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

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—mole...

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Autores principales: Drees, Alissa, Trinh, Tung Lam, Fischer, Markus
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10054347/
https://www.ncbi.nlm.nih.gov/pubmed/36986556
http://dx.doi.org/10.3390/ph16030457
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author Drees, Alissa
Trinh, Tung Lam
Fischer, Markus
author_facet Drees, Alissa
Trinh, Tung Lam
Fischer, Markus
author_sort Drees, Alissa
collection PubMed
description 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.
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spelling pubmed-100543472023-03-30 The Influence of Protein Charge and Molecular Weight on the Affinity of Aptamers Drees, Alissa Trinh, Tung Lam Fischer, Markus Pharmaceuticals (Basel) Brief Report 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. MDPI 2023-03-18 /pmc/articles/PMC10054347/ /pubmed/36986556 http://dx.doi.org/10.3390/ph16030457 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Brief Report
Drees, Alissa
Trinh, Tung Lam
Fischer, Markus
The Influence of Protein Charge and Molecular Weight on the Affinity of Aptamers
title The Influence of Protein Charge and Molecular Weight on the Affinity of Aptamers
title_full The Influence of Protein Charge and Molecular Weight on the Affinity of Aptamers
title_fullStr The Influence of Protein Charge and Molecular Weight on the Affinity of Aptamers
title_full_unstemmed The Influence of Protein Charge and Molecular Weight on the Affinity of Aptamers
title_short The Influence of Protein Charge and Molecular Weight on the Affinity of Aptamers
title_sort influence of protein charge and molecular weight on the affinity of aptamers
topic Brief Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10054347/
https://www.ncbi.nlm.nih.gov/pubmed/36986556
http://dx.doi.org/10.3390/ph16030457
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