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Antibodies and Aptamers Used as Molecular Recognition Components in Sensing...
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Antibodies and Aptamers Used as Molecular Recognition Components in Sensing Platforms

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

Deadline for manuscript submissions: closed (30 September 2024) | Viewed by 10396

Special Issue Editor

Dr. Iwona Grabowska

E-Mail Website
Guest Editor
Department of Biosensors, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima Str. 10, 10-693 Olsztyn, Poland
Interests: electrochemical biosensors; redox-active layers; medical diagnostics; analytical chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The interfacial molecular recognition phenomenon is a key aspect taken into account in the developed sensor systems. The type of the probe molecule and its spatial arrangement undeniably determine the properties of the bio interface. There has been ongoing competition between antibodies and aptamers used as molecular recognition components in sensing platforms. Indeed, the number of available aptamer molecules is still insufficient to directly compare them with existing antibodies. However, due to the increasing awareness of the significant advantages of aptamers over conventional antibodies, an increasing demand for aptamer-based diagnostics is expected within the next few years. Aptamers are characterized by a high efficiency toward specific analytes, less immunogenicity as compared with antibodies, ease of synthesis and minimum cost. They can bind large and small molecules as well. On the other hand, comparative experimental studies, based on aptamers and antibodies used as molecular probes under equivalent conditions, are limited, and the results are ambiguous regarding the advantages and disadvantages of each bioreceptor type.

Considering the importance of this topic, the main goal of this Special Issue is to collect original research manuscripts or reviews, including electrochemical, optical and other existing methodologies. The purpose of this SI is to underline the efficiency of antibodies vs. aptamers used as molecular recognition components in sensing platforms.  

Dr. Iwona Grabowska
Guest Editor

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Keywords

  • aptasensors
  • immunosensors
  • electrochemical systems
  • optical systems
  • molecular recognition

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Published Papers (3 papers)

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Research

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17 pages, 3538 KiB  
Article
Novel DNA Aptamers to Dickkopf-1 Protein and Their Application in Colorimetric Sandwich Assays for Target Detection in Patients with Axial Spondyloarthritis
by Elizaveta A. Shatunova, Anastasia S. Rychkova, Mariya I. Meschaninova, Marsel R. Kabilov, Alexey E. Tupikin, Yuliya D. Kurochkina, Maksim A. Korolev and Mariya A. Vorobyeva
Int. J. Mol. Sci. 2024, 25(22), 12214; https://doi.org/10.3390/ijms252212214 - 14 Nov 2024
Viewed by 1056
Abstract
Chronic immunoinflammatory rheumatic diseases, such as axial spondyloarthritis (AxSpA), are accompanied by a dysregulation of bone remodeling. Among potential biomarkers of bone metabolism, the Wnt pathway antagonist, Dickkopf-1 (DKK-1), is of particular interest because of its potential to reflect a shift towards joint [...] Read more.
Chronic immunoinflammatory rheumatic diseases, such as axial spondyloarthritis (AxSpA), are accompanied by a dysregulation of bone remodeling. Among potential biomarkers of bone metabolism, the Wnt pathway antagonist, Dickkopf-1 (DKK-1), is of particular interest because of its potential to reflect a shift towards joint ossification or osteoporosis, but its diagnostic value needs validation. There is still a lack of stable and efficient methods of measuring serum DKK-1 levels suitable for longitude studies. The use of aptamer-based diagnostic assays could be very promising for this purpose. We generated novel anti-DKK-1 DNA aptamers from a combinatorial library with a pre-defined sequence pattern in the randomized region. This approach showed high efficacy, as only four SELEX rounds of selection produced high-affinity aptamers with dissociation constants ranging from 1.3 to 3.7 nM. A family of their truncated versions was also developed by rational design. Novel DNA aptamers functioned as capture components in a microplate ELISA-like assay with HRP-conjugated anti-DKK-1 antibody as a reporter component. We succeeded in revealing the aptamer/aptamer sandwich pairs that provided an aptamer-only sandwich colorimetric assay. The aptamer/antibody colorimetric test systems were also examined in the analyses of blood serum from AxSpA patients and shown sufficient workability. However, in a number of cases we registered significant differences between assays based on TD10 and DK4 aptamers and made some suggestions about the origin of this effect. Full article
(This article belongs to the Special Issue Antibodies and Aptamers Used as Molecular Recognition Components in Sensing Platforms)
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14 pages, 2344 KiB  
Article
Matrix Background Screening of an ssDNA Aptamer and Its Identification Against Lactopontin
by Chao Zhu, Ziru Feng, Mengmeng Yan, Hongxia Du, Tengfei Li and Jiangsheng Mao
Int. J. Mol. Sci. 2024, 25(21), 11832; https://doi.org/10.3390/ijms252111832 - 4 Nov 2024
Cited by 1 | Viewed by 1172
Abstract
Lactopontin (LPN) is a highly phosphorylated O-glycosylated acidic protein closely associated with infant gut, brain, and immune development, and its recognition is urgent due to its rising application in fortified dairy products and infant formula. In this study, an ssDNA aptamer against LPN [...] Read more.
Lactopontin (LPN) is a highly phosphorylated O-glycosylated acidic protein closely associated with infant gut, brain, and immune development, and its recognition is urgent due to its rising application in fortified dairy products and infant formula. In this study, an ssDNA aptamer against LPN was obtained, among which two kinds of matrix-background-assisted systematic evolution of ligands via exponential enrichment (SELEX) approaches were performed and compared. The direct approach was to utilize the sample matrix as the mixing-incubation background between the ssDNA library and LPN that can theoretically increase screening pressure and simulate practical application scenarios. The indirect approach was to utilize a PBS buffer as a screening background and to include counter-screening steps that adopt the “sample matrix” as a whole as the counter-screening target. Their screening evolutions were monitored through qPCR assays from sequence diversity convergences of each sub-library based on the change in the proportion of hetero- and homo-duplexes from the dissociation curve and melting temperature, which were also verified from the sequence statistics of high-throughput sequencing. The common sequence of Seq.I1II3 from the two approaches was finally fished out as the aptamer through multiple analyses of combining the sequence frequency, secondary structures, homology, and binding assessments, which was demonstrated good specificity and low-nanomolar affinity by qPCR assay (KD, 5.9 nM). In addition, molecular docking and a dynamics simulation were performed for their binding site prediction and affinity confirmation. This study provides a potential identifying element and a basis for accelerating the development of methods for LPN detection in dairy products. Full article
(This article belongs to the Special Issue Antibodies and Aptamers Used as Molecular Recognition Components in Sensing Platforms)
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Review

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27 pages, 2298 KiB  
Review
New Insights into Aptamers: An Alternative to Antibodies in the Detection of Molecular Biomarkers
by Michaela Domsicova, Jana Korcekova, Alexandra Poturnayova and Albert Breier
Int. J. Mol. Sci. 2024, 25(13), 6833; https://doi.org/10.3390/ijms25136833 - 21 Jun 2024
Cited by 19 | Viewed by 7676
Abstract
Aptamers are short oligonucleotides with single-stranded regions or peptides that recently started to transform the field of diagnostics. Their unique ability to bind to specific target molecules with high affinity and specificity is at least comparable to many traditional biorecognition elements. Aptamers are [...] Read more.
Aptamers are short oligonucleotides with single-stranded regions or peptides that recently started to transform the field of diagnostics. Their unique ability to bind to specific target molecules with high affinity and specificity is at least comparable to many traditional biorecognition elements. Aptamers are synthetically produced, with a compact size that facilitates deeper tissue penetration and improved cellular targeting. Furthermore, they can be easily modified with various labels or functional groups, tailoring them for diverse applications. Even more uniquely, aptamers can be regenerated after use, making aptasensors a cost-effective and sustainable alternative compared to disposable biosensors. This review delves into the inherent properties of aptamers that make them advantageous in established diagnostic methods. Furthermore, we will examine some of the limitations of aptamers, such as the need to engage in bioinformatics procedures in order to understand the relationship between the structure of the aptamer and its binding abilities. The objective is to develop a targeted design for specific targets. We analyse the process of aptamer selection and design by exploring the current landscape of aptamer utilisation across various industries. Here, we illuminate the potential advantages and applications of aptamers in a range of diagnostic techniques, with a specific focus on quartz crystal microbalance (QCM) aptasensors and their integration into the well-established ELISA method. This review serves as a comprehensive resource, summarising the latest knowledge and applications of aptamers, particularly highlighting their potential to revolutionise diagnostic approaches. Full article
(This article belongs to the Special Issue Antibodies and Aptamers Used as Molecular Recognition Components in Sensing Platforms)
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