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Applications of Nucleic Acids in Chemistry and Biology

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A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Applied Biosciences and Bioengineering".

Deadline for manuscript submissions: closed (15 April 2022) | Viewed by 53602

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Special Issue Editors

Prof. Dr. Michal Sobkowski

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Guest Editor

Inst Bioorgan Chem, Polish Academy of Sciences, 61-174 Poznan, Poland
Interests: nucleotide analogues; oligonucleotides; nucleic acids; chemistry organic; phosphorus chemistry; H-phosphonates; P-chiral compounds; stereochemistry; stereocontrolled synthesis

Prof. Dr. Adam Kraszewski

E-Mail Website1 Website2
Guest Editor

Institute of Bio-Organic Chemistry, Polish Academy of Sciences, 61-174 Poznan, Poland
Interests: bioorganic chemistry; nucleotide chemistry; nucleotide analogues; antiviral pro-nucleotides; anticancer pro-nucleotides; oligonucleotides; oligonucleotide analogues; DNA; RNA

Dr. Joanna Romanowska

E-Mail Website
Guest Editor

Inst Bioorgan Chem, Polish Academy of Sciences, 61-174 Poznan, Poland
Interests: medicinal chemistry; bioorganic chemistry; organophosphorus chemistry; chemistry of nucleotides; pro-drugs; pro-nucleotides; H-phosphonates

Special Issue Information

Dear Colleagues,

Since the discovery of DNA structure and its role in the storage of genetic information, nucleic acids have fascinated chemists and biologists. The achievements of Watson and Crick were followed by outstanding development in the chemistry of nucleic acids, which allowed molecular biologists to easily access nucleosides, nucleotides, and oligonucleotides—natural, or bearing a plethora of various modifications. Some examples include antiviral and anticancer nucleoside analogues, their pro-nucleotide derivatives, or therapeutic oligonucleotides designed for various applications, e.g. in antigene, antisense, aptamer, or RNAi therapeutic strategies.

Despite the excellent progress made on synthetic methods and an improved understanding of the mechanisms of the biological activity of nucleic acid-derived compounds, there is a continuously increasing demand for new analogues and novel strategies for their applications.

In this Special Issue, both high-quality reviews and original research articles that are likely to significantly advance the field are welcome. The reviews should give readers a perspective of the directions in which the chemistry and biology of nucleic acids is developing, or is likely to develop, in the near or distant future. Experimental papers should present significant achievements in rational design, isolation, characterization, synthesis, biological evaluation and applications of compounds, in the broad scope of nucleic acids chemistry. Exemplary topics of interest include synthetic methods and strategies; chemical, physical, and biological properties; new concepts of modified oligonucleotides and their applications; structural studies (e.g. NMR, X-ray, AFM, cryoEM); synthetic biology and the biotechnology of nucleic acids. QSAR, molecular modeling and other computational studies of nucleic acid derivatives are also welcome.

Manuscripts are expected to contain a brief description of the state of the art in this field, and a statement on the importance of the research being submitted. Due to the broadness of this Special Issue, the leading topic of the manuscript should be provided (please choose from the list):

Chemistry
Chemical biology
Molecular biology
Synthetic biology
Nucleic acid structure
Ribozymes, DNAzymes
Non-biological applications of nucleic acids
Computational studies
Other

Keywords

bioorganic chemistry
bioinorganic chemistry
biological activity
nucleoside derivatives
nucleotide derivatives
therapeutic oligonucleotides
pharmaceutical chemistry
prodrugs
pronucleotides
molecular biology
synthetic biology
nucleic acid structure
nucleic acid quadruplexes
gene
genome
genomics
ribozymes
DNAzymes
DNA
RNA

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Published Papers (12 papers)

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Research

Jump to: Review

9 pages, 833 KiB

Open AccessArticle

A Method to Produce vsiRNAs in Plants with Cross-Kingdom Gene Silencing Capacity

by Hernán de Jesús Villanueva-Alonzo, Ana Paulina Haro-Álvarez, Arturo A. Alvarado-Segura, Raúl Enrique Valle-Gough, Juan Gualberto Collí-Mull, Alberto Cal-Torres, Víctor Ermilo Arana-Argáez, Julio César Torres-Romero, Oscar Alberto Moreno-Valenzuela, Geovanny Nic-Can, Benjamín Abraham Ayil-Gutiérrez and Karla Y. Acosta-Viana

Appl. Sci. 2022, 12(11), 5329; https://doi.org/10.3390/app12115329 - 25 May 2022

Viewed by 2437

Abstract

Plants have evolved defense mechanisms to suppress viral transcription and replication by transcriptional and post-transcriptional gene silencing mediated by virus-derived small interfering RNAs (vsiRNAs). Based on this response, virus-induced gene silencing (VIGS)-based technology has been developed to silence target genes on either host plants or insect pests. This mechanism could also be used for the silencing of genes of interest in the medical field. We used the VIGS vector pEuMV-YP:Krt18, which was obtained by inserting the Mus musculus (M. musculus) Krt18 sequence into pEuMV-YP:ΔAV1. The objective was to evaluate the capacity of pEuMV-YP:Krt18 to induce Nicotiana benthamiana (N. benthamiana) production of vsiRNAs of a specific sequence that belongs to neither the plant genome nor the wild virus genome, which were used to induce cross-kingdom gene silencing between plants and mammals. The percentage of vsiRNA for each viral gene was calculated from an sRNA library of N. benthamiana plants infected by pEuMV-YP: Krt18. When the vsiRNAs were characterized, it was found that they corresponded to all the genes of the pEuMV-YP:Krt18 vector. These vsiRNAs induced the silencing of the Krt18 gene in M. musculus macrophages, supporting the ability to use VIGS vectors in plants as biofactories for the production of sRNAs that induce gene silencing in mammals. Full article

(This article belongs to the Special Issue Applications of Nucleic Acids in Chemistry and Biology)

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17 pages, 1718 KiB

Open AccessArticle

Liposomes as Carriers for the Delivery of Efavirenz in Combination with Glutathione—An Approach to Combat Opportunistic Infections

by Vanaja Kenchappa, Ruoqiong Cao, Vishwanath Venketaraman and Guru V. Betageri

Appl. Sci. 2022, 12(3), 1468; https://doi.org/10.3390/app12031468 - 29 Jan 2022

Cited by 5 | Viewed by 2972

Abstract

Human immunodeficiency virus (HIV)-infected individuals display an enhanced production of reactive oxygen species (ROS). This reduction of antioxidant capacity in host tissues has been related to the decrease in total levels of ROS scavengers such as glutathione (GSH). Prevention of opportunistic infections due to a weakened immune system is becoming a key strategy along with HIV elimination. Research in these directions is clearly warranted, especially a combination of antiretrovirals and antioxidants to ameliorate oxidative stress, improve intracellular uptake and target viral reservoirs. Hence, we aimed to formulate liposomes loaded with the antiretroviral drug efavirenz (EFA) in the presence of glutathione, as these carriers can be engineered to enhance the ability to reach the target reservoirs. The goal of the present work was to investigate the intracellular uptake of EFA-loaded liposome (with and without GSH) by human monocytic leukemia cells (THP-1 cells) and examine cell viability and ROS scavenging activity. Results obtained provided significant data as follows: (i) treatment with EFA and GSH combination could enhance the uptake and reduce cytotoxicity; (ii) encapsulation of EFA into liposomes increased its levels in the macrophages, which was further enhanced in the presence of GSH; (iii) delivery of EFA in the presence of GSH quenched the intracellular ROS, which was significantly higher when delivered via liposomes. Data revealed that a combination of EFA and GSH encompasses advantages; hence, GSH supplementation could be a safe and cost-effective treatment to slow the development of HIV infection and produce an immune-enhancing effect. Full article

(This article belongs to the Special Issue Applications of Nucleic Acids in Chemistry and Biology)

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16 pages, 5207 KiB

Open AccessArticle

Anti-Aging Effects of Polyoxometalates on Skin

by Katsuyuki Fujinami, Katsuaki Dan, Toshiko Tanaka-Kagawa and Ikuo Kawamura

Appl. Sci. 2021, 11(24), 11948; https://doi.org/10.3390/app112411948 - 15 Dec 2021

Cited by 3 | Viewed by 2784

Abstract

Excessive reactive oxygen species (ROS) generation by inflammation and glycation contributes to various aging-related changes in the body. Therefore, inhibiting ROS production can prevent wrinkles, maculae, dullness, and slackness in skin. To assess the anti-aging effects of two polyoxometalates (PMs: VB2 and VB3) on skin, this study investigated whether they ameliorated the anti-aging responses of normal human dermal fibroblasts (NHDF) to oxidative stress due to ad-vanced glycation end products (AGEs) or H₂O₂ exposure. Compared with the mRNA expression levels of AGE receptors in cells exposed to AGEs alone, an additional treatment with VB2 or VB3 significantly increased the expression levels of FEEL-1, FEEL-2, and RAGE. Under AGE-induced stress conditions, the expression levels of five heat shock proteins were markedly increased by the VB treatments. Conversely, VBs suppressed the induction of cell death and intracellular ROS production. VBs also exerted prophylactic effects on these harmful events under stress conditions. Furthermore, VB treatments were found to prevent both the suppression of AQP-1/AQP-3 expression and the suppression of hyaluronan and elastin production induced via H₂O₂ exposure. These results show the potential of VB2 and VB3 as anti-aging agents. Full article

(This article belongs to the Special Issue Applications of Nucleic Acids in Chemistry and Biology)

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12 pages, 1373 KiB

Open AccessArticle

MiR-486-3p and MiR-938—Important Inhibitors of Pacemaking Ion Channels and/or Markers of Immune Cells

by Abimbola J Aminu, Maria Petkova, Weixuan Chen, Zeyuan Yin, Vlad S Kuzmin, Andrew J Atkinson and Halina Dobrzynski

Appl. Sci. 2021, 11(23), 11366; https://doi.org/10.3390/app112311366 - 1 Dec 2021

Cited by 4 | Viewed by 2524

Abstract

The sinus node (SN) is the heart’s primary pacemaker and has a unique expression of pacemaking ion channels and immune cell markers. The role of microribonucleic acids (miRNAs) in control of ion channels and immune function of the sinus node is not well understood. We have recently shown that hsa-miR-486-3p downregulates the main pacemaking channel HCN4 in the SN. In addition, we recently demonstrated that immune cells are significantly more abundant in the SN compared to the right atrium. The aim of this study was to validate the previously predicted interactions between miRNAs and mRNAs of key Ca²⁺ ion channels (involved in peacemaking) and mRNA of TPSAB1—(a mast cells marker) using luciferase assay. We now show that miR-486 significantly downregulates Ca_v1.3, Ca_v3.1, and TPSAB1-mediated luciferase activity, while miR-938 significantly downregulates only TPSAB1-mediated luciferase activity. This makes miR-486-3p a potential therapeutic target in the treatment of SN dysfunctions. Full article

(This article belongs to the Special Issue Applications of Nucleic Acids in Chemistry and Biology)

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14 pages, 5886 KiB

Open AccessFeature PaperArticle

Multilevel Gene Regulation Using Switchable Transcription Terminator and Toehold Switch in Escherichia coli

by Seongho Hong, Jeongwon Kim and Jongmin Kim

Appl. Sci. 2021, 11(10), 4532; https://doi.org/10.3390/app11104532 - 16 May 2021

Cited by 8 | Viewed by 3664

Abstract

Nucleic acid-based regulatory components provide a promising toolbox for constructing synthetic biological circuits due to their design flexibility and seamless integration towards complex systems. In particular, small-transcriptional activating RNA (STAR) and toehold switch as regulators of transcription and translation steps have shown a large library size and a wide dynamic range, meeting the criteria to scale up genetic circuit construction. Still, there are limited attempts to integrate the heterogeneous regulatory components for multilevel regulatory circuits in living cells. In this work, inspired by the design principle of STAR, we designed several switchable transcription terminators starting from natural and synthetic terminators. These switchable terminators could be designed to respond to specific RNA triggers with minimal sequence constraints. When combined with toehold switches, the switchable terminators allow simultaneous control of transcription and translation processes to minimize leakage in Escherichia coli. Further, we demonstrated a set of logic gates implementing 2-input AND circuits and multiplexing capabilities to control two different output proteins. This study shows the potential of novel switchable terminator designs that can be computationally designed and seamlessly integrated with other regulatory components, promising to help scale up the complexity of synthetic gene circuits in living cells. Full article

(This article belongs to the Special Issue Applications of Nucleic Acids in Chemistry and Biology)

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10 pages, 1584 KiB

Open AccessArticle

Comparative Analysis of Cell-Free miR-205-5p, let-7f-5p, and miR-483-5p Expression in Ovarian Cell Cultures and Plasma Samples of Patients with Ovarian Cancer

by Éva Márton, Alexandra Varga, Beáta Soltész, András Penyige, János Lukács, Róbert Póka, Bálint Nagy and Melinda Szilágyi

Appl. Sci. 2021, 11(4), 1735; https://doi.org/10.3390/app11041735 - 16 Feb 2021

Cited by 3 | Viewed by 2007

Abstract

The term liquid biopsy reveals a non-invasive diagnostic method that might be based on the quantification of cell-free microRNAs in body fluids. However, the identification of candidates for liquid biopsy is challenging. Our aim was to compare the cell-free expression of miR-483-5p, miR-205-5p, and let-7f-5p in ovarian cell cultures and plasma samples of patients with ovarian cancer. Both the intracellular and cell-free expression of miR-205-5p and let-7f-5p proved to be higher in the Estrogen Receptor α (ERα) expressing PEO1 cell-line than in the estrogen non-sensitive A2780. Moreover, the expression of let-7f-5p was up-regulated in response to estradiol exposure that was diminished after the addition of an ERα selective antagonist. MiR-483-5p had lower intracellular and cell-free expression in PEO1. All these miRNAs had detectable expression level in plasma samples, among which miR-205-5p proved to be overexpressed in the plasma samples of patients with ovarian tumors compared to healthy controls and possessed an acceptable diagnostic potential with ROC-AUC 0.683 (95% CI 0.57–0.795). Functional annotation clustering of the target genes of miR-205-5p revealed several clusters involved in cancer development. We suggest that miR-205-5p might be a promising biomarker candidate in ovarian cancer that should be further analyzed in larger sample size. Full article

(This article belongs to the Special Issue Applications of Nucleic Acids in Chemistry and Biology)

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14 pages, 1841 KiB

Open AccessArticle

Application of Antiviral Polyoxometalates to Living Environments—Antiviral Moist Hand Towels and Stationery Items

by Katsuaki Dan, Katsuyuki Fujinami, Hajime Sumitomo, Yasuaki Ogiwara, Shigehiko Suhara, Yoshiharu Konno, Mitsuhiro Sawada, Yusuke Soga, Atsushi Takada, Keita Takanashi, Kenji Watanabe and Tatsuo Shinozuka

Appl. Sci. 2020, 10(22), 8246; https://doi.org/10.3390/app10228246 - 20 Nov 2020

Cited by 6 | Viewed by 3078

Abstract

Safe, secure, and environmentally friendly active substances should be developed. VB (virus block) refers to an antibacterial/antiviral mixture of two kinds of polyoxometalates (PMs), i.e., K₁₁H[(VO)₃(SbW₉O₃₃)₂]·27H₂O (VB2) and α-Na₂[SbW₉O₃₃]⁹⁻ (VB3), and polyhexamethylene biguanide (PHMB). VB was demonstrated to exert antiviral effects on cultured cells. The effects were maintained even in hygiene products or solids. The antiviral effects were analyzed by reverse transcription–polymerase chain reaction (RT–PCR), and the results were correlated with TCID50, potentially eliminating the need for handling infectious viruses. VB was demonstrated to be extremely effective (up to 99.99% inhibition) in cultured cells, with antibacterial/antiviral effects maintained in VB-containing hygiene products. VB was applied to solids, demonstrating their high applicability and versatility. VB withstands high temperatures regardless of materials because its effects are enhanced by more frequent contact with viruses and bacteria due to the increased surface area of the compound. Full article

(This article belongs to the Special Issue Applications of Nucleic Acids in Chemistry and Biology)

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14 pages, 697 KiB

Open AccessArticle

In Vitro and in Silico Analysis of miR-125a with rs12976445 Polymorphism in Breast Cancer Patients

by Tomasz P. Lehmann, Joanna Miskiewicz, Natalia Szostak, Marta Szachniuk, Sylwia Grodecka-Gazdecka and Paweł P. Jagodziński

Appl. Sci. 2020, 10(20), 7275; https://doi.org/10.3390/app10207275 - 17 Oct 2020

Cited by 5 | Viewed by 2682

Abstract

Background: Breast cancer affects over 2 million women yearly. Its early detection allows for successful treatment, which motivates to research factors that enable an accurate diagnosis. miR-125a is one of them, correlating with different types of cancer. For example, the miR-125a level decreases in breast cancer tissues; polymorphisms in the miR-125a encoding gene are related to prostate cancer and the risk of radiotherapy-induced pneumonitis. Methods: In this work, we investigated two variants of rs12976445 polymorphism in the context of breast cancer. We analyzed the data of 175 blood samples from breast cancer patients and compared them with the control data from 129 control samples. Results: We observed the tendency that in breast cancer cases TT genotype appeared slightly more frequent over CC and CT genotypes (statistically nonsignificant). The TT genotype appeared also to be more frequent among human epidermal growth factor receptor 2 (HER2) positive patients, compared to HER2 negative. In silico modelling showed that the presence of uridine (U) diminished the probability of pri-miR-125a binding to NOVA1 and HNRNPK proteins. We demonstrated that U and C -variants could promote different RNA folding patterns and provoke alternative protein binding. Conclusions: U-variant may imply a lower miR-125a expression in breast cancer. Full article

(This article belongs to the Special Issue Applications of Nucleic Acids in Chemistry and Biology)

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Review

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17 pages, 20039 KiB

Open AccessReview

Overview of Methods for Large-Scale RNA Synthesis

by Marcin Ryczek, Martyna Pluta, Leszek Błaszczyk and Agnieszka Kiliszek

Appl. Sci. 2022, 12(3), 1543; https://doi.org/10.3390/app12031543 - 31 Jan 2022

Cited by 5 | Viewed by 8834

Abstract

In recent years, it has become clear that RNA molecules are involved in almost all vital cellular processes and pathogenesis of human disorders. The functional diversity of RNA comes from its structural richness. Although composed of only four nucleotides, RNA molecules present a plethora of secondary and tertiary structures critical for intra and intermolecular contacts with other RNAs and ligands (proteins, small metabolites, etc.). In order to fully understand RNA function it is necessary to define its spatial structure. Crystallography, nuclear magnetic resonance and cryogenic electron microscopy have demonstrated considerable success in determining the structures of biologically important RNA molecules. However, these powerful methods require large amounts of sample. Despite their limitations, chemical synthesis and in vitro transcription are usually employed to obtain milligram quantities of RNA for structural studies, delivering simple and effective methods for large-scale production of homogenous samples. The aim of this paper is to provide an overview of methods for large-scale RNA synthesis with emphasis on chemical synthesis and in vitro transcription. We also present our own results of testing the efficiency of these approaches in order to adapt the material acquisition strategy depending on the desired RNA construct. Full article

(This article belongs to the Special Issue Applications of Nucleic Acids in Chemistry and Biology)

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26 pages, 3596 KiB

Open AccessFeature PaperReview

Acyclic Nucleic Acids with Phosphodiester Linkages—Synthesis, Properties and Potential Applications

by Agnieszka Tomaszewska-Antczak and Piotr Guga

Appl. Sci. 2021, 11(24), 12125; https://doi.org/10.3390/app112412125 - 20 Dec 2021

Cited by 4 | Viewed by 3260

Abstract

This review summarizes the synthetic efforts on acyclic analogs of nucleic acids and provides information on the most interesting features of selected classes of such compounds. The selection includes the following types of analogs: Flexible (FNA), Unlocked (UNA), Glycol (GNA), Butyl (BuNA), Threoninol (TNA) and Serinol Nucleic Acids (SNA). These classes of analogs are discussed in terms of their synthetic methods, the thermal stability of their homo- and hetero-duplexes and their applicability in biological and biochemical research and nanotechnology. Full article

(This article belongs to the Special Issue Applications of Nucleic Acids in Chemistry and Biology)

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28 pages, 10809 KiB

Open AccessReview

Nucleoside Di- and Triphosphates as a New Generation of Anti-HIV Pronucleotides. Chemical and Biological Aspects

by Marta Rachwalak, Joanna Romanowska, Michal Sobkowski and Jacek Stawinski

Appl. Sci. 2021, 11(5), 2248; https://doi.org/10.3390/app11052248 - 4 Mar 2021

Cited by 1 | Viewed by 4662

Abstract

This review provides a short account of the chemical synthesis of nucleoside di- and triphosphates on a historical background, together with the use of this class of compounds as potential pronucleotides in anti-HIV therapy. Full article

(This article belongs to the Special Issue Applications of Nucleic Acids in Chemistry and Biology)

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16 pages, 554 KiB

Open AccessFeature PaperReview

Copy Number Variation: Methods and Clinical Applications

by Ondrej Pös, Jan Radvanszky, Jakub Styk, Zuzana Pös, Gergely Buglyó, Michal Kajsik, Jaroslav Budis, Bálint Nagy and Tomas Szemes

Appl. Sci. 2021, 11(2), 819; https://doi.org/10.3390/app11020819 - 16 Jan 2021

Cited by 33 | Viewed by 11606

Abstract

Gains and losses of large segments of genomic DNA, known as copy number variants (CNVs) gained considerable interest in clinical diagnostics lately, as particular forms may lead to inherited genetic diseases. In recent decades, researchers developed a wide variety of cytogenetic and molecular methods with different detection capabilities to detect clinically relevant CNVs. In this review, we summarize methodological progress from conventional approaches to current state of the art techniques capable of detecting CNVs from a few bases up to several megabases. Although the recent rapid progress of sequencing methods has enabled precise detection of CNVs, determining their functional effect on cellular and whole-body physiology remains a challenge. Here, we provide a comprehensive list of databases and bioinformatics tools that may serve as useful assets for researchers, laboratory diagnosticians, and clinical geneticists facing the challenge of CNV detection and interpretation. Full article

(This article belongs to the Special Issue Applications of Nucleic Acids in Chemistry and Biology)

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