Engineering Aptamers for Biomedical Applications II

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Cell Biology and Pathology".

Deadline for manuscript submissions: closed (15 February 2021) | Viewed by 21522

Special Issue Editors


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Guest Editor
Istituto per l'Endocrinologia e Oncologia Sperimentale "G. Salvatore", Via Tommaso De Amicis 95 Via S. Pansini 5, 80145 Naples, Italy
Interests: RNA therapeutics; delivery of nucleic acid therapeutics; aptamer; tumor microenvironment; signal transduction; microRNA; targeted therapy
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Guest Editor
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Akademgorodok 50, 660036 Krasnoyarsk, Russia
Interests: aptamer selection; characterization; applications for clinics

Special Issue Information

Dear Colleagues,

This Special Issue, “Engineering Aptamers for Biomedical Applications II”, will mainly focus on the more recent advances in the development of highly stable and specific aptamers suitable as therapeutic and diagnostic agents.

The introduction of modifications in the nucleic acids backbone, the expansion of genetic variability in nucleobases, and the generation of enzymes able to catalyze the synthesis of modified aptamers is revealing as invaluable advantage in the design of aptamer ligands in biomedicine. Aptamers obtained with nucleic acid variants exhibit high stability in circulating fluids, target binding affinity, and specificity, thus potentially improving their applicability as therapeutics and/or as diagnostic tools.

We cordially invite authors in the field to submit original research or review articles pertaining to this important and fast-progressing field of biomedicine.

Dr. Vittorio de Franciscis
Dr. Anna Kichkailo
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 submissions that pass pre-check are 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. Biomedicines 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 2600 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

  • Aptamer probes and therapeutics;
  • Biosensors;
  • ODN nanotechnology;
  • Ribozymes/DNAzymes evolution;
  • Combinatorial therapy;
  • Molecular evolution;
  • Expanded genetics

Published Papers (5 papers)

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Research

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12 pages, 1121 KiB  
Article
Evaluation of Aptamers as Affinity Reagents for an Enhancement of SRM-Based Detection of Low-Abundance Proteins in Blood Plasma
by Sergey Radko, Konstantin Ptitsyn, Svetlana Novikova, Yana Kiseleva, Alexander Moysa, Leonid Kurbatov, Maria Mannanova, Victor Zgoda, Elena Ponomarenko, Andrey Lisitsa and Alexander Archakov
Biomedicines 2020, 8(5), 133; https://doi.org/10.3390/biomedicines8050133 - 24 May 2020
Cited by 3 | Viewed by 2866
Abstract
Selected reaction monitoring (SRM) is a mass spectrometric technique characterized by the exceptionally high selectivity and sensitivity of protein detection. However, even with this technique, the quantitative detection of low- and ultralow-abundance proteins in blood plasma, which is of great importance for the [...] Read more.
Selected reaction monitoring (SRM) is a mass spectrometric technique characterized by the exceptionally high selectivity and sensitivity of protein detection. However, even with this technique, the quantitative detection of low- and ultralow-abundance proteins in blood plasma, which is of great importance for the search and verification of novel protein disease markers, is a challenging task due to the immense dynamic range of protein abundance levels. One approach used to overcome this problem is the immunoaffinity enrichment of target proteins for SRM analysis, employing monoclonal antibodies. Aptamers appear as a promising alternative to antibodies for affinity enrichment. Here, using recombinant protein SMAD4 as a model target added at known concentrations to human blood plasma and SRM as a detection method, we investigated a relationship between the initial amount of the target protein and its amount in the fraction enriched with SMAD4 by an anti-SMAD4 DNA-aptamer immobilized on magnetic beads. It was found that the aptamer-based enrichment provided a 30-fold increase in the sensitivity of SRM detection of SMAD4. These results indicate that the aptamer-based affinity enrichment of target proteins can be successfully employed to improve quantitative detection of low-abundance proteins by SRM in undepleted human blood plasma. Full article
(This article belongs to the Special Issue Engineering Aptamers for Biomedical Applications II)
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13 pages, 3459 KiB  
Article
Aptamer-Conjugated Tb(III)-Doped Silica Nanoparticles for Luminescent Detection of Leukemia Cells
by Yaroslav A. Grechkin, Svetlana L. Grechkina, Emil A. Zaripov, Svetlana V. Fedorenko, Asiya R. Mustafina and Maxim V. Berezovski
Biomedicines 2020, 8(1), 14; https://doi.org/10.3390/biomedicines8010014 - 13 Jan 2020
Cited by 16 | Viewed by 4000
Abstract
DNA aptamers have many benefits for cell imaging, such as high affinity and specificity, easiness of chemical functionalization, and low cost of production. Among known aptamers, Sgc8-aptamer was selected against acute lymphoblastic leukemia cells with a dissociation constant in a nanomolar range. The [...] Read more.
DNA aptamers have many benefits for cell imaging, such as high affinity and specificity, easiness of chemical functionalization, and low cost of production. Among known aptamers, Sgc8-aptamer was selected against acute lymphoblastic leukemia cells with a dissociation constant in a nanomolar range. The aptamer was previously used for the covalent coupling with fluorescent and magnetic nanoparticles, as well as for the fabrication of aptamer-based biosensors. Among commonly used fluorescent tags, lanthanide nanoparticles offer stable luminescence with narrow, well-resolved emission peaks and the absence of photoblinking. In other words, lanthanide nanoparticles could serve as luminescence reporters and be used in biosensing. In our study, we conjugated amino- and carboxyl-modified silica-coated terbium (III) thiacalix[4]arenesulfonate luminescent nanoparticles with Sgc8-aptamer and showed the ability of the aptamer-conjugated nanoparticles to detect leukemia cells using fluorescence microscopy. In addition, we conducted a cell viability assay and confirmed that the nanoparticles do not induce spontaneous cell apoptosis or necrosis and could be potentially used for bioimaging applications. Full article
(This article belongs to the Special Issue Engineering Aptamers for Biomedical Applications II)
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Review

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20 pages, 904 KiB  
Review
Non-Invasive Delivery of Therapeutics into the Brain: The Potential of Aptamers for Targeted Delivery
by Bakhtiar Bukari, Rasika M. Samarasinghe, Jinjutha Noibanchong and Sarah L. Shigdar
Biomedicines 2020, 8(5), 120; https://doi.org/10.3390/biomedicines8050120 - 14 May 2020
Cited by 29 | Viewed by 4395
Abstract
The blood-brain barrier (BBB) is a highly specialised network of blood vessels that effectively separates the brain environment from the circulatory system. While there are benefits, in terms of keeping pathogens from entering the brain, the BBB also complicates treatments of brain pathologies [...] Read more.
The blood-brain barrier (BBB) is a highly specialised network of blood vessels that effectively separates the brain environment from the circulatory system. While there are benefits, in terms of keeping pathogens from entering the brain, the BBB also complicates treatments of brain pathologies by preventing efficient delivery of macromolecular drugs to diseased brain tissue. Although current non-invasive strategies of therapeutics delivery into the brain, such as focused ultrasound and nanoparticle-mediated delivery have shown various levels of successes, they still come with risks and limitations. This review discusses the current approaches of therapeutic delivery into the brain, with a specific focus on non-invasive methods. It also discusses the potential for aptamers as alternative delivery systems and several reported aptamers with promising preliminary results. Full article
(This article belongs to the Special Issue Engineering Aptamers for Biomedical Applications II)
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14 pages, 1723 KiB  
Review
Aptamers Increase Biocompatibility and Reduce the Toxicity of Magnetic Nanoparticles Used in Biomedicine
by Galina S. Zamay, Tatiana N. Zamay, Kirill A. Lukyanenko and Anna S. Kichkailo
Biomedicines 2020, 8(3), 59; https://doi.org/10.3390/biomedicines8030059 - 14 Mar 2020
Cited by 33 | Viewed by 5063
Abstract
Aptamer-based approaches are very promising tools in nanomedicine. These small single-stranded DNA or RNA molecules are often used for the effective delivery and increasing biocompatibility of various therapeutic agents. Recently, magnetic nanoparticles (MNPs) have begun to be successfully applied in various fields of [...] Read more.
Aptamer-based approaches are very promising tools in nanomedicine. These small single-stranded DNA or RNA molecules are often used for the effective delivery and increasing biocompatibility of various therapeutic agents. Recently, magnetic nanoparticles (MNPs) have begun to be successfully applied in various fields of biomedicine. The use of MNPs is limited by their potential toxicity, which depends on their biocompatibility. The functionalization of MNPs by ligands increases biocompatibility by changing the charge and shape of MNPs, preventing opsonization, increasing the circulation time of MNPs in the blood, thus shielding iron ions and leading to the accumulation of MNPs only in the necessary organs. Among various ligands, aptamers, which are synthetic analogs of antibodies, turned out to be the most promising for the functionalization of MNPs. This review describes the factors that determine MNPs’ biocompatibility and affect their circulation time in the bloodstream, biodistribution in organs and tissues, and biodegradation. The work also covers the role of the aptamers in increasing MNPs’ biocompatibility and reducing toxicity. Full article
(This article belongs to the Special Issue Engineering Aptamers for Biomedical Applications II)
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15 pages, 11061 KiB  
Review
A Mini-Review: Clinical Development and Potential of Aptamers for Thrombotic Events Treatment and Monitoring
by Alex T. Ponce and Ka Lok Hong
Biomedicines 2019, 7(3), 55; https://doi.org/10.3390/biomedicines7030055 - 26 Jul 2019
Cited by 26 | Viewed by 4400
Abstract
The unique opportunity for aptamer uses in thrombotic events has sparked a considerable amount of research in the area. The short half-lives of unmodified aptamers in vivo remain one of the major challenges in therapeutic aptamers. Much of the incremental successful therapeutic aptamer [...] Read more.
The unique opportunity for aptamer uses in thrombotic events has sparked a considerable amount of research in the area. The short half-lives of unmodified aptamers in vivo remain one of the major challenges in therapeutic aptamers. Much of the incremental successful therapeutic aptamer stories were due to modifications in the aptamer bases. This mini-review briefly summarizes the successes and challenges in the clinical development of aptamers for thrombotic events, and highlights some of the most recent developments in using aptamers for anticoagulation monitoring. Full article
(This article belongs to the Special Issue Engineering Aptamers for Biomedical Applications II)
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