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Beyond the Canonical DNA Double-Helix: Supramolecular Assemblies of Chemically Modified...
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Beyond the Canonical DNA Double-Helix: Supramolecular Assemblies of Chemically Modified Nucleic Acids and their Applications

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

Deadline for manuscript submissions: closed (15 October 2021) | Viewed by 14113

Special Issue Editor

Dr. Arnaud Gissot

E-Mail Website
Guest Editor
CNRS, INSERM, ARNA, UMR 5320, U1212, Université de Bordeaux, F-33000 Bordeaux, France
Interests: nucleic acids; amphiphiles; supramolecular assemblies; organic synthesis

Special Issue Information

Dear Colleagues,

Nucleic acids and more particularly DNA are central for life on Earth. Beyond the central dogma of molecular biology that converts the double-stranded DNA into mRNAs followed by proteins, nucleic acids were later found to serve many other roles such as enzymes (ribozymes), receptors (natural riboswitchs and artificial aptamers) and regulators of genetic expression (RNA interference, antisense, etc.). Many of these phenomena do not necessarily rely on the traditional Watson–Crick base pairing scheme. While the level of control and complexity achieved by nature in the building of nucleic acid-based supramolecular assemblies is outstanding, chemists have long sought to improve or impart these assemblies with new properties through chemical modification and/or conjugation to other molecules. This Special Issue intends to cover all aspects of chemically modified supramolecular assemblies of artificial nucleic acids and their applications that do not primarily capitalize on conventional Watson–Crick base pairing; or when the biophysics of the DNA duplexes are purposely altered—for instance, in nanoparticle–DNA conjugates. The topics covered range from the design and biophysics of such artificial systems based on both hard and soft matter to their application in diagnosis, catalysis, biomedical devices, etc.

Dr. Arnaud Gissot
Guest Editor

Manuscript Submission Information

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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.

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Keywords

  • DNA
  • RNA
  • Chemically modified nucleic acids
  • Conjugated nucleic acids
  • Supramolecular assemblies
  • Soft matter
  • Nanoparticle–DNA conjugates
  • G-quadruplex
  • i-motif
  • Aptamers
  • Triplex
  • Origami
  • Spherical nucleic acids
  • Diagnosis
  • Biophysics
  • Molecular recognition
  • DNA/RNAzyme

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Published Papers (3 papers)

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Research

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17 pages, 48624 KiB  
Article
Unified Nanotechnology Format: One Way to Store Them All
by David Kuťák, Erik Poppleton, Haichao Miao, Petr Šulc and Ivan Barišić
Molecules 2022, 27(1), 63; https://doi.org/10.3390/molecules27010063 - 23 Dec 2021
Cited by 7 | Viewed by 4278
Abstract
The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate [...] Read more.
The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle. Full article
(This article belongs to the Special Issue Beyond the Canonical DNA Double-Helix: Supramolecular Assemblies of Chemically Modified Nucleic Acids and their Applications)
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23 pages, 4293 KiB  
Article
A Combined Experimental and Computational Study of Halogen and Hydrogen Bonding in Molecular Salts of 5-Bromocytosine
by Massimiliano Aschi, Giorgia Toto Brocchi and Gustavo Portalone
Molecules 2021, 26(11), 3111; https://doi.org/10.3390/molecules26113111 - 23 May 2021
Cited by 1 | Viewed by 4209
Abstract
Although natural or artificial modified pyrimidine nucleobases represent important molecules with valuable properties as constituents of DNA and RNA, no systematic analyses of the structural aspects of bromo derivatives of cytosine have appeared so far in the literature. In view of the biochemical [...] Read more.
Although natural or artificial modified pyrimidine nucleobases represent important molecules with valuable properties as constituents of DNA and RNA, no systematic analyses of the structural aspects of bromo derivatives of cytosine have appeared so far in the literature. In view of the biochemical and pharmaceutical relevance of these compounds, six different crystals containing proton-transfer derivatives of 5-bromocytosine are prepared and analyzed in the solid-state by single crystal X-ray diffraction. All six compounds are organic salts, with proton transfer occurring to the Nimino atom of the pyridine ring. Experimental results are then complemented with Hirshfeld surface analysis to quantitively evaluate the contribution of different intermolecular interactions in the crystal packing. Furthermore, theoretical calculations, based on different arrangements of molecules extracted from the crystal structure determinations, are carried out to analyze the formation mechanism of halogen bonds (XBs) in these compounds and provide insights into the nature and strength of the observed interactions. The results show that the supramolecular architectures of the six molecular salts involve extensive classical intermolecular hydrogen bonds. However, in all but one proton-transfer adducts, weak to moderate XBs are revealed by C–Br…O short contacts between the bromine atom in the fifth position, which acts as XB donor (electron acceptor). Moreover, the lone pair electrons of the oxygen atom of adjacent pyrimidine nucleobases and/or counterions or water molecules, which acts as XB acceptor (electron donor). Full article
(This article belongs to the Special Issue Beyond the Canonical DNA Double-Helix: Supramolecular Assemblies of Chemically Modified Nucleic Acids and their Applications)
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Review

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22 pages, 5722 KiB  
Review
Roles of G4-DNA and G4-RNA in Class Switch Recombination and Additional Regulations in B-Lymphocytes
by Ophélie Dézé, Brice Laffleur and Michel Cogné
Molecules 2023, 28(3), 1159; https://doi.org/10.3390/molecules28031159 - 24 Jan 2023
Cited by 7 | Viewed by 4775
Abstract
Mature B cells notably diversify immunoglobulin (Ig) production through class switch recombination (CSR), allowing the junction of distant “switch” (S) regions. CSR is initiated by activation-induced deaminase (AID), which targets cytosines adequately exposed within single-stranded DNA of transcribed targeted S regions, with a [...] Read more.
Mature B cells notably diversify immunoglobulin (Ig) production through class switch recombination (CSR), allowing the junction of distant “switch” (S) regions. CSR is initiated by activation-induced deaminase (AID), which targets cytosines adequately exposed within single-stranded DNA of transcribed targeted S regions, with a specific affinity for WRCY motifs. In mammals, G-rich sequences are additionally present in S regions, forming canonical G-quadruplexes (G4s) DNA structures, which favor CSR. Small molecules interacting with G4-DNA (G4 ligands), proved able to regulate CSR in B lymphocytes, either positively (such as for nucleoside diphosphate kinase isoforms) or negatively (such as for RHPS4). G4-DNA is also implicated in the control of transcription, and due to their impact on both CSR and transcriptional regulation, G4-rich sequences likely play a role in the natural history of B cell malignancies. Since G4-DNA stands at multiple locations in the genome, notably within oncogene promoters, it remains to be clarified how it can more specifically promote legitimate CSR in physiology, rather than pathogenic translocation. The specific regulatory role of G4 structures in transcribed DNA and/or in corresponding transcripts and recombination hereby appears as a major issue for understanding immune responses and lymphomagenesis. Full article
(This article belongs to the Special Issue Beyond the Canonical DNA Double-Helix: Supramolecular Assemblies of Chemically Modified Nucleic Acids and their Applications)
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