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Aptamers: Functional and Structural Studies

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (15 January 2024) | Viewed by 5896

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Dr. Anna Pasternak

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Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61704 Poznan, Poland
Interests: aptamers; modified oligonucleotides; G-quadruplexes; triplexes; i-motif; RNA; DNA; therapeutic oligonucleotides; diagnostics; theranostics; cancer treatment; nucleic acids thermodynamics

Special Issue Information

Dear Colleagues,

Aptamers are short fragments of nucleic acids that form specific, unique, and stable structures that bind target molecules with high affinity and selectivity. They are often named chemical antibodies, but in contrast to antibodies, they are characterized by the ease of their synthesis and storage, low production costs and minor batch-to-batch variability, negligible immunogenicity, a broad repertoire of targets, and the feasibility of chemical modifications. Most aptamers are developed in vitro using a SELEX procedure; however, some naturally occurring aptamers were also sparsely found to be the elements of cell machinery. Due to the unquestionable benefits that they provide, aptamers can be applied as therapeutics, biosensors, or diagnostics in diverse areas including modern biotechnology, molecular biology, and biomedicine.

This Special Issue aims to cover fundamental aspects of aptamers, changing trends in aptamer technology, and their innovative applications in biotechnological and biomedical fields. We welcome submissions of research articles and reviews.

Dr. Anna Pasternak
Guest Editor

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Keywords

aptamers
RNA
DNA
therapeutics
diagnostics
theranostics
biosensors

Published Papers (6 papers)

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Research

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13 pages, 974 KiB

Open AccessArticle

A Multi-Faceted Binding Assessment of Aptamers Targeting the SARS-CoV-2 Spike Protein

by Laia Civit, Nima Moradzadeh, Anna Jonczyk, Patrick Neckermann, Benedikt Asbach, David Peterhoff, Ralf Wagner, Michael Famulok, Günter Mayer, Jørgen Kjems and Julián Valero

Int. J. Mol. Sci. 2024, 25(9), 4642; https://doi.org/10.3390/ijms25094642 - 24 Apr 2024

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Abstract

The COVID-19 pandemic has underscored the critical need for the advancement of diagnostic and therapeutic platforms. These platforms rely on the rapid development of molecular binders that should facilitate surveillance and swift intervention against viral infections. In this study, we have evaluated by three independent research groups the binding characteristics of various published RNA and DNA aptamers targeting the spike protein of the SARS-CoV-2 virus. For this comparative analysis, we have employed different techniques such as biolayer interferometry (BLI), enzyme-linked oligonucleotide assay (ELONA), and flow cytometry. Our data show discrepancies in the reported specificity and affinity among several of the published aptamers and underline the importance of standardized methods, the impact of biophysical techniques, and the controls used for aptamer characterization. We expect our results to contribute to the selection and application of suitable aptamers for the detection of SARS-CoV-2. Full article

(This article belongs to the Special Issue Aptamers: Functional and Structural Studies)

22 pages, 2230 KiB

Open AccessArticle

The Development and Characterisation of ssDNA Aptamers via a Modified Cell-SELEX Methodology for the Detection of Human Red Blood Cells

by Hayley Costanzo, James Gooch, Sireethorn Tungsirisurp and Nunzianda Frascione

Int. J. Mol. Sci. 2024, 25(3), 1814; https://doi.org/10.3390/ijms25031814 - 02 Feb 2024

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Abstract

Blood is one of the most commonly found biological fluids at crime scenes, with the detection and identification of blood holding a high degree of evidential value. It can provide not only information about the nature of the crime but can also lead to identification via DNA profiling. Presumptive tests for blood are usually sensitive but not specific, so small amounts of the substrate can be detected, but false-positive results are often encountered, which can be misleading. Novel methods for the detection of red blood cells based on aptamer–target interactions may be able to overcome these issues. Aptamers are single-stranded DNA or RNA sequences capable of undergoing selective antigen association due to three-dimensional structure formation. The use of aptamers as a target-specific moiety poses several advantages and has the potential to replace antibodies within immunoassays. Aptamers are cheaper to produce, display no batch-to-batch variation and can allow for a wide range of chemical modifications. They can help limit cross-reactivity, which is a hindrance to current forensic testing methods. Within this study, a modified Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process was used to generate aptamers against whole red blood cells. Obtained aptamer pools were analysed via massively parallel sequencing to identify viable sequences that demonstrate a high affinity for the target. Using bioinformatics platforms, aptamer candidates were identified via their enrichment profiles. Binding characterisation was also conducted on two selected aptamer candidates via fluorescent microscopy and qPCR to visualise and quantify aptamer binding. The potential for these aptamers is broad as they can be utilised within a range of bioassays for not only forensic applications but also other analytical science and medical applications. Potential future work includes the incorporation of developed aptamers into a biosensing platform that can be used at crime scenes for the real-time detection of human blood. Full article

(This article belongs to the Special Issue Aptamers: Functional and Structural Studies)

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35 pages, 11177 KiB

Open AccessArticle

Aptamer-Based Recognition of Breast Tumor Cells: A New Era for Breast Cancer Diagnosis

by Natassia Silva de Araújo, Aline dos Santos Moreira, Rayane da Silva Abreu, Valdemir Vargas Junior, Deborah Antunes, Julia Badaró Mendonça, Tayanne Felippe Sassaro, Arnon Dias Jurberg, Rafaella Ferreira-Reis, Nina Carrossini Bastos, Priscila Valverde Fernandes, Ana Carolina Ramos Guimarães, Wim Maurits Sylvain Degrave, Tatiana Martins Tilli and Mariana Caldas Waghabi

Int. J. Mol. Sci. 2024, 25(2), 840; https://doi.org/10.3390/ijms25020840 - 10 Jan 2024

Viewed by 878

Abstract

Breast cancer is one of the leading causes of death among women worldwide and can be classified into four major distinct molecular subtypes based on the expression of specific receptors. Despite significant advances, the lack of biomarkers for detailed diagnosis and prognosis remains a major challenge in the field of oncology. This study aimed to identify short single-stranded oligonucleotides known as aptamers to improve breast cancer diagnosis. The Cell-SELEX technique was used to select aptamers specific to the MDA-MB-231 tumor cell line. After selection, five aptamers demonstrated specific recognition for tumor breast cell lines and no binding to non-tumor breast cells. Validation of aptamer specificity revealed recognition of primary and metastatic tumors of all subtypes. In particular, AptaB4 and AptaB5 showed greater recognition of primary tumors and metastatic tissue, respectively. Finally, a computational biology approach was used to identify potential aptamer targets, which indicated that CSKP could interact with AptaB4. These results suggest that aptamers are promising in breast cancer diagnosis and treatment due to their specificity and selectivity. Full article

(This article belongs to the Special Issue Aptamers: Functional and Structural Studies)

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16 pages, 2009 KiB

Open AccessArticle

Simplified PCR-Based Quantification of Proteins with DNA Aptamers and Methylcellulose as a Blocking Agent

by Oleksij Redcenko, Magda Tumova and Petr Draber

Int. J. Mol. Sci. 2024, 25(1), 347; https://doi.org/10.3390/ijms25010347 - 26 Dec 2023

Viewed by 826

Abstract

Due to their unique three-dimensional structure, DNA or RNA oligonucleotide aptamers bind to various molecules with high affinity and specificity. Aptamers, alone or in combination with antibodies, can be used to sensitively quantify target molecules by quantitative real-time polymerase chain reaction (qPCR). However, the assays are often complicated and unreliable. In this study, we explored the feasibility of performing the entire assay on wells of routinely used polypropylene PCR plates. We found that polypropylene wells efficiently bind proteins. This allows the entire assay to be run in a single well. To minimize nonspecific binding of the assay components to the polypropylene wells, we tested various blocking agents and identified methylcellulose as an effective alternative to the commonly used BSA. Methylcellulose not only demonstrates comparable or superior blocking capabilities but also offers the advantage of a well-defined composition and non-animal origin. Our findings support the utilization of aptamers, either alone or in combination with antibodies, for sensitive quantification of selected molecules immobilized in polypropylene PCR wells in a streamlined one-well qPCR assay under well-defined conditions. Full article

(This article belongs to the Special Issue Aptamers: Functional and Structural Studies)

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13 pages, 3776 KiB

Open AccessArticle

Label-Free Electrochemical Aptasensor for Sensitive Detection of Malachite Green Based on AuNPs/MWCNTs@TiO₂ Nanocomposites

by Zanlin Chen, Haiming Li, Miaojia Xie, Fengguang Zhao and Shuangyan Han

Int. J. Mol. Sci. 2023, 24(13), 10594; https://doi.org/10.3390/ijms241310594 - 24 Jun 2023

Cited by 1 | Viewed by 1149

Abstract

This study proposes a label-free aptamer biosensor for the sensitive detection of malachite green(MG) using gold nanoparticles/multi-walled carbon nanotubes @ titanium dioxide(AuNPs/MWCNTs@TiO₂). The nanocomposite provides a large surface area and good electrical conductivity, improving current transfer and acting as a platform for aptamer immobilization. The aptamer and the complementary chain(cDNA) are paired by base complementary to form the recognition element and fixed on the AuNPs by sulfhydryl group, which was modified on the cDNA. Since DNA is negatively charged, the redox probe in the electrolyte is less exposed to the electrode surface under the repulsion of the negative charge, resulting in a low-electrical signal level. When MG is present, the aptamer is detached from the cDNA and binds to MG, the DNA on the electrode surface is reduced, and the rejection of the redox probe is weakened, which leads to an enhanced electrical signal and enables the detection of MG concentration by measuring the change in the electrical signal. Under the best experimental conditions, the sensor demonstrates a good linear relationship for the detection of MG from 0.01 to 1000 ng/mL, the limit of detection (LOD)is 8.68 pg/mL. This sensor is stable, specific, and reproducible, allowing for the detection of various small-molecule pollutants by changing the aptamer, providing an effective method for detecting small-molecule pollutants. Full article

(This article belongs to the Special Issue Aptamers: Functional and Structural Studies)

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Review

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22 pages, 387 KiB

Open AccessReview

Aptamers: A Cutting-Edge Approach for Gram-Negative Bacterial Pathogen Identification

by María Guadalupe Córdova-Espinoza, Rosa González-Vázquez, Rolando Rafik Barron-Fattel, Raquel Gónzalez-Vázquez, Marco Antonio Vargas-Hernández, Exsal Manuel Albores-Méndez, Ana Laura Esquivel-Campos, Felipe Mendoza-Pérez, Lino Mayorga-Reyes, María Angélica Gutiérrez-Nava, Karen Medina-Quero and Alejandro Escamilla-Gutiérrez

Int. J. Mol. Sci. 2024, 25(2), 1257; https://doi.org/10.3390/ijms25021257 - 19 Jan 2024

Viewed by 1158

Abstract

Early and accurate diagnoses of pathogenic microorganisms is essential to correctly identify diseases, treating infections, and tracking disease outbreaks associated with microbial infections, to develop precautionary measures that allow a fast and effective response in epidemics and pandemics, thus improving public health. Aptamers are a class of synthetic nucleic acid molecules with the potential to be used for medical purposes, since they can be directed towards any target molecule. Currently, the use of aptamers has increased because they are a useful tool in the detection of specific targets. We present a brief review of the use of aptamers to detect and identify bacteria or even some toxins with clinical importance. This work describes the advances in the technology of aptamers, with the purpose of providing knowledge to develop new aptamers for diagnoses and treatment of different diseases caused by infectious microorganisms. Full article

(This article belongs to the Special Issue Aptamers: Functional and Structural Studies)

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