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Topical Collection "New Frontiers in Nucleic Acid Chemistry"

A topical collection in Molecules (ISSN 1420-3049). This collection belongs to the section "Molecular Diversity".

Editors

Collection Editor
Prof. Dr. Ramon Eritja

Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, CIBER-BBN, Jordi Girona 18-26, 08034 Barcelona, Spain
Website | E-Mail
Interests: nucleic acid chemistry; DNA and RNA analogs: synthesis applications, molecular tools; RNA interference; DNA nanotechnology; G-quadruplex; Triplex, artificial DNA
Collection Editor
Prof. Dr. Lajos Kovacs

Nucleic Acids Laboratory, Department of Medicinal Chemistry, Universtiy of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
Website | E-Mail
Fax: +36 62 42 59 71
Interests: G quadruplexes; supramolecular chemistry; synthetic organic chemistry of carbohydrates; nucleobases; nucleosides; C-nucleosides; peptide nucleic acids; heterocycles; protecting groups
Collection Editor
Prof. Dr. Daniela Montesarchio

Department of Chemical Sciences, University of Naples “Federico II”, via Cinthia 4, 80126 Naples, Italy
Website | E-Mail
Interests: nucleic acid chemistry; nucleoside and nucleotide analogs: modified and conjugated oligonucleotides; G-quadruplex; carbohydrate analogs and glyco-conjugates; synthetic ionophores; nucleolipids and their applications in drug delivery

Topical Collection Information

Dear Colleagues,

After the success of the Special Issues “Nucleic Acid Analogs”, edited by Molecules in 2012, and “Frontiers in Nucleic Acid Chemistry”, edited in 2015, we are happy to announce the launch of a Topical Collection on these topics. Synthetic oligonucleotides have become essential tools for biological, biomedical, and nanotechnology researches and have also shown promising results in therapeutics and diagnostics. Novel oligonucleotide derivatives with tailored properties are being continuously developed since their specific recognition and unique folding characteristics allow to obtain potential drugs or drug delivery agents, biosensors, diagnostic agents, etc. Along with this development, nucleic acid research is taking new directions as well: synthesis and applications of even more complex molecules, like synthetic RNA analogues (peptide nucleic acids, locked nucleic acids, morpholino oligos, conjugates, etc.), highly informative analytical methods (e.g., those based on mass spectrometry), study of higher-order structures (triple and quadruple helices), investigation of molecular electronic devices based on smart, self-assembling oligonucleotide analogues, to name just a few. The study of the properties of modified nucleic acids brings together many different branches of science, such as molecular biology, chemistry, biochemistry, medicinal chemistry, medicine, materials science, and synthetic biology.

The Topical Collection of Molecules, “New Frontiers in Nucleic Acid Chemistry”, will concentrate on the latest developments in nucleic acids chemistry. We cordially invite all the researchers involved in this exciting field to contribute to the continuing success of the Topical Collection “New Frontiers in Nucleic Acid Chemistry”.

Dr. Ramon Eritja
Dr. Lajos Kovács
Dr. Daniela Montesarchio
Collection 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 collection 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 monthly 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 1800 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

  • modified oligonucleotides
  • artificial nucleic acids
  • xeno nucleic acids
  • synthetic genes
  • oligonucleotide conjugates
  • nucleoside/nucleotide analogs
  • G-quadruplex
  • i-motif
  • triplex
  • antisense
  • siRNA
  • RNA interference
  • antiviral activity
  • anticancer activity
  • DNA nanobiotechnology
  • nanomaterials
  • aptamers
  • biosensors
  • surface-plasmon resonance
  • fluorescent nucleic acids
  • locked nucleic acids
  • unlocked nucleic acids
  • peptide nucleic acids
  • DNA repair
  • base-modified DNA
  • DNA polymerase
  • circular nucleic acids
  • NMR of nucleic acids
  • mass spectrometry of nucleic acids
  • biophysical studies

Related Special Issues

Published Papers (5 papers)

2017

Jump to: 2016

Open AccessArticle The Molecular Effect of Diagnostic Absorbed Doses from 131I on Papillary Thyroid Cancer Cells In Vitro
Molecules 2017, 22(6), 993; doi:10.3390/molecules22060993
Received: 14 April 2017 / Revised: 12 June 2017 / Accepted: 13 June 2017 / Published: 15 June 2017
PDF Full-text (2236 KB) | HTML Full-text | XML Full-text
Abstract
Diagnostic whole-body scan is a standard procedure in patients with thyroid cancer prior to the application of a therapeutic dose of 131I. Unfortunately, administration of the radioisotope in a diagnostic dose may decrease further radioiodine uptake—the phenomenon called “thyroid stunning”. We estimated
[...] Read more.
Diagnostic whole-body scan is a standard procedure in patients with thyroid cancer prior to the application of a therapeutic dose of 131I. Unfortunately, administration of the radioisotope in a diagnostic dose may decrease further radioiodine uptake—the phenomenon called “thyroid stunning”. We estimated radiation absorbed dose-dependent changes in genetic material, in particular in the sodium iodide symporter (NIS) gene promoter, and the NIS protein level in a K1 cell line derived from the metastasis of a human papillary thyroid carcinoma exposed to 131I in culture. The different activities applied were calculated to result in absorbed doses of 5, 10 and 20 Gy. Radioiodine did not affect the expression of the NIS gene at the mRNA level, however, we observed significant changes in the NIS protein level in K1 cells. The decrease of the NIS protein level observed in the cells subjected to the lowest absorbed dose was paralleled by a significant increase in 8-oxo-dG concentrations (p < 0.01) and followed by late activation of the DNA repair pathways. Our findings suggest that the impact of 131I radiation on thyroid cells, in the range compared to doses absorbed during diagnostic procedures, is not linear and depends on various factors including the cellular components of thyroid pathology. Full article
Figures

Figure 1

Open AccessReview Evolution of Complex Target SELEX to Identify Aptamers against Mammalian Cell-Surface Antigens
Molecules 2017, 22(2), 215; doi:10.3390/molecules22020215
Received: 20 December 2016 / Accepted: 24 January 2017 / Published: 30 January 2017
Cited by 3 | PDF Full-text (2434 KB) | HTML Full-text | XML Full-text
Abstract
The demand has increased for sophisticated molecular tools with improved detection limits. Such molecules should be simple in structure, yet stable enough for clinical applications. Nucleic acid aptamers (NAAs) represent a class of molecules able to meet this demand. In particular, aptamers, a
[...] Read more.
The demand has increased for sophisticated molecular tools with improved detection limits. Such molecules should be simple in structure, yet stable enough for clinical applications. Nucleic acid aptamers (NAAs) represent a class of molecules able to meet this demand. In particular, aptamers, a class of small nucleic acid ligands that are composed of single-stranded modified/unmodified RNA/DNA molecules, can be evolved from a complex library using Systematic Evolution of Ligands by EXponential enrichment (SELEX) against almost any molecule. Since its introduction in 1990, in stages, SELEX technology has itself undergone several modifications, improving selection and broadening the repertoire of targets. This review summarizes these milestones that have pushed the field forward, allowing researchers to generate aptamers that can potentially be applied as therapeutic and diagnostic agents. Full article
Figures

Figure 1

2016

Jump to: 2017

Open AccessArticle Synthesis and Biological Evaluation of Triazolyl 13α-Estrone–Nucleoside Bioconjugates
Molecules 2016, 21(9), 1212; doi:10.3390/molecules21091212
Received: 28 July 2016 / Revised: 2 September 2016 / Accepted: 6 September 2016 / Published: 10 September 2016
Cited by 1 | PDF Full-text (2934 KB) | HTML Full-text | XML Full-text
Abstract
2′-Deoxynucleoside conjugates of 13α-estrone were synthesized by applying the copper-catalyzed alkyne–azide click reaction (CuAAC). For the introduction of the azido group the 5′-position of the nucleosides and a propargyl ether functional group on the 3-hydroxy group of 13α-estrone were chosen. The best yields
[...] Read more.
2′-Deoxynucleoside conjugates of 13α-estrone were synthesized by applying the copper-catalyzed alkyne–azide click reaction (CuAAC). For the introduction of the azido group the 5′-position of the nucleosides and a propargyl ether functional group on the 3-hydroxy group of 13α-estrone were chosen. The best yields were realized in our hands when the 3′-hydroxy groups of the nucleosides were protected by acetyl groups and the 5′-hydroxy groups were modified by the tosyl–azide exchange method. The commonly used conditions for click reaction between the protected-5′-azidonucleosides and the steroid alkyne was slightly modified by using 1.5 equivalent of Cu(I) catalyst. All the prepared conjugates were evaluated in vitro by means of MTT assays for antiproliferative activity against a panel of human adherent cell lines (HeLa, MCF-7 and A2780) and the potential inhibitory activity of the new conjugates on human 17β-hydroxysteroid dehydrogenase 1 (17β-HSD1) was investigated via in vitro radiosubstrate incubation. Some protected conjugates displayed moderate antiproliferative properties against a panel of human adherent cancer cell lines (the protected cytidine conjugate proved to be the most potent with IC50 value of 9 μM). The thymidine conjugate displayed considerable 17β-HSD1 inhibitory activity (IC50 = 19 μM). Full article
Figures

Open AccessArticle DNA Three Way Junction Core Decorated with Amino Acids-Like Residues-Synthesis and Characterization
Molecules 2016, 21(9), 1082; doi:10.3390/molecules21091082
Received: 5 July 2016 / Revised: 8 August 2016 / Accepted: 10 August 2016 / Published: 23 August 2016
PDF Full-text (1251 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Construction and physico-chemical behavior of DNA three way junction (3WJ) functionalized by protein-like residues (imidazole, alcohol and carboxylic acid) at unpaired positions at the core is described. One 5′-C(S)-propargyl-thymidine nucleotide was specifically incorporated on each strand to react through a post
[...] Read more.
Construction and physico-chemical behavior of DNA three way junction (3WJ) functionalized by protein-like residues (imidazole, alcohol and carboxylic acid) at unpaired positions at the core is described. One 5′-C(S)-propargyl-thymidine nucleotide was specifically incorporated on each strand to react through a post synthetic CuACC reaction with either protected imidazolyl-, hydroxyl- or carboxyl-azide. Structural impacts of 5′-C(S)-functionalization were investigated to evaluate how 3WJ flexibility/stability is affected. Full article
Figures

Open AccessArticle Chemical Incorporation of Chain-Terminating Nucleoside Analogs as 3′-Blocking DNA Damage and Their Removal by Human ERCC1-XPF Endonuclease
Molecules 2016, 21(6), 766; doi:10.3390/molecules21060766
Received: 13 May 2016 / Accepted: 3 June 2016 / Published: 11 June 2016
Cited by 1 | PDF Full-text (2286 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Nucleoside/nucleotide analogs that lack the 3′-hydroxy group are widely utilized for HIV therapy. These chain-terminating nucleoside analogs (CTNAs) block DNA synthesis after their incorporation into growing DNA, leading to the antiviral effects. However, they are also considered to be DNA damaging agents, and
[...] Read more.
Nucleoside/nucleotide analogs that lack the 3′-hydroxy group are widely utilized for HIV therapy. These chain-terminating nucleoside analogs (CTNAs) block DNA synthesis after their incorporation into growing DNA, leading to the antiviral effects. However, they are also considered to be DNA damaging agents, and tyrosyl-DNA phosphodiesterase 1, a DNA repair enzyme, is reportedly able to remove such CTNA-modifications of DNA. Here, we have synthesized phosphoramidite building blocks of representative CTNAs, such as acyclovir, abacavir, carbovir, and lamivudine, and oligonucleotides with the 3′-CTNAs were successfully synthesized on solid supports. Using the chemically synthesized oligonucleotides, we investigated the excision of the 3′-CTNAs in DNA by the human excision repair cross complementing protein 1-xeroderma pigmentosum group F (ERCC1-XPF) endonuclease, which is one of the main components of the nucleotide excision repair pathway. A biochemical analysis demonstrated that the ERCC1-XPF endonuclease cleaved 2–7 nt upstream from the 3′-blocking CTNAs, and that DNA synthesis by the Klenow fragment was resumed after the removal of the CTNAs, suggesting that ERCC1-XPF participates in the repair of the CTNA-induced DNA damage. Full article
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