summarize recent advances in biomarker detection using electrochemical aptasensors. The principles of detection, sensitivity, selectivity, and other important factors in aptasensor performance are investigated. Finally, advantages and challenges of the developed aptasensors are discussed. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Open AccessReview

Applications in Which Aptamers Are Needed or Wanted in Diagnostics and Therapeutics

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John G. Bruno

Pharmaceuticals 2022, 15(6), 693; https://doi.org/10.3390/ph15060693 - 01 Jun 2022

Cited by 4 | Viewed by 1355

Abstract

One strategy for bringing aptamers more into the mainstream of biomedical diagnostics and therapeutics is to exploit niche applications where aptamers are truly needed or wanted for their innate differences versus antibodies. This brief review article highlights some of those relatively rare applications [...] Read more.

One strategy for bringing aptamers more into the mainstream of biomedical diagnostics and therapeutics is to exploit niche applications where aptamers are truly needed or wanted for their innate differences versus antibodies. This brief review article highlights some of those relatively rare applications in which aptamers are necessary or better suited to the user requirements than antibodies with explanations for why the aptamer is a necessary or superior choice. These situations include when no commercial antibody exists, when antibodies are excessively difficult to develop against a particular target because the target is highly toxic to host animals, when antibodies fail to discriminate closely related targets, when a smaller size is preferable to penetrate a tissue, when humanized monoclonal antibodies are too expensive and when the target is rapidly evolving or mutating. Examples of each are provided to illustrate these points. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Open AccessReview

Aptamer-Based Lateral Flow Assays: Current Trends in Clinical Diagnostic Rapid Tests

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Marjan Majdinasab

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Mihaela Badea

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Jean Louis Marty

Pharmaceuticals 2022, 15(1), 90; https://doi.org/10.3390/ph15010090 - 13 Jan 2022

Cited by 15 | Viewed by 4225

Abstract

The lateral flow assay (LFA) is an extensively used paper-based platform for the rapid and on-site detection of different analytes. The method is user-friendly with no need for sophisticated operation and only includes adding sample. Generally, antibodies are employed as the biorecognition elements [...] Read more.

The lateral flow assay (LFA) is an extensively used paper-based platform for the rapid and on-site detection of different analytes. The method is user-friendly with no need for sophisticated operation and only includes adding sample. Generally, antibodies are employed as the biorecognition elements in the LFA. However, antibodies possess several disadvantages including poor stability, high batch-to-batch variation, long development time, high price and need for ethical approval and cold chain. Because of these limitations, aptamers screened by an in vitro process can be a good alternative to antibodies as biorecognition molecules in the LFA. In recent years, aptamer-based LFAs have been investigated for the detection of different analytes in point-of-care diagnostics. In this review, we summarize the applications of aptamer technology in LFAs in clinical diagnostic rapid tests for the detection of biomarkers, microbial analytes, hormones and antibiotics. Performance, advantages and drawbacks of the developed assays are also discussed. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Open AccessReview

Aptamer Applications in Neuroscience

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Meric Ozturk

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Marit Nilsen-Hamilton

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Muslum Ilgu

Pharmaceuticals 2021, 14(12), 1260; https://doi.org/10.3390/ph14121260 - 03 Dec 2021

Cited by 9 | Viewed by 3281

Abstract

Being the predominant cause of disability, neurological diseases have received much attention from the global health community. Over a billion people suffer from one of the following neurological disorders: dementia, epilepsy, stroke, migraine, meningitis, Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, amyotrophic lateral sclerosis, [...] Read more.

Being the predominant cause of disability, neurological diseases have received much attention from the global health community. Over a billion people suffer from one of the following neurological disorders: dementia, epilepsy, stroke, migraine, meningitis, Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, amyotrophic lateral sclerosis, Huntington’s disease, prion disease, or brain tumors. The diagnosis and treatment options are limited for many of these diseases. Aptamers, being small and non-immunogenic nucleic acid molecules that are easy to chemically modify, offer potential diagnostic and theragnostic applications to meet these needs. This review covers pioneering studies in applying aptamers, which shows promise for future diagnostics and treatments of neurological disorders that pose increasingly dire worldwide health challenges. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Open AccessReview

Aptamer Applications in Emerging Viral Diseases

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Arne Krüger

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Ana Paula de Jesus Santos

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Vanessa de Sá

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Henning Ulrich

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Carsten Wrenger

Pharmaceuticals 2021, 14(7), 622; https://doi.org/10.3390/ph14070622 - 28 Jun 2021

Cited by 10 | Viewed by 3475

Abstract

Aptamers are single-stranded DNA or RNA molecules which are submitted to a process denominated SELEX. SELEX uses reiterative screening of a random oligonucleotide library to identify high-affinity binders to a chosen target, which may be a peptide, protein, or entire cells or viral [...] Read more.

Aptamers are single-stranded DNA or RNA molecules which are submitted to a process denominated SELEX. SELEX uses reiterative screening of a random oligonucleotide library to identify high-affinity binders to a chosen target, which may be a peptide, protein, or entire cells or viral particles. Aptamers can rival antibodies in target recognition, and benefit from their non-proteic nature, ease of modification, increased stability, and pharmacokinetic properties. This turns them into ideal candidates for diagnostic as well as therapeutic applications. Here, we review the recent accomplishments in the development of aptamers targeting emerging viral diseases, with emphasis on recent findings of aptamers binding to coronaviruses. We focus on aptamer development for diagnosis, including biosensors, in addition to aptamer modifications for stabilization in body fluids and tissue penetration. Such aptamers are aimed at in vivo diagnosis and treatment, such as quantification of viral load and blocking host cell invasion, virus assembly, or replication, respectively. Although there are currently no in vivo applications of aptamers in combating viral diseases, such strategies are promising for therapy development in the future. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Open AccessReview

Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors

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Zachary J. Tickner

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Michael Farzan

Pharmaceuticals 2021, 14(6), 554; https://doi.org/10.3390/ph14060554 - 10 Jun 2021

Cited by 10 | Viewed by 4077 | Correction

Abstract

Vectors developed from adeno-associated virus (AAV) are powerful tools for in vivo transgene delivery in both humans and animal models, and several AAV-delivered gene therapies are currently approved for clinical use. However, AAV-mediated gene therapy still faces several challenges, including limited vector packaging [...] Read more.

Vectors developed from adeno-associated virus (AAV) are powerful tools for in vivo transgene delivery in both humans and animal models, and several AAV-delivered gene therapies are currently approved for clinical use. However, AAV-mediated gene therapy still faces several challenges, including limited vector packaging capacity and the need for a safe, effective method for controlling transgene expression during and after delivery. Riboswitches, RNA elements which control gene expression in response to ligand binding, are attractive candidates for regulating expression of AAV-delivered transgene therapeutics because of their small genomic footprints and non-immunogenicity compared to protein-based expression control systems. In addition, the ligand-sensing aptamer domains of many riboswitches can be exchanged in a modular fashion to allow regulation by a variety of small molecules, proteins, and oligonucleotides. Riboswitches have been used to regulate AAV-delivered transgene therapeutics in animal models, and recently developed screening and selection methods allow rapid isolation of riboswitches with novel ligands and improved performance in mammalian cells. This review discusses the advantages of riboswitches in the context of AAV-delivered gene therapy, the subsets of riboswitch mechanisms which have been shown to function in human cells and animal models, recent progress in riboswitch isolation and optimization, and several examples of AAV-delivered therapeutic systems which might be improved by riboswitch regulation. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Open AccessFeature PaperReview

Logic Gates Based on DNA Aptamers

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Mariia Andrianova

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Alexander Kuznetsov

Pharmaceuticals 2020, 13(11), 417; https://doi.org/10.3390/ph13110417 - 23 Nov 2020

Cited by 10 | Viewed by 3046

Abstract

DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based [...] Read more.

DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based on aptamers for the purposes of medicine and analytical chemistry. The review considers different approaches to the creation of logic gates and identifies the general algorithms of their creation, as well as describes the methods of obtaining an output signal which can be divided into optical and electrochemical. Aptameric logic gates based on DNA origami and DNA nanorobots are also shown. The information presented in this article can be useful when creating new logic gates using existing aptamers and aptamers that will be selected in the future. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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Other

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Open AccessBrief Report

The Influence of Protein Charge and Molecular Weight on the Affinity of Aptamers

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Alissa Drees

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Tung Lam Trinh

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Markus Fischer

Pharmaceuticals 2023, 16(3), 457; https://doi.org/10.3390/ph16030457 - 18 Mar 2023

Viewed by 768

Abstract

Aptamers offer several advantages over antibodies. However, to ensure high affinity and specificity, a better understanding of the interactions between the nucleic-acid-based aptamers and their targets is mandatory. Therefore, we investigated the influence of two physical properties of proteins—molecular mass and charge—on the [...] Read more.

Aptamers offer several advantages over antibodies. However, to ensure high affinity and specificity, a better understanding of the interactions between the nucleic-acid-based aptamers and their targets is mandatory. Therefore, we investigated the influence of two physical properties of proteins—molecular mass and charge—on the affinity of nucleic-acid-based aptamers. For this purpose, first, the affinity of two random oligonucleotides towards twelve proteins was determined. No binding was observed for proteins with a negative net charge towards the two oligonucleotides, while up to nanomolar affinity was determined for positively charged proteins with a high pI value. Second, a literature analysis comprising 369 aptamer–peptide/protein pairs was performed. The dataset included 296 different target peptides and proteins and is thus currently one of the largest databases for aptamers for proteins and peptides. The targets considered covered isoelectric points of 4.1–11.8 and a molecular weight range of 0.7–330 kDa, while the dissociation constants ranged from 50 fM to 29.5 µM. This also revealed a significant inverse correlation between the protein’s isoelectric point and the affinity of aptamers. In contrast, no trend was observed between the affinity and the molecular weight of the target protein with either approach. Full article

(This article belongs to the Special Issue Potential of the Aptamers to Fill Therapeutic and Diagnostic Gaps)

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