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Special Issue "The Polymorphic World of G-Quadruplexes: From Structural Insights to Functional Activity-2nd Edition"

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: 30 June 2021.

Special Issue Editors

Dr. Aldo Galeone
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Guest Editor
Department of Pharmacy, Università degli Studi di Napoli Federico II, Naples, Italy
Interests: G-quadruplex; nucleic acid secondary structures; aptamers; nucleic acid chemistry
Special Issues and Collections in MDPI journals
Dr. Veronica Esposito
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Guest Editor
Department of Pharmacy, Università degli Studi di Napoli Federico II, Naples, Italy
Interests: G-quadruplex; aptamers; nucleic acid chemistry; nuclear magnetic resonance; molecular modelling
Special Issues and Collections in MDPI journals
Dr. Antonella Virgilio
Website
Guest Editor
Department of Pharmacy, Università degli Studi di Napoli Federico II, Naples, Italy
Interests: G-quadruplex; aptamers; nucleic acid chemistry; circular dichroism; electrophoresis
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

G-quadruplex structures are secondary conformations of nucleic acids, whose constitutive unit is the G-tetrad or G-quartet. This building block consists of a square planar arrangement of four guanosines, in which each base is associated to the adjacent ones through four hydrogen bonds. The stacking of two or more G-tetrad units can form larger and more stable structures. The occurrance of monovalent cations, between two adjacent G-tetrads or also in the center of a G-tetrad, further contributes to the structural stability of the G-quadruplex complexes. The biological significance of these DNA or RNA structures is witnessed by their occurrence or potential formation in several regions of the human genome, such as telomeres, genes promoters, and transcription start sites. Furthermore, they can be involved in the regulation of gene expression and telomere maintenance. However, the importance of the G-quadruplex structures is not confined to genetics and molecular biological research. In fact, thanks to their remarkable stability and outstanding variability, these structures constitute the scaffolds of several DNA or RNA aptamers, with important applications in pharmaceutics, analytics, and diagnostics. Furthermore, suitable G-quadruplexes are also endowed with catalytic properties. Moreover, considering their self-assembly properties, G-quadruplexes are often exploited in building nanostructures and in developing nanodevices.

This Special Issue will concern a selection of original research, review articles, and commentaries focused on diverse topics, with particular attention on the relationship between the structural features of the G-quadruplexes and their functional role.

Dr. Aldo Galeone
Dr. Veronica Esposito
Dr. Antonella Virgilio
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 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • G-quadruplex thermodynamics
  • G-quadruplex CD and fluorescence spectroscopy
  • G-quadruplex synthesis
  • G-quadruplex properties
  • G-quadruplex structure
  • G-quadruplex dynamics
  • G-quadruplex folding
  • G-quadruplex biological functions
  • G-quadruplex aptamers
  • G-quadruplex as a therapeutic target
  • Catalytic G-quadruplexes

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Published Papers (3 papers)

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Research

Open AccessArticle
The Functional Role of Loops and Flanking Sequences of G-Quadruplex Aptamer to the Hemagglutinin of Influenza a Virus
Int. J. Mol. Sci. 2021, 22(5), 2409; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22052409 - 27 Feb 2021
Abstract
Nucleic acid aptamers are generally accepted as promising elements for the specific and high-affinity binding of various biomolecules. It has been shown for a number of aptamers that the complexes with several related proteins may possess a similar affinity. An outstanding example is [...] Read more.
Nucleic acid aptamers are generally accepted as promising elements for the specific and high-affinity binding of various biomolecules. It has been shown for a number of aptamers that the complexes with several related proteins may possess a similar affinity. An outstanding example is the G-quadruplex DNA aptamer RHA0385, which binds to the hemagglutinins of various influenza A virus strains. These hemagglutinins have homologous tertiary structures but moderate-to-low amino acid sequence identities. Here, the experiment was inverted, targeting the same protein using a set of related, parallel G-quadruplexes. The 5′- and 3′-flanking sequences of RHA0385 were truncated to yield parallel G-quadruplex with three propeller loops that were 7, 1, and 1 nucleotides in length. Next, a set of minimal, parallel G-quadruplexes with three single-nucleotide loops was tested. These G-quadruplexes were characterized both structurally and functionally. All parallel G-quadruplexes had affinities for both recombinant hemagglutinin and influenza virions. In summary, the parallel G-quadruplex represents a minimal core structure with functional activity that binds influenza A hemagglutinin. The flanking sequences and loops represent additional features that can be used to modulate the affinity. Thus, the RHA0385–hemagglutinin complex serves as an excellent example of the hypothesis of a core structure that is decorated with additional recognizing elements capable of improving the binding properties of the aptamer. Full article
Open AccessArticle
Aptamers Against the β-Conglutin Allergen: Insights into the Behavior of the Shortest Multimeric(Intra)Molecular DNA G-Quadruplex
Int. J. Mol. Sci. 2021, 22(3), 1150; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22031150 - 24 Jan 2021
Abstract
In previous work, a 93-mer aptamer was selected against the anaphylactic allergen, β-conglutin and truncated to an 11-mer, improving the affinity by two orders of magnitude, whilst maintaining the specificity. This 11-mer was observed to fold in a G-quadruplex, and preliminary results indicated [...] Read more.
In previous work, a 93-mer aptamer was selected against the anaphylactic allergen, β-conglutin and truncated to an 11-mer, improving the affinity by two orders of magnitude, whilst maintaining the specificity. This 11-mer was observed to fold in a G-quadruplex, and preliminary results indicated the existence of a combination of monomeric and higher-order structures. Building on this previous work, in the current study, we aimed to elucidate a deeper understanding of the structural forms of this 11-mer and the effect of the structure on its binding ability. A battery of techniques including polyacrylamide gel electrophoresis, high-performance liquid chromatography in combination with electrospray ionization time-of-flight mass spectrometry, matrix-assisted laser desorption/ionization time-of-flight, thermal binding analysis, circular dichroism and nuclear magnetic resonance were used to probe the structure of both the 11-mer and the 11-mer flanked with TT- at either the 5′ or 3′ end or at both ends. The TT-tail at the 5′ end hinders stacking effects and effectively enforces the 11-mer to maintain a monomeric form. The 11-mer and the TT- derivatives of the 11-mer were also evaluated for their ability to bind its cognate target using microscale thermophoresis and surface plasmon resonance, and biolayer interferometry confirmed the nanomolar affinity of the 11-mer. All the techniques utilized confirmed that the 11-mer was found to exist in a combination of monomeric and higher-order structures, and that independent of the structural form present, nanomolar affinity was observed. Full article
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Open AccessArticle
Effect of DNA Glycosylases OGG1 and Neil1 on Oxidized G-Rich Motif in the KRAS Promoter
Int. J. Mol. Sci. 2021, 22(3), 1137; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22031137 - 24 Jan 2021
Abstract
The promoter of the Kirsten ras (KRAS) proto-oncogene contains, upstream of the transcription start site, a quadruplex-forming motif called 32R with regulatory functions. As guanine under oxidative stress can be oxidized to 8-oxoguanine (8OG), we investigated the capacity of glycosylases 8-oxoguanine [...] Read more.
The promoter of the Kirsten ras (KRAS) proto-oncogene contains, upstream of the transcription start site, a quadruplex-forming motif called 32R with regulatory functions. As guanine under oxidative stress can be oxidized to 8-oxoguanine (8OG), we investigated the capacity of glycosylases 8-oxoguanine glycosylase (OGG1) and endonuclease VIII-like 1 (Neil1) to excise 8OG from 32R, either in duplex or G-quadruplex (G4) conformation. We found that OGG1 efficiently excised 8OG from oxidized 32R in duplex but not in G4 conformation. By contrast, glycosylase Neil1 showed more activity on the G4 than the duplex conformation. We also found that the excising activity of Neil1 on folded 32R depended on G4 topology. Our data suggest that Neil1, besides being involved in base excision repair pathway (BER), could play a role on KRAS transcription. Full article
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