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Chemistry of Nucleic Acids: From Structure to Biological Interactions

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 818

Special Issue Editors


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Guest Editor
Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
Interests: ruthenium complexes; platinum complexes; benzodifuran compounds; anticancer drugs; nanosystems; nanomaterials; oligonucleotides; G-quadruplex; aptamers; thrombin binding aptamers
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Guest Editor Assistant
Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
Interests: oligonucleotides; G-quadruplex; aptamers; proteins; nanosystems; interactions; anticancer drugs

Special Issue Information

Dear Colleagues,

Nucleic acids, primarily DNA and RNA, are versatile structures crucial for cellular function and regulation as well as for genetic information storage and transmission. Beyond their well-known canonical structures, such as the double helix of DNA and the single-stranded form of RNA, these molecules exhibit a wide range of noncanonical conformations, including G-quadruplexes, i-motifs, and triplexes, which are essential for biological regulation and interaction with other biomolecules.

The chemistry of nucleic acid structures can influence their biological activities and interactions with proteins, lipids, small molecules, and other nucleic acids. Understanding these interactions is crucial for developing novel therapeutic approaches and gaining deeper insights into cellular processes.

In addition, nucleic acids can themselves be therapeutic agents, which act as aptamers, and, thus, binds to high-affinity specific protein targets involved in the most important diseases.

This Special Issue of Molecules will include both regular articles and reviews, and it aims to explore the latest advancements in the chemical understanding of nucleic acids, from their intrinsic structural features to their dynamic interactions with other biomolecules. This Special Issue will focus on both canonical and noncanonical nucleic acid structures, highlighting their roles in cellular processes and therapeutic applications.

Contributions dealing with nucleic acid structure, stability, and interactions with other biomolecules are of great relevance to this Special Issue. Studies concerning nucleic acids with potential applications in therapy, diagnostics, and analytics are particularly welcome. Contributions focused on the molecular mechanisms that govern nucleic acid folding, stability, and recognition will be also highly appreciated.

Topics of interest for this Special Issue include, but are not limited to, the following:

  • chemistry of nucleic acids;
  • synthesis/improvement of nucleic acid structures;
  • physicochemical studies, thermodynamics, and kinetics of nucleic acids;
  • aptamers and their functional role in aptamer-related diseases;
  • interactions of nucleic acid structures with other components, ranging from small molecules to large proteins;
  • nucleic acids in the development of drug delivery systems.

Dr. Claudia Riccardi
Guest Editor

Dr. Federica D'Aria
Guest Editor Assistant

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. 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 2700 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

  • nucleic acid structures and function
  • modified nucleic acids
  • nucleic acid-targeting ligands
  • physicochemical studies of nucleic acids
  • thermodynamics and kinetics of nucleic acid structures
  • structure–function relationship of nucleic acids
  • nucleic acid–protein interactions
  • aptamers

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Published Papers (1 paper)

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Research

21 pages, 4223 KiB  
Article
Exploring the G-Quadruplex Formation of AS1411 Derivatives
by Pedro Lourenço, David Moreira, André Miranda, Jéssica Lopes-Nunes, Izamara Maocha, Tiago Santos, Pedro L. Ferreira, Fani Sousa, Artur Paiva and Carla Cruz
Molecules 2025, 30(8), 1673; https://doi.org/10.3390/molecules30081673 - 8 Apr 2025
Viewed by 371
Abstract
AS1411 is a G-quadruplex (G4) aptamer that binds tightly to nucleolin (NCL) on the cell surface and has shown strong anticancer effects. However, this aptamer is highly polymorphic, presenting different types of G4s, which may hinder its preclinical application. Several modifications have been [...] Read more.
AS1411 is a G-quadruplex (G4) aptamer that binds tightly to nucleolin (NCL) on the cell surface and has shown strong anticancer effects. However, this aptamer is highly polymorphic, presenting different types of G4s, which may hinder its preclinical application. Several modifications have been made to decrease the polymorphism of this aptamer. In this work, we designed six AS1411 derivatives by substituting guanine with thymine in the central linker and modifying the number of thymines either in the linker itself and/or at both ends of the sequence. The G4 formation, stability, and NCL binding were evaluated by several biophysical techniques and computational and cell studies. Overall, a decrease in polymorphism of G4-forming sequences compared to AS1411 is observed by size exclusion chromatography (SEC) and circular dichroism (CD) spectroscopy in the presence of potassium salt. The melting experiments reveal a higher ability of the derivatives without thymine at both sequence ends to form a G4, consistent with the G4H score predictions. Additionally, it is possible to conclude that deletions of T in the central core increase the ability to form G4. Moreover, the AS1411 derivatives bind NCL with high affinity (KD values in the 10−9 M range), particularly the sequences with only thymine modifications in the central linker. In silico studies reveal structural insights and demonstrate that AS1411 derivatives interact with NCL, establishing multiple interactions with the different domains, thereby further supporting the experimental findings. By using a lung cancer cell line with high cell surface NCL expression, we evaluate the internalization and uptake of AS1411 derivatives, identifying the derivative-lacking thymines in the central core as the ones with the highest internalization and cellular uptake. Full article
(This article belongs to the Special Issue Chemistry of Nucleic Acids: From Structure to Biological Interactions)
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