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Nucleosides and Nucleotides
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Nucleosides and Nucleotides

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

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 23715

Special Issue Editor

Dr. David R. W. Hodgson

E-Mail Website
Guest Editor
Department of Chemistry, Durham University, Lower Mountjoy, Stockton Road, Durham DH1 3LE, UK
Interests: nucleosides; nucleotides; DNA; RNA; mechanism; bioconjugation; physical organic; kinetics

Special Issue Information

Dear Colleagues,

Nucleosides and nucleotides continue to underpin key areas of medicinal chemistry; chemical biology; biotechnology; and, more recently, synthetic biology and nucleic acids-based materials. The preparation of nucleoside-based antivirals is even more pertinent in the current climate, alongside nucleic acids-based technologies that provide the foundations for the detection of viral infections. Despite this plethora of critical applications, the chemistry of nucleoside and nucleotide transformations remains challenging, and this Special Issue aims to share new synthetic insights and applications of nucleoside and nucleotide chemistry.

Dr. David R. W. Hodgson
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.

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

  • Synthesis of nucleosides, nucleotides, and their analogues
  • Phosphorus chemistry—preparation of (poly)phosphates and analogues
  • Chemical biology of nucleosides and nucleotides—applications towards biological challenges
  • Medicinal chemistry

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Published Papers (5 papers)

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Research

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16 pages, 2808 KiB  
Article
Synthesis of Polyanionic C5-Modified 2′-Deoxyuridine and 2′-Deoxycytidine-5′-Triphosphates and Their Properties as Substrates for DNA Polymerases
by Claire Dutson, Esther Allen, Mark J. Thompson, Joseph H. Hedley, Heather E. Murton and David M. Williams
Molecules 2021, 26(8), 2250; https://doi.org/10.3390/molecules26082250 - 13 Apr 2021
Cited by 5 | Viewed by 2599
Abstract
Modified 2′-deoxyribonucleotide triphosphates (dNTPs) have widespread applications in both existing and emerging biomolecular technologies. For such applications it is an essential requirement that the modified dNTPs be substrates for DNA polymerases. To date very few examples of C5-modified dNTPs bearing negatively charged functionality [...] Read more.
Modified 2′-deoxyribonucleotide triphosphates (dNTPs) have widespread applications in both existing and emerging biomolecular technologies. For such applications it is an essential requirement that the modified dNTPs be substrates for DNA polymerases. To date very few examples of C5-modified dNTPs bearing negatively charged functionality have been described, despite the fact that such nucleotides might potentially be valuable in diagnostic applications using Si-nanowire-based detection systems. Herein we have synthesised C5-modified dUTP and dCTP nucleotides each of which are labelled with an dianionic reporter group. The reporter group is tethered to the nucleobase via a polyethylene glycol (PEG)-based linkers of varying length. The substrate properties of these modified dNTPs with a variety of DNA polymerases have been investigated to study the effects of varying the length and mode of attachment of the PEG linker to the nucleobase. In general, nucleotides containing the PEG linker tethered to the nucleobase via an amide rather than an ether linkage proved to be the best substrates, whilst nucleotides containing PEG linkers from PEG6 to PEG24 could all be incorporated by one or more DNA polymerase. The polymerases most able to incorporate these modified nucleotides included Klentaq, Vent(exo-) and therminator, with incorporation by Klenow(exo-) generally being very poor. Full article
(This article belongs to the Special Issue Nucleosides and Nucleotides)
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25 pages, 2243 KiB  
Article
Probing the Binding Requirements of Modified Nucleosides with the DNA Nuclease SNM1A
by Eva-Maria Dürr and Joanna F. McGouran
Molecules 2021, 26(2), 320; https://doi.org/10.3390/molecules26020320 - 9 Jan 2021
Cited by 6 | Viewed by 3281
Abstract
SNM1A is a nuclease that is implicated in DNA interstrand crosslink repair and, as such, its inhibition is of interest for overcoming resistance to chemotherapeutic crosslinking agents. However, the number and identity of the metal ion(s) in the active site of SNM1A are [...] Read more.
SNM1A is a nuclease that is implicated in DNA interstrand crosslink repair and, as such, its inhibition is of interest for overcoming resistance to chemotherapeutic crosslinking agents. However, the number and identity of the metal ion(s) in the active site of SNM1A are still unconfirmed, and only a limited number of inhibitors have been reported to date. Herein, we report the synthesis and evaluation of a family of malonate-based modified nucleosides to investigate the optimal positioning of metal-binding groups in nucleoside-derived inhibitors for SNM1A. These compounds include ester, carboxylate and hydroxamic acid malonate derivatives which were installed in the 5′-position or 3′-position of thymidine or as a linkage between two nucleosides. Evaluation as inhibitors of recombinant SNM1A showed that nine of the twelve compounds tested had an inhibitory effect at 1 mM concentration. The most potent compound contains a hydroxamic acid malonate group at the 5′-position. Overall, our studies advance the understanding of requirements for nucleoside-derived inhibitors for SNM1A and indicate that groups containing a negatively charged group in close proximity to a metal chelator, such as hydroxamic acid malonates, are promising structures in the design of inhibitors. Full article
(This article belongs to the Special Issue Nucleosides and Nucleotides)
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Review

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21 pages, 3116 KiB  
Review
Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies
by Lukasz T. Olenginski, Kehinde M. Taiwo, Regan M. LeBlanc and Theodore K. Dayie
Molecules 2021, 26(18), 5581; https://doi.org/10.3390/molecules26185581 - 14 Sep 2021
Cited by 8 | Viewed by 3629
Abstract
RNA structural research lags behind that of proteins, preventing a robust understanding of RNA functions. NMR spectroscopy is an apt technique for probing the structures and dynamics of RNA molecules in solution at atomic resolution. Still, RNA analysis by NMR suffers from spectral [...] Read more.
RNA structural research lags behind that of proteins, preventing a robust understanding of RNA functions. NMR spectroscopy is an apt technique for probing the structures and dynamics of RNA molecules in solution at atomic resolution. Still, RNA analysis by NMR suffers from spectral overlap and line broadening, both of which worsen for larger RNAs. Incorporation of stable isotope labels into RNA has provided several solutions to these challenges. In this review, we summarize the benefits and limitations of various methods used to obtain isotope-labeled RNA building blocks and how they are used to prepare isotope-labeled RNA for NMR structure and dynamics studies. Full article
(This article belongs to the Special Issue Nucleosides and Nucleotides)
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14 pages, 9176 KiB  
Review
Site-Specific Fluorescent Labeling of RNA Interior Positions
by Barry S. Cooperman
Molecules 2021, 26(5), 1341; https://doi.org/10.3390/molecules26051341 - 3 Mar 2021
Cited by 3 | Viewed by 3257
Abstract
The introduction of fluorophores into RNA for both in vitro and in cellulo studies of RNA function and cellular distribution is a subject of great current interest. Here I briefly review methods, some well-established and others newly developed, which have been successfully exploited [...] Read more.
The introduction of fluorophores into RNA for both in vitro and in cellulo studies of RNA function and cellular distribution is a subject of great current interest. Here I briefly review methods, some well-established and others newly developed, which have been successfully exploited to site-specifically fluorescently label interior positions of RNAs, as a guide to investigators seeking to apply this approach to their studies. Most of these methods can be applied directly to intact RNAs, including (1) the exploitation of natural posttranslational modifications, (2) the repurposing of enzymatic transferase reactions, and (3) the nucleic acid-assisted labeling of intact RNAs. In addition, several methods are described in which specifically labeled RNAs are prepared de novo. Full article
(This article belongs to the Special Issue Nucleosides and Nucleotides)
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27 pages, 1614 KiB  
Review
Nucleotide Sugars in Chemistry and Biology
by Satu Mikkola
Molecules 2020, 25(23), 5755; https://doi.org/10.3390/molecules25235755 - 6 Dec 2020
Cited by 51 | Viewed by 9157
Abstract
Nucleotide sugars have essential roles in every living creature. They are the building blocks of the biosynthesis of carbohydrates and their conjugates. They are involved in processes that are targets for drug development, and their analogs are potential inhibitors of these processes. Drug [...] Read more.
Nucleotide sugars have essential roles in every living creature. They are the building blocks of the biosynthesis of carbohydrates and their conjugates. They are involved in processes that are targets for drug development, and their analogs are potential inhibitors of these processes. Drug development requires efficient methods for the synthesis of oligosaccharides and nucleotide sugar building blocks as well as of modified structures as potential inhibitors. It requires also understanding the details of biological and chemical processes as well as the reactivity and reactions under different conditions. This article addresses all these issues by giving a broad overview on nucleotide sugars in biological and chemical reactions. As the background for the topic, glycosylation reactions in mammalian and bacterial cells are briefly discussed. In the following sections, structures and biosynthetic routes for nucleotide sugars, as well as the mechanisms of action of nucleotide sugar-utilizing enzymes, are discussed. Chemical topics include the reactivity and chemical synthesis methods. Finally, the enzymatic in vitro synthesis of nucleotide sugars and the utilization of enzyme cascades in the synthesis of nucleotide sugars and oligosaccharides are briefly discussed. Full article
(This article belongs to the Special Issue Nucleosides and Nucleotides)
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