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Special Issue "Aptamers: Successes, Limitations and Future Directions"

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

Deadline for manuscript submissions: 31 October 2019

Special Issue Editor

Guest Editor
Dr. Laura Cerchia

Institute of Experimental Endocrinology and Oncology "G. Salvatore" (IEOS) – National Research Council of Italy (CNR), Via S. Pansini 5, 80131 Naples, Italy
Website | E-Mail
Phone: + 39 0815455751
Interests: oligonucleotide aptamer, cell-SELEX technology, targeting delivery system, cancer biomarker discovery, cancer cell biology and signaling, targeted therapy, chemotherapy resistance, glioblastoma, triple-negative breast cancers

Special Issue Information

Dear Colleagues,

Aptamers, generated by the systematic evolution of ligands by exponential enrichment (SELEX) process, are short, artificial, single-stranded oligonucleotides that, similarly to antibodies, interact at high affinity with their targets by recognizing a specific three-dimensional structure. They offer suitable features for analytical, diagnostic, and therapeutic applications, including easy manufacturing and great reproducibility from batch-to-batch, structural stability, and low/absent immunogenicity. Because of their nucleic acid nature, the rational design of advanced strategies to manipulate aptamers for wide-ranging applications is greatly simplified over antibodies.

This Special Issue will include original research articles and review articles on all aspects of aptamer research, including aptamer selection technology, engineering/modification strategies, analytical applications, imaging modalities, nanotechnology, diagnostics, and therapeutics. It aims to attract contributions highlighting problems, solutions, and future directions in the development of aptamers as molecular recognition elements from basic research toward diverse commercial applications.

Dr. Laura Cerchia
Guest Editor

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 semimonthly 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
  • Aptamer diagnostics
  • Aptamer therapeutics
  • Aptamer imaging
  • Aptamer sensors
  • Aptamer nanotechnology
  • Aptamer nanomedicine
  • Targeted delivery systems
  • SELEX

Published Papers (2 papers)

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Research

Jump to: Review

Open AccessArticle
Energy Transfer as A Driving Force in Nucleic Acid–Protein Interactions
Molecules 2019, 24(7), 1443; https://doi.org/10.3390/molecules24071443
Received: 11 March 2019 / Revised: 10 April 2019 / Accepted: 11 April 2019 / Published: 11 April 2019
PDF Full-text (1992 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Many nucleic acid–protein structures have been resolved, though quantitative structure-activity relationship remains unclear in many cases. Thrombin complexes with G-quadruplex aptamers are striking examples of a lack of any correlation between affinity, interface organization, and other common parameters. Here, we tested the hypothesis [...] Read more.
Many nucleic acid–protein structures have been resolved, though quantitative structure-activity relationship remains unclear in many cases. Thrombin complexes with G-quadruplex aptamers are striking examples of a lack of any correlation between affinity, interface organization, and other common parameters. Here, we tested the hypothesis that affinity of the aptamer–protein complex is determined with the capacity of the interface to dissipate energy of binding. Description and detailed analysis of 63 nucleic acid–protein structures discriminated peculiarities of high-affinity nucleic acid–protein complexes. The size of the amino acid sidechain in the interface was demonstrated to be the most significant parameter that correlates with affinity of aptamers. This observation could be explained in terms of need of efficient energy transfer from interacting residues. Application of energy dissipation theory provided an illustrative tool for estimation of efficiency of aptamer–protein complexes. These results are of great importance for a design of efficient aptamers. Full article
(This article belongs to the Special Issue Aptamers: Successes, Limitations and Future Directions)
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Review

Jump to: Research

Open AccessReview
Recent Advances in Aptamer Discovery and Applications
Molecules 2019, 24(5), 941; https://doi.org/10.3390/molecules24050941
Received: 25 January 2019 / Revised: 3 March 2019 / Accepted: 4 March 2019 / Published: 7 March 2019
Cited by 1 | PDF Full-text (3324 KB) | HTML Full-text | XML Full-text
Abstract
Aptamers are short, single-stranded DNA, RNA, or synthetic XNA molecules that can be developed with high affinity and specificity to interact with any desired targets. They have been widely used in facilitating discoveries in basic research, ensuring food safety and monitoring the environment. [...] Read more.
Aptamers are short, single-stranded DNA, RNA, or synthetic XNA molecules that can be developed with high affinity and specificity to interact with any desired targets. They have been widely used in facilitating discoveries in basic research, ensuring food safety and monitoring the environment. Furthermore, aptamers play promising roles as clinical diagnostics and therapeutic agents. This review provides update on the recent advances in this rapidly progressing field of research with particular emphasis on generation of aptamers and their applications in biosensing, biotechnology and medicine. The limitations and future directions of aptamers in target specific delivery and real-time detection are also discussed. Full article
(This article belongs to the Special Issue Aptamers: Successes, Limitations and Future Directions)
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Graphical abstract

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

  1. Author: J. Carlos Penedo

Affiliation: University of St Andrews, SUPA School of Physics and Astronomy, St. Andrews, United Kingdom

  1. Type of the paper: Review

Tentative title: G-quadruplex-forming aptamers – characteristics, applications and perspectives

Authors: Carolina Roxo, Weronika Kotkowiak, Anna Pasternak

Affiliations: Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, PAS, Poznan, Poland

3. Type of the paper: review
Authors: Natalia Komarova, Alexander Kuznetsov
Affiliation: Scientific-Manufacturing Complex Technological Centre, 1–7 Shokin Square, Zelenograd, 124498 Moscow, Russia
  1. Author: Yu. Ivanov, Tatyana Pleshakova

Affiliation: Bonn Pharmazeutisches Institut, Rheinische Friedrich-Wilhelms-Universität

Title: Aptamers for detection of Hepatite C virus particals by silicon nanowire field-effect-transistor

  1. Authors: Walhan Alshaer 1,*, Mohammad Ismail 2, Ezzaldin Alesawi 2, Hamdi Al Nusirat 3, Said I. Ismail 2,4

Affiliation: 1.Cell Therapy Center, The University of Jordan, Amman, Jordan; 2. Faculty of Medicine, The University of Jordan, Amman, Jordan; 3. Faculty of Science, The University of Jordan, Amman, Jordan; 4. Qatar Genome Project, Qatar Foundation, Doha, Qatar

Abstract: Soon after they were first described in 1990, Aptamers we largely recognized as a new class of biological ligands that can rival antibodies in various analytical, diagnostic and therapeutic applications. Aptamers are short single stranded RNA or DNA oligonucleotides capable of folding into complex 3D structures, enabling them to bind a large variety of target molecules ranging from small ions to whole cells. Their high binding specificity and affinity is comparable to antibodies but they are superior with regards to being easy to manufacture, having a long shelf life, simplistic chemical modification, in addition to low toxicity and immunogenicity.  In the past 3 decades, aptamers have been used in a plethora of therapeutic and drug delivery systems that involve innovative delivery mechanisms and carrying various types of drug cargos. However, the successful translation of aptamers research from bench- to bedside has been challenged by several limitations that slowdown the realization of the promising aptamers applications as therapeutics at the clinical level. The main limitations include the susceptibility for degradation by nucleases, fast renal clearance, low thermal stability, and the limited functional groups diversity. The salvation of such limitations can be in the chemistry of aptamers. The currentreview will focus on the recent arts of aptamers chemistry that have been evolved to refine the pharmacological properties of aptamers. Moreover, this review will analyze advantages and disadvantages of such chemical modifications and how they impact the pharmacological properties of aptamers. Finally, this review will end with future directions that may improve the applications of aptamers in therapeutics.

Keywords: Aptamers, Drug delivery, Nanocarriers, chemical modifications.

  1. Author: Maria DeRosa

Affiliation: Chemistry Department, Carleton University, Ottawa, Ontario, Canada

7. Author: Sarah Shigdar

Affiliation: School of Medicine Deakin University, Geelong, Victoria 3128, Australia


 

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