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Current Trends in Applications of Cytosine-rich Oligonucleotides

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

Deadline for manuscript submissions: closed (1 April 2021) | Viewed by 3059

Special Issue Editors


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Guest Editor
Department of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland
Interests: G-quadruplex; DNAzyme; DNA probes; Bioassay development; bioanalysis
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Department of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland
Interests: G-quadruplex; i-motif; DNA probes; DNA-templated silver nanoclusters Bioassay development; bioanalysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Functional nucleic-acids are very attractive in terms of their applications in biotechnology and nanotechnology. Among many different types of functional nucleic acids there is growing interest in cytosine-rich oligonucleotides. A characteristic feature of oligonucleotides rich in cytosine (C-rich) is their ability to fold into a tetraplex called I-motif proceeded by cytosine protonation. The pH-dependent I-motif formation has found applications in many areas, i.e., in the design of molecular sensing devices, nanomachines, nanoswitches, electrodes, and other intelligent nanosurfaces or nanomaterials. Moreover, C-rich oligonucleotides can promote triplex structure formation and serve as efficient templates for fluorescent silver nanoclusters (AgNCs). On the other hand, C-rich sequences have been found in eukaryotic genomes, and some proteins can selectively bind I-motif structures; therefore, such sequences are biologically relevant. Recent trends concerning C-rich oligonucleotides as well as other functional nucleic acids include the diagnostic and therapeutic applications of this kind of biomaterials. This Special Issue aims to provide an opportunity to share new knowledge, developments, and applications of cytosine-rich functional nucleic acids.

Prof. Dr. Bernard Juskowiak
Dr. Anna Renata Dembska
Guest Editors

Manuscript Submission Information

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Keywords

  • Cytosine-rich oligonucleotide
  • I-motif
  • pH sensors
  • Silver nanoclusters AgNCs
  • Nanocontainers
  • Molecular logic gates
  • Fluorescence probes
  • Triplex

Published Papers (1 paper)

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Research

12 pages, 2459 KiB  
Article
Co-Localization of DNA i-Motif-Forming Sequences and 5-Hydroxymethyl-cytosines in Human Embryonic Stem Cells
by Yogini P. Bhavsar-Jog, Eric Van Dornshuld, Tracy A. Brooks, Gregory S. Tschumper and Randy M. Wadkins
Molecules 2019, 24(19), 3619; https://doi.org/10.3390/molecules24193619 - 08 Oct 2019
Cited by 4 | Viewed by 2628
Abstract
G-quadruplexes (G4s) and i-motifs (iMs) are tetraplex DNA structures. Sequences capable of forming G4/iMs are abundant near the transcription start sites (TSS) of several genes. G4/iMs affect gene expression in vitro. Depending on the gene, the presence of G4/iMs can enhance or suppress [...] Read more.
G-quadruplexes (G4s) and i-motifs (iMs) are tetraplex DNA structures. Sequences capable of forming G4/iMs are abundant near the transcription start sites (TSS) of several genes. G4/iMs affect gene expression in vitro. Depending on the gene, the presence of G4/iMs can enhance or suppress expression, making it challenging to discern the underlying mechanism by which they operate. Factors affecting G4/iM structures can provide additional insight into their mechanism of regulation. One such factor is epigenetic modification. The 5-hydroxymethylated cytosines (5hmCs) are epigenetic modifications that occur abundantly in human embryonic stem cells (hESC). The 5hmCs, like G4/iMs, are known to participate in gene regulation and are also enriched near the TSS. We investigated genomic co-localization to assess the possibility that these two elements may play an interdependent role in regulating genes in hESC. Our results indicate that amongst 15,760 G4/iM-forming locations, only 15% have 5hmCs associated with them. A detailed analysis of G4/iM-forming locations enriched in 5hmC indicates that most of these locations are in genes that are associated with cell differentiation, proliferation, apoptosis and embryogenesis. The library generated from our analysis is an important resource for investigators exploring the interdependence of these DNA features in regulating expression of selected genes in hESC. Full article
(This article belongs to the Special Issue Current Trends in Applications of Cytosine-rich Oligonucleotides)
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