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Special Issue "Aptamers: Past, Present, and Future"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Molecular Diversity".

Deadline for manuscript submissions: closed (15 September 2015)

Special Issue Editors

Guest Editor
Dr. Alain O.A. Miller

CilBiotech sa, c/o UMons-Rue de l'Epargne 56, B-7000 Mons, Belgium
Website | E-Mail
Phone: +32 (0) 65374 578
Interests: stem cells; aptamers; antibodies; Large-scale cultivation of human adhering cells; Dynamic growth medium technology (development of aptamer-based biosensors)
Guest Editor
Dr. Jean Jacques Vanden Eynde

Formerly head of the Department of Organic Chemistry (FS), University of Mons-UMONS, 7000 Mons, Belgium
Website | E-Mail
Interests: heterocycles; microwave-induced synthesis; medicinal chemistry; green chemistry

Special Issue Information

Dear Colleagues,

Nucleic acid aptamer libraries are large arrays of randomly distributed (usually 40-60 nucleotides long) single-stranded nucleic acid molecules, provided with fixed 5’ and 3’ ends.

Individual aptamers display numerous sequence-dependent folds (“cavities”) capable of accommodating small molecules, as well as molecular clusters (“aptatopes”) present on target molecules (generally proteins). Following 8-12 rounds of in vitro selection by the SELEX method (Systematic Evolution of Ligands by EXponential enrichment), it is possible to generate aptamers with increased affinity and specificity towards a given target.

Due to their huge sequence complexity (1014–1015 combinatorial variants), aptamer libraries constitute unique tools for clinicians, pharma, and biotech industries to develop innovative applications, including human primary/pluripotent stem cells low-abundance protein atlases, the elimination of trace contaminants during monoclonal antibody purification, etc.

Cell-specific aptamer probes for intracellular and membrane proteins, the construction of biosensors, miniaturized biological circuits, and artificial extracellular matrix-based scaffolds represent many developments that critically depend upon aptamers. These developments open new avenues for clinical applications in oncology, diabetes, cardiovascular diseases, etc.

This Special Issue aims to be a forum for newcomers and specialists, and will provide an opportunity for them to present recent and novel results in the blooming field of aptamers technology and applications.

Dr. Alain O.A. Miller
Dr. Jean Jacques Vanden Eynde
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • aptamers
  • SELEX
  • oligonucleotides
  • nuclei acids
  • DNA
  • RNA
  • amplification
  • PCR
  • RT-PCR
  • spiegelmers
  • Cell-specific aptamers (cell sorting)
  • Organismal proteome of low abundance proteins
  • Therapeutic aptamers (pri-miRNA/siRNA/nanoparticles)

Related Special Issue

Published Papers (15 papers)

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Research

Jump to: Review

Open AccessArticle Binding of Harmine Derivatives to DNA: A Spectroscopic Investigation
Molecules 2017, 22(11), 1831; doi:10.3390/molecules22111831
Received: 28 September 2017 / Revised: 20 October 2017 / Accepted: 24 October 2017 / Published: 27 October 2017
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Abstract
Harmine belongs to a group of β-carboline alkaloids endowed with antitumor properties. Harmine and its derivatives are thought to bind to DNA and interfere with topoisomerase activities. We investigated the base-dependent binding of harmine, and three of its synthetic anticancer-active derivatives to the
[...] Read more.
Harmine belongs to a group of β-carboline alkaloids endowed with antitumor properties. Harmine and its derivatives are thought to bind to DNA and interfere with topoisomerase activities. We investigated the base-dependent binding of harmine, and three of its synthetic anticancer-active derivatives to the genomic DNA from calf thymus and two synthetic 20-mer double helices, the poly(dG-dC)·poly(dG-dC) and the poly(dA-dT)·poly(dA-dT), by means of UV-Vis and circular dichroism (CD) spectroscopies. The data show that the DNA binding and stabilising properties of the investigated derivatives are base pair-dependent. These results could be used as a guide to design and develop further bioactive analogues. Full article
(This article belongs to the collection New Frontiers in Nucleic Acid Chemistry)
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Open AccessArticle The Molecular Effect of Diagnostic Absorbed Doses from 131I on Papillary Thyroid Cancer Cells In Vitro
Molecules 2017, 22(6), 993; doi:10.3390/molecules22060993
Received: 14 April 2017 / Revised: 12 June 2017 / Accepted: 13 June 2017 / Published: 15 June 2017
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Abstract
Diagnostic whole-body scan is a standard procedure in patients with thyroid cancer prior to the application of a therapeutic dose of 131I. Unfortunately, administration of the radioisotope in a diagnostic dose may decrease further radioiodine uptake—the phenomenon called “thyroid stunning”. We estimated
[...] Read more.
Diagnostic whole-body scan is a standard procedure in patients with thyroid cancer prior to the application of a therapeutic dose of 131I. Unfortunately, administration of the radioisotope in a diagnostic dose may decrease further radioiodine uptake—the phenomenon called “thyroid stunning”. We estimated radiation absorbed dose-dependent changes in genetic material, in particular in the sodium iodide symporter (NIS) gene promoter, and the NIS protein level in a K1 cell line derived from the metastasis of a human papillary thyroid carcinoma exposed to 131I in culture. The different activities applied were calculated to result in absorbed doses of 5, 10 and 20 Gy. Radioiodine did not affect the expression of the NIS gene at the mRNA level, however, we observed significant changes in the NIS protein level in K1 cells. The decrease of the NIS protein level observed in the cells subjected to the lowest absorbed dose was paralleled by a significant increase in 8-oxo-dG concentrations (p < 0.01) and followed by late activation of the DNA repair pathways. Our findings suggest that the impact of 131I radiation on thyroid cells, in the range compared to doses absorbed during diagnostic procedures, is not linear and depends on various factors including the cellular components of thyroid pathology. Full article
(This article belongs to the collection New Frontiers in Nucleic Acid Chemistry)
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Open AccessArticle Synthesis and Biological Evaluation of Triazolyl 13α-Estrone–Nucleoside Bioconjugates
Molecules 2016, 21(9), 1212; doi:10.3390/molecules21091212
Received: 28 July 2016 / Revised: 2 September 2016 / Accepted: 6 September 2016 / Published: 10 September 2016
Cited by 2 | PDF Full-text (2934 KB) | HTML Full-text | XML Full-text
Abstract
2′-Deoxynucleoside conjugates of 13α-estrone were synthesized by applying the copper-catalyzed alkyne–azide click reaction (CuAAC). For the introduction of the azido group the 5′-position of the nucleosides and a propargyl ether functional group on the 3-hydroxy group of 13α-estrone were chosen. The best yields
[...] Read more.
2′-Deoxynucleoside conjugates of 13α-estrone were synthesized by applying the copper-catalyzed alkyne–azide click reaction (CuAAC). For the introduction of the azido group the 5′-position of the nucleosides and a propargyl ether functional group on the 3-hydroxy group of 13α-estrone were chosen. The best yields were realized in our hands when the 3′-hydroxy groups of the nucleosides were protected by acetyl groups and the 5′-hydroxy groups were modified by the tosyl–azide exchange method. The commonly used conditions for click reaction between the protected-5′-azidonucleosides and the steroid alkyne was slightly modified by using 1.5 equivalent of Cu(I) catalyst. All the prepared conjugates were evaluated in vitro by means of MTT assays for antiproliferative activity against a panel of human adherent cell lines (HeLa, MCF-7 and A2780) and the potential inhibitory activity of the new conjugates on human 17β-hydroxysteroid dehydrogenase 1 (17β-HSD1) was investigated via in vitro radiosubstrate incubation. Some protected conjugates displayed moderate antiproliferative properties against a panel of human adherent cancer cell lines (the protected cytidine conjugate proved to be the most potent with IC50 value of 9 μM). The thymidine conjugate displayed considerable 17β-HSD1 inhibitory activity (IC50 = 19 μM). Full article
(This article belongs to the collection New Frontiers in Nucleic Acid Chemistry)
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Open AccessArticle DNA Three Way Junction Core Decorated with Amino Acids-Like Residues-Synthesis and Characterization
Molecules 2016, 21(9), 1082; doi:10.3390/molecules21091082
Received: 5 July 2016 / Revised: 8 August 2016 / Accepted: 10 August 2016 / Published: 23 August 2016
PDF Full-text (1251 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Construction and physico-chemical behavior of DNA three way junction (3WJ) functionalized by protein-like residues (imidazole, alcohol and carboxylic acid) at unpaired positions at the core is described. One 5′-C(S)-propargyl-thymidine nucleotide was specifically incorporated on each strand to react through a post
[...] Read more.
Construction and physico-chemical behavior of DNA three way junction (3WJ) functionalized by protein-like residues (imidazole, alcohol and carboxylic acid) at unpaired positions at the core is described. One 5′-C(S)-propargyl-thymidine nucleotide was specifically incorporated on each strand to react through a post synthetic CuACC reaction with either protected imidazolyl-, hydroxyl- or carboxyl-azide. Structural impacts of 5′-C(S)-functionalization were investigated to evaluate how 3WJ flexibility/stability is affected. Full article
(This article belongs to the collection New Frontiers in Nucleic Acid Chemistry)
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Open AccessArticle Chemical Incorporation of Chain-Terminating Nucleoside Analogs as 3′-Blocking DNA Damage and Their Removal by Human ERCC1-XPF Endonuclease
Molecules 2016, 21(6), 766; doi:10.3390/molecules21060766
Received: 13 May 2016 / Accepted: 3 June 2016 / Published: 11 June 2016
Cited by 1 | PDF Full-text (2286 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Nucleoside/nucleotide analogs that lack the 3′-hydroxy group are widely utilized for HIV therapy. These chain-terminating nucleoside analogs (CTNAs) block DNA synthesis after their incorporation into growing DNA, leading to the antiviral effects. However, they are also considered to be DNA damaging agents, and
[...] Read more.
Nucleoside/nucleotide analogs that lack the 3′-hydroxy group are widely utilized for HIV therapy. These chain-terminating nucleoside analogs (CTNAs) block DNA synthesis after their incorporation into growing DNA, leading to the antiviral effects. However, they are also considered to be DNA damaging agents, and tyrosyl-DNA phosphodiesterase 1, a DNA repair enzyme, is reportedly able to remove such CTNA-modifications of DNA. Here, we have synthesized phosphoramidite building blocks of representative CTNAs, such as acyclovir, abacavir, carbovir, and lamivudine, and oligonucleotides with the 3′-CTNAs were successfully synthesized on solid supports. Using the chemically synthesized oligonucleotides, we investigated the excision of the 3′-CTNAs in DNA by the human excision repair cross complementing protein 1-xeroderma pigmentosum group F (ERCC1-XPF) endonuclease, which is one of the main components of the nucleotide excision repair pathway. A biochemical analysis demonstrated that the ERCC1-XPF endonuclease cleaved 2–7 nt upstream from the 3′-blocking CTNAs, and that DNA synthesis by the Klenow fragment was resumed after the removal of the CTNAs, suggesting that ERCC1-XPF participates in the repair of the CTNA-induced DNA damage. Full article
(This article belongs to the collection New Frontiers in Nucleic Acid Chemistry)
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Open AccessArticle Identification of RNA Oligonucleotides Binding to Several Proteins from Potential G-Quadruplex Forming Regions in Transcribed Pre-mRNA
Molecules 2015, 20(11), 20832-20840; doi:10.3390/molecules201119733
Received: 15 September 2015 / Revised: 6 November 2015 / Accepted: 12 November 2015 / Published: 23 November 2015
Cited by 1 | PDF Full-text (2165 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
G-quadruplexes (G4s) are noncanonical DNA/RNA structures formed by guanine-rich sequences. Recently, G4s have been found not only in aptamers but also in the genomic DNA and transcribed RNA. In this study, we identified new RNA oligonucleotides working as aptamers by focusing on G4-forming
[...] Read more.
G-quadruplexes (G4s) are noncanonical DNA/RNA structures formed by guanine-rich sequences. Recently, G4s have been found not only in aptamers but also in the genomic DNA and transcribed RNA. In this study, we identified new RNA oligonucleotides working as aptamers by focusing on G4-forming RNAs located within the pre-mRNA. We showed that the G4 in the 5′ UTR and first intron of VEGFA bound to the protein encoded in VEGFA gene, VEGF165, with high affinity. Moreover, G4-forming RNAs located within the PDGFA and the PDGFB introns bound to PDGF-AA and PDGF-BB, respectively, indicating that G4 in the pre-mRNA could be an aptamer. It had been reported that the putative G4-forming RNA sequences are located in some parts of most genes, thus our strategy for aptamer identification could be applicable to other proteins. It has been reported that some G4-forming RNAs in 5′ UTRs are involved in translation control; however, G4-forming excised intronic RNA function has not been revealed previously. Therefore, these findings could not only contribute to the identification of RNA aptamers but also provide new insights into the biological functioning of G4-forming RNAs located within intronic RNA sequences. Full article
(This article belongs to the Special Issue Aptamers: Past, Present, and Future)
Open AccessArticle Fluorescent Sensor for PH Monitoring Based on an i-Motif- – Switching Aptamer Containing a Tricyclic Cytosine Analogue (tC)
Molecules 2015, 20(10), 18511-18525; doi:10.3390/molecules201018511
Received: 31 August 2015 / Revised: 24 September 2015 / Accepted: 6 October 2015 / Published: 9 October 2015
Cited by 6 | PDF Full-text (932 KB) | HTML Full-text | XML Full-text
Abstract
There are cytosine-rich regions in the genome that bind protons with high specificity. Thus protonated C-rich sequence may undergo folding to tetraplex structures called i-motifs. Therefore, one can regard such specific C-rich oligonucleotides as aptamers that recognize protons and undergo conformational transitions. Proper
[...] Read more.
There are cytosine-rich regions in the genome that bind protons with high specificity. Thus protonated C-rich sequence may undergo folding to tetraplex structures called i-motifs. Therefore, one can regard such specific C-rich oligonucleotides as aptamers that recognize protons and undergo conformational transitions. Proper labeling of the aptamer with a fluorescent tag constitutes a platform to construct a pH-sensitive aptasensor. Since the hemiprotonated C-C+ base pairs are responsible for the folded tetraplex structure of i-motif, we decided to substitute one of cytosines in an aptamer sequence with its fluorescent analogue, 1,3-diaza-2-oxophenothiazine (tC). In this paper we report on three tC-modified fluorescent probes that contain RET related sequences as a proton recognizing aptamer. Results of the circular dichroism (CD), UV absorption melting experiments, and steady-state fluorescence measurements of these tC-modified i-motif probes are presented and discussed. The pH-induced i-motif formation by the probes resulted in fluorescence quenching of tC fluorophore. Efficiency of quenching was related to the pH variations. Suitability of the sensor for monitoring pH changes was also demonstrated. Full article
(This article belongs to the Special Issue Aptamers: Past, Present, and Future)
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Open AccessArticle RNA Aptamers as Molecular Tools to Study the Functionality of the Hepatitis C Virus CRE Region
Molecules 2015, 20(9), 16030-16047; doi:10.3390/molecules200916030
Received: 30 July 2015 / Revised: 25 August 2015 / Accepted: 29 August 2015 / Published: 2 September 2015
Cited by 3 | PDF Full-text (1043 KB) | HTML Full-text | XML Full-text
Abstract
Background: Hepatitis C virus (HCV) contains a (+) ssRNA genome with highly conserved structural, functional RNA domains, many of them with unknown roles for the consecution of the viral cycle. Such genomic domains are candidate therapeutic targets. This study reports the functional characterization
[...] Read more.
Background: Hepatitis C virus (HCV) contains a (+) ssRNA genome with highly conserved structural, functional RNA domains, many of them with unknown roles for the consecution of the viral cycle. Such genomic domains are candidate therapeutic targets. This study reports the functional characterization of a set of aptamers targeting the cis-acting replication element (CRE) of the HCV genome, an essential partner for viral replication and also involved in the regulation of protein synthesis. Methods: Forty-four aptamers were tested for their ability to interfere with viral RNA synthesis in a subgenomic replicon system. Some of the most efficient inhibitors were further evaluated for their potential to affect the recruitment of the HCV RNA-dependent RNA polymerase (NS5B) and the viral translation in cell culture. Results: Four aptamers emerged as potent inhibitors of HCV replication by direct interaction with functional RNA domains of the CRE, yielding a decrease in the HCV RNA levels higher than 90%. Concomitantly, one of them also induced a significant increase in viral translation (>50%). The three remaining aptamers efficiently competed with the binding of the NS5B protein to the CRE. Conclusions: Present findings confirm the potential of the CRE as an anti-HCV target and support the use of aptamers as molecular tools for investigating the functionality of RNA domains in viral genomes. Full article
(This article belongs to the Special Issue Aptamers: Past, Present, and Future)
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Review

Jump to: Research

Open AccessReview Evolution of Complex Target SELEX to Identify Aptamers against Mammalian Cell-Surface Antigens
Molecules 2017, 22(2), 215; doi:10.3390/molecules22020215
Received: 20 December 2016 / Accepted: 24 January 2017 / Published: 30 January 2017
Cited by 8 | PDF Full-text (2434 KB) | HTML Full-text | XML Full-text
Abstract
The demand has increased for sophisticated molecular tools with improved detection limits. Such molecules should be simple in structure, yet stable enough for clinical applications. Nucleic acid aptamers (NAAs) represent a class of molecules able to meet this demand. In particular, aptamers, a
[...] Read more.
The demand has increased for sophisticated molecular tools with improved detection limits. Such molecules should be simple in structure, yet stable enough for clinical applications. Nucleic acid aptamers (NAAs) represent a class of molecules able to meet this demand. In particular, aptamers, a class of small nucleic acid ligands that are composed of single-stranded modified/unmodified RNA/DNA molecules, can be evolved from a complex library using Systematic Evolution of Ligands by EXponential enrichment (SELEX) against almost any molecule. Since its introduction in 1990, in stages, SELEX technology has itself undergone several modifications, improving selection and broadening the repertoire of targets. This review summarizes these milestones that have pushed the field forward, allowing researchers to generate aptamers that can potentially be applied as therapeutic and diagnostic agents. Full article
(This article belongs to the collection New Frontiers in Nucleic Acid Chemistry)
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Open AccessReview Methods for Improving Aptamer Binding Affinity
Molecules 2016, 21(4), 421; doi:10.3390/molecules21040421
Received: 21 December 2015 / Revised: 6 March 2016 / Accepted: 22 March 2016 / Published: 28 March 2016
Cited by 14 | PDF Full-text (2132 KB) | HTML Full-text | XML Full-text
Abstract
Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to
[...] Read more.
Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to achieve desired binding affinities. The optimization of primary sequences and stabilization of aptamer conformations are the main approaches to refining the binding properties of aptamers. In particular, sequence optimization using combined in silico sequence recombinations and in vitro functional evaluations is effective for the improvement of binding affinities, however, the binding affinities of aptamers are limited by the low hydrophobicity of nucleic acids. Accordingly, introduction of hydrophobic moieties into aptamers expands the diversity of interactions between aptamers and targets. Moreover, construction of multivalent aptamers by connecting aptamers that recognize distinct epitopes is an attractive approach to substantial increases in binding affinity. In addition, binding affinities can be tuned by optimizing the scaffolds of multivalent constructs. In this review, we summarize the various techniques for improving the binding affinities of aptamers. Full article
(This article belongs to the Special Issue Aptamers: Past, Present, and Future)
Open AccessReview Oligonucleotide Functionalised Microbeads: Indispensable Tools for High-Throughput Aptamer Selection
Molecules 2015, 20(12), 21298-21312; doi:10.3390/molecules201219766
Received: 22 September 2015 / Revised: 21 October 2015 / Accepted: 12 November 2015 / Published: 1 December 2015
Cited by 4 | PDF Full-text (1479 KB) | HTML Full-text | XML Full-text
Abstract
The functionalisation of microbeads with oligonucleotides has become an indispensable technique for high-throughput aptamer selection in SELEX protocols. In addition to simplifying the separation of binding and non-binding aptamer candidates, microbeads have facilitated the integration of other technologies such as emulsion PCR (ePCR)
[...] Read more.
The functionalisation of microbeads with oligonucleotides has become an indispensable technique for high-throughput aptamer selection in SELEX protocols. In addition to simplifying the separation of binding and non-binding aptamer candidates, microbeads have facilitated the integration of other technologies such as emulsion PCR (ePCR) and Fluorescence Activated Cell Sorting (FACS) to high-throughput selection techniques. Within these systems, monoclonal aptamer microbeads can be individually generated and assayed to assess aptamer candidate fitness thereby helping eliminate stochastic effects which are common to classical SELEX techniques. Such techniques have given rise to aptamers with 1000 times greater binding affinities when compared to traditional SELEX. Another emerging technique is Fluorescence Activated Droplet Sorting (FADS) whereby selection does not rely on binding capture allowing evolution of a greater diversity of aptamer properties such as fluorescence or enzymatic activity. Within this review we explore examples and applications of oligonucleotide functionalised microbeads in aptamer selection and reflect upon new opportunities arising for aptamer science. Full article
(This article belongs to the Special Issue Aptamers: Past, Present, and Future)
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Open AccessReview DNA Aptamers in the Diagnosis and Treatment of Human Diseases
Molecules 2015, 20(12), 20979-20997; doi:10.3390/molecules201219739
Received: 15 September 2015 / Revised: 16 November 2015 / Accepted: 16 November 2015 / Published: 25 November 2015
Cited by 4 | PDF Full-text (787 KB) | HTML Full-text | XML Full-text
Abstract
Aptamers have a promising role in the field of life science and have been extensively researched for application as analytical tools, therapeutic agents and as vehicles for targeted drug delivery. Compared with RNA aptamers, DNA aptamers have inherent advantages in stability and facility
[...] Read more.
Aptamers have a promising role in the field of life science and have been extensively researched for application as analytical tools, therapeutic agents and as vehicles for targeted drug delivery. Compared with RNA aptamers, DNA aptamers have inherent advantages in stability and facility of generation and synthesis. To better understand the specific potential of DNA aptamers, an overview of the progress in the generation and application of DNA aptamers in human disease diagnosis and therapy are presented in this review. Special attention is given to researches that are relatively close to practical application. DNA aptamers are expected to have great potential in the diagnosis and treatment of human diseases. Full article
(This article belongs to the Special Issue Aptamers: Past, Present, and Future)
Open AccessReview Generation of Aptamers with an Expanded Chemical Repertoire
Molecules 2015, 20(9), 16643-16671; doi:10.3390/molecules200916643
Received: 13 August 2015 / Revised: 28 August 2015 / Accepted: 1 September 2015 / Published: 14 September 2015
Cited by 36 | PDF Full-text (1388 KB) | HTML Full-text | XML Full-text
Abstract
The enzymatic co-polymerization of modified nucleoside triphosphates (dN*TPs and N*TPs) is a versatile method for the expansion and exploration of expanded chemical space in SELEX and related combinatorial methods of in vitro selection. This strategy can be exploited to generate aptamers with improved
[...] Read more.
The enzymatic co-polymerization of modified nucleoside triphosphates (dN*TPs and N*TPs) is a versatile method for the expansion and exploration of expanded chemical space in SELEX and related combinatorial methods of in vitro selection. This strategy can be exploited to generate aptamers with improved or hitherto unknown properties. In this review, we discuss the nature of the functionalities appended to nucleoside triphosphates and their impact on selection experiments. The properties of the resulting modified aptamers will be described, particularly those integrated in the fields of biomolecular diagnostics, therapeutics, and in the expansion of genetic systems (XNAs). Full article
(This article belongs to the Special Issue Aptamers: Past, Present, and Future)
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Open AccessReview A Highlight of Recent Advances in Aptamer Technology and Its Application
Molecules 2015, 20(7), 11959-11980; doi:10.3390/molecules200711959
Received: 8 June 2015 / Revised: 23 June 2015 / Accepted: 25 June 2015 / Published: 30 June 2015
Cited by 49 | PDF Full-text (1254 KB) | HTML Full-text | XML Full-text
Abstract
Aptamers and SELEX (systematic evolution of ligands by exponential enrichment) technology have gained increasing attention over the past 25 years. Despite their functional similarity to protein antibodies, oligonucleotide aptamers have many unique properties that are suitable for clinical applications and industrialization. Aptamers may
[...] Read more.
Aptamers and SELEX (systematic evolution of ligands by exponential enrichment) technology have gained increasing attention over the past 25 years. Despite their functional similarity to protein antibodies, oligonucleotide aptamers have many unique properties that are suitable for clinical applications and industrialization. Aptamers may be superior to antibodies in fields such as biomarker discovery, in vitro and in vivo diagnosis, precisely controlled drug release, and targeted therapy. However, aptamer commercialization has not occurred as quickly as expected, and few aptamer-based products have yet successfully entered clinical and industrial use. Thus, it is important to critically review some technical barriers of aptamer and SELEX technology per se that may impede aptamer development and application. To date, how to rapidly obtain aptamers with superior bioavailability over antibodies remains the key issue. In this review, we discuss different chemical and structural modification strategies aimed to enhance aptamer bioavailability. We also discuss improvements to SELEX process steps to shorten the selection period and improve the SELEX process success rate. Applications in which aptamers are particularly suited and perform differently or superior to antibodies are briefly introduced. Full article
(This article belongs to the Special Issue Aptamers: Past, Present, and Future)
Open AccessReview Predicting the Uncertain Future of Aptamer-Based Diagnostics and Therapeutics
Molecules 2015, 20(4), 6866-6887; doi:10.3390/molecules20046866
Received: 19 March 2015 / Revised: 4 April 2015 / Accepted: 7 April 2015 / Published: 16 April 2015
Cited by 35 | PDF Full-text (1435 KB) | HTML Full-text | XML Full-text
Abstract
Despite the great promise of nucleic acid aptamers in the areas of diagnostics and therapeutics for their facile in vitro development, lack of immunogenicity and other desirable properties, few truly successful aptamer-based products exist in the clinical or other markets. Core reasons for
[...] Read more.
Despite the great promise of nucleic acid aptamers in the areas of diagnostics and therapeutics for their facile in vitro development, lack of immunogenicity and other desirable properties, few truly successful aptamer-based products exist in the clinical or other markets. Core reasons for these commercial deficiencies probably stem from industrial commitment to antibodies including a huge financial investment in humanized monoclonal antibodies and a general ignorance about aptamers and their performance among the research and development community. Given the early failures of some strong commercial efforts to gain government approval and bring aptamer-based products to market, it may seem that aptamers are doomed to take a backseat to antibodies forever. However, the key advantages of aptamers over antibodies coupled with niche market needs that only aptamers can fill and more recent published data still point to a bright commercial future for aptamers in areas such as infectious disease and cancer diagnostics and therapeutics. As more researchers and entrepreneurs become familiar with aptamers, it seems inevitable that aptamers will at least be considered for expanded roles in diagnostics and therapeutics. This review also examines new aptamer modifications and attempts to predict new aptamer applications that could revolutionize biomedical technology in the future and lead to marketed products. Full article
(This article belongs to the Special Issue Aptamers: Past, Present, and Future)
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