Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
6.7
4.6
Journals
Molecules
Special Issues
Organic Synthesis and Functional Evaluation of Nucleic Acids
molecules-logo
Submit to Molecules Review for Molecules Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Organic Synthesis and Functional Evaluation of Nucleic Acids

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

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 4926

Special Issue Editor

Dr. Yosuke Taniguchi

E-Mail Website
Guest Editor
Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
Interests: bioorganic and synthetic chemistry; RNA editing; functional oligonucleotide; nucleoside damage; nucleotide derivatives; artificial nucleic acids

Special Issue Information

Dear Colleagues,

Newly synthetic nucleoside derivatives that have been produced through the organic synthesis process provide a great deal of useful information in the field of biochemistry, nucleic acid medicine, and biotechnology. For example, nucleosides and nucleotides have enzyme-inhibitory activities or antiviral activities, and oligonucleotides have gene regulatory functions, and so on. In addition, artificial nucleic acids that can form special higher-order structures play a very important role in the elucidation of life phenomena. However, nucleic acid chemists design and chemically synthesize various nucleic acid derivatives because nucleic acid derivatives with such novel functions must be chemically synthesized. 

This Special Issue provides an opportunity for researchers in a wide range of fields to share and discuss the latest results on the chemical synthesis of nucleosides, nucleotides, and oligonucleotides, including artificial nucleic acids and their functions. This issue of the journal solicits submissions of short reports, original papers, and review articles related to the synthesis of nucleic acid derivatives and their functional evaluation.

Dr. Yosuke Taniguchi
Guest Editor

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 submissions that pass pre-check are 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. 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

  • organic synthesis of nucleic acids
  • functional evaluation of nucleic acids
  • nucleosides
  • nucleotides
  • nucleic acids
  • oligonucleotides

Published Papers (3 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

13 pages, 3110 KiB  
Article
Synthesis and Behavior of DNA Oligomers Containing the Ambiguous Z-Nucleobase 5-Aminoimidazole-4-carboxamide
by Yuhei Nogi, Noriko Saito-Tarashima, Sangita Karanjit and Noriaki Minakawa
Molecules 2023, 28(7), 3265; https://doi.org/10.3390/molecules28073265 - 06 Apr 2023
Viewed by 1488
Abstract
5-Amino-1-β-D-ribofuranosylimidazole-4-carboxamide 5′-monophosphate (ZMP) is a central intermediate in de novo purine nucleotide biosynthesis. Its nucleobase moiety, 5-aminoimidazole-4-carboxamide (Z-base), is considered an ambiguous base that can pair with any canonical base owing to the rotatable nature of its 5-carboxamide group. This idea of ambiguous [...] Read more.
5-Amino-1-β-D-ribofuranosylimidazole-4-carboxamide 5′-monophosphate (ZMP) is a central intermediate in de novo purine nucleotide biosynthesis. Its nucleobase moiety, 5-aminoimidazole-4-carboxamide (Z-base), is considered an ambiguous base that can pair with any canonical base owing to the rotatable nature of its 5-carboxamide group. This idea of ambiguous base pairing due to free rotation of the carboxamide has been applied to designing mutagenic antiviral nucleosides, such as ribavirin and T-705. However, the ambiguous base-pairing ability of Z-base has not been elucidated, because the synthesis of Z-base-containing oligomers is problematic. Herein, we propose a practical method for the synthesis of Z-base-containing DNA oligomers based on the ring-opening reaction of an N1-dinitrophenylhypoxanthine (HxaDNP) base. Thermal denaturation studies of the resulting oligomers revealed that the Z-base behaves physiologically as an A-like nucleobase, preferentially forming pairs with T. We tested the behavior of Z-base-containing DNA oligomers in enzyme-catalyzed reactions: in single nucleotide insertion, Klenow fragment DNA polymerase recognized Z-base as an A-like analog and incorporated dTTP as a complementary nucleotide to Z-base in the DNA template; in PCR amplification, Taq DNA polymerase similarly incorporated dTTP as a complementary nucleotide to Z-base. Our findings will contribute to the development of new mutagenic antiviral nucleoside analogs. Full article
(This article belongs to the Special Issue Organic Synthesis and Functional Evaluation of Nucleic Acids)
►▼ Show Figures

Figure 1

17 pages, 3985 KiB  
Article
Synthesis of 6-Alkynylated Purine-Containing DNA via On-Column Sonogashira Coupling and Investigation of Their Base-Pairing Properties
by Hidenori Okamura, Giang Hoang Trinh, Zhuoxin Dong, Wenjue Fan and Fumi Nagatsugi
Molecules 2023, 28(4), 1766; https://doi.org/10.3390/molecules28041766 - 13 Feb 2023
Cited by 2 | Viewed by 1530
Abstract
Synthetic unnatural base pairs have been proven to be attractive tools for the development of DNA-based biotechnology. Our group has very recently reported on alkynylated purine–pyridazine pairs, which exhibit selective and stable base-pairing via hydrogen bond formation between pseudo-nucleobases in the major groove [...] Read more.
Synthetic unnatural base pairs have been proven to be attractive tools for the development of DNA-based biotechnology. Our group has very recently reported on alkynylated purine–pyridazine pairs, which exhibit selective and stable base-pairing via hydrogen bond formation between pseudo-nucleobases in the major groove of duplex DNA. In this study, we attempted to develop an on-column synthesis methodology of oligodeoxynucleotides (ODNs) containing alkynylated purine derivatives to systematically explore the relationship between the structure and the corresponding base-pairing ability. Through Sonogashira coupling of the ethynyl pseudo-nucleobases and CPG-bound ODNs containing 6-iodopurine, we have demonstrated the synthesis of the ODNs containing three NPu derivatives (NPu1, NPu2, NPu3) as well as three OPu derivatives (OPu1, OPu2, OPu3). The base-pairing properties of each alkynylated purine derivative revealed that the structures of pseudo-nucleobases influence the base pair stability and selectivity. Notably, we found that OPu1 bearing 2-pyrimidinone exhibits higher stability to the complementary NPz than the original OPu, thereby demonstrating the potential of the on-column strategy for convenient screening of the alkynylated purine derivatives with superior pairing ability. Full article
(This article belongs to the Special Issue Organic Synthesis and Functional Evaluation of Nucleic Acids)
►▼ Show Figures

Figure 1

12 pages, 1100 KiB  
Article
Antisense Gapmers with LNA-Wings and (S)-5′-C-Aminopropyl-2′-arabinofluoro-nucleosides Could Efficiently Suppress the Expression of KNTC2
by Yujun Zhou, Shuichi Sakamoto and Yoshihito Ueno
Molecules 2022, 27(21), 7384; https://doi.org/10.3390/molecules27217384 - 30 Oct 2022
Viewed by 1173
Abstract
Previously reported (S)-5′-C-aminopropyl-2′-arabinofluoro-thymidine (5ara-T) and newly synthesized (S)-5′-C-aminopropyl-2′-arabinofluoro-5-methyl-cytidine (5ara-MeC) analogs were incorporated into a series of antisense gapmers containing multiple phosphorothioate (PS) linkages and locked nucleic acids (LNAs) in [...] Read more.
Previously reported (S)-5′-C-aminopropyl-2′-arabinofluoro-thymidine (5ara-T) and newly synthesized (S)-5′-C-aminopropyl-2′-arabinofluoro-5-methyl-cytidine (5ara-MeC) analogs were incorporated into a series of antisense gapmers containing multiple phosphorothioate (PS) linkages and locked nucleic acids (LNAs) in their wing regions. The functional properties of the gapmers were further evaluated in vitro. Compared with the positive control, for the LNA-wing full PS gapmer without 5ara modification, it was revealed that each gapmer could have a high affinity and be thermally stable under biological conditions. Although the cleavage pattern was obviously changed; gapmers with 5ara modification could still efficiently activate E. coli RNase H1. In addition, incorporating one 5ara modification into the two phosphodiester linkages could reverse the destabilization in enzymatic hydrolysis caused by fewer PS linkages. In vitro cellular experiments were also performed, and the Lipofectamine® 2000 (LFA)+ group showed relatively higher antisense activity than the LFA-free group. KN5ara-10, which contains fewer PS linkages, showed similar or slightly better antisense activity than the corresponding full PS-modified KN5ara-3. Hence, KN5ara-10 may be the most promising candidate for KNTC2-targeted cancer therapy. Full article
(This article belongs to the Special Issue Organic Synthesis and Functional Evaluation of Nucleic Acids)
►▼ Show Figures

Graphical abstract

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-3
Back to TopTop