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Special Issue "Oligonucleotides Application to Nano- and Biotechnology (DNA Origami, DNA Machine)"

A special issue of Molecules (ISSN 1420-3049).

Deadline for manuscript submissions: 31 October 2018

Special Issue Editors

Guest Editor
Prof. Dr. Shigeki Sasaki

Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
Website | E-Mail
Interests: functional oligonucleotides; therapeutic oligonucleotide; medicinal chemistry; drug delivery; molecular therapy; nano-medicine
Guest Editor
Dr. Marcel Hollenstein

Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
Website | E-Mail
Interests: synthesis of modified nucleoside triphosphates and nucleoside analogues for their use in selection experiments to isolate aptamers and catalytic nucleic acids for their application as imaging and therapeutic agents; enzymatic construction of artificial metal base-pairs for an expansion of the genetic code

Special Issue Information

Dear Colleagues,

Progress in organic synthesis, molecular biology, and nanotechnology has made nucleic acids leading elements in numerous applications. For instance, DNA oligonucleotides are the fundamental building elements for the construction of DNA origamis, nanodevices, and nanomachines. Oligonucleotides are also essential in the development of the antisense therapy strategy and other related gene silencing methods. Conjugation of oligonucleotides to other biopolymers and/or chemical entities, such as cell penetrating peptides or metal complexes is a highly developing field of research. Lastly, the advent of SELEX has made aptamers and DNAzymes popular tools for biosensing and therapeutic applications and the inclusion of modified triphosphates broadens the scope of these functional nucleic acids. Therefore, in this Special Issue on oligonucleotides, we welcome research articles and comprehensive reviews in all mentioned areas.

Prof. Dr. Shigeki Sasaki
Dr. Marcel Hollenstein
Guest 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 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 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

  • DNA nanotechnology
  • aptamers
  • DNAzymes
  • oligonucleotide sensors
  • antisense oligonucleotides
  • therapeutic oligonucleotides
  • modified nucleoside triphosphates
  • modified oligonucleotides
  • synthesis of oligonucleotides
  • oligonucleotide conjugates

Published Papers (5 papers)

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Research

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Open AccessFeature PaperCommunication Shaping Rolling Circle Amplification Products into DNA Nanoparticles by Incorporation of Modified Nucleotides and Their Application to In Vitro and In Vivo Delivery of a Photosensitizer
Molecules 2018, 23(7), 1833; https://doi.org/10.3390/molecules23071833
Received: 10 June 2018 / Revised: 17 July 2018 / Accepted: 20 July 2018 / Published: 23 July 2018
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Abstract
Rolling circle amplification (RCA) is a robust way to generate DNA constructs, which are promising materials for biomedical applications including drug delivery because of their high biocompatibility. To be employed as a drug delivery platform, however, the DNA materials produced by RCA need
[...] Read more.
Rolling circle amplification (RCA) is a robust way to generate DNA constructs, which are promising materials for biomedical applications including drug delivery because of their high biocompatibility. To be employed as a drug delivery platform, however, the DNA materials produced by RCA need to be shaped into nanoparticles that display both high cellular uptake efficiency and nuclease resistance. Here, we showed that the DNA nanoparticles (DNPs) can be prepared with RCA and modified nucleotides that have side-chains appended on the nucleobase are capable of interacting with the DNA strands of the resulting RCA products. The incorporation of the modified nucleotides improved cellular uptake efficiency and nuclease resistance of the DNPs. We also demonstrated that these DNPs could be employed as carriers for the delivery of a photosensitizer into cancer cells to achieve photodynamic therapy upon irradiation at both the in vitro and in vivo levels. Full article
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Open AccessFeature PaperArticle Aptamer Display on Diverse DNA Polyhedron Supports
Molecules 2018, 23(7), 1695; https://doi.org/10.3390/molecules23071695
Received: 29 June 2018 / Revised: 9 July 2018 / Accepted: 9 July 2018 / Published: 11 July 2018
Cited by 1 | PDF Full-text (2928 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
DNA aptamers are important tools for molecular recognition, particularly for a new generation of tools for biomedicine based on nucleic acid nanostructures. Here, we investigated the relative abilities of different shapes and sizes of DNA polyhedra to display an aptamer which binds to
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DNA aptamers are important tools for molecular recognition, particularly for a new generation of tools for biomedicine based on nucleic acid nanostructures. Here, we investigated the relative abilities of different shapes and sizes of DNA polyhedra to display an aptamer which binds to the malaria biomarker Plasmodium falciparum lactate dehydrogenase (PfLDH). The aptamer was shown to perform an Aptamer-Tethered Enzyme Capture (APTEC) assay with the hypothesis that the display of the aptamer above the surface through the use of a polyhedron may lead to better sensitivity than use of the aptamer alone. We compared different numbers of points of contact, different shapes, including tetrahedron, square, and pentagon-based pyramids, as well as prisms. We also investigated the optimal height of display of the structure. Our results demonstrated that the display of an aptamer on an optimized nanostructure improved sensitivity up to 6-fold relative to the aptamer alone in the APTEC assay. Other important factors included multiple basal points of contact with the surface, a tetrahedron proved superior to the more complex shaped structures, and height above the surface only made minor differences to efficacy. The display of an aptamer on a nanostructure may be beneficial for higher sensitivity aptamer-mediated malaria diagnosis. Aptamer displays using DNA nanostructure polyhedron supports could be a useful approach in a variety of applications. Full article
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Review

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Open AccessReview Oligonucleotides Targeting Telomeres and Telomerase in Cancer
Molecules 2018, 23(9), 2267; https://doi.org/10.3390/molecules23092267
Received: 26 July 2018 / Revised: 27 August 2018 / Accepted: 4 September 2018 / Published: 5 September 2018
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Abstract
Telomeres and telomerase have become attractive targets for the development of anticancer therapeutics due to their involvement in cancer cell immortality. Currently, several therapeutics have been developed that directly target telomerase and telomeres, such as telomerase inhibitors and G-quadruplex stabilizing ligands. Telomere-specific oligonucleotides
[...] Read more.
Telomeres and telomerase have become attractive targets for the development of anticancer therapeutics due to their involvement in cancer cell immortality. Currently, several therapeutics have been developed that directly target telomerase and telomeres, such as telomerase inhibitors and G-quadruplex stabilizing ligands. Telomere-specific oligonucleotides that reduce telomerase activity and disrupt telomere architecture are also in development as novel anticancer therapeutics. Specifically, GRN163L and T-oligos have demonstrated promising anticancer activity in multiple cancers types via induction of potent DNA damage responses. Currently, several miRNAs have been implicated in the regulation of telomerase activity and may prove to be valuable targets in the development of novel therapies by reducing expression of telomerase subunits. Targeting miRNAs that are known to increase expression of telomerase subunits may be another strategy to reduce carcinogenesis. This review aims to provide a comprehensive understanding of current oligonucleotide-based anticancer therapies that target telomeres and telomerase. These studies may help design novel therapeutic approaches to overcome the challenges of oligonucleotide therapy in a clinical setting. Full article
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Open AccessReview DNA Origami Nanomachines
Molecules 2018, 23(7), 1766; https://doi.org/10.3390/molecules23071766
Received: 5 July 2018 / Accepted: 17 July 2018 / Published: 18 July 2018
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Abstract
DNA can assemble various molecules and nanomaterials in a programmed fashion and is a powerful tool in the nanotechnology and biology research fields. DNA also allows the construction of desired nanoscale structures via the design of DNA sequences. Structural nanotechnology, especially DNA origami,
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DNA can assemble various molecules and nanomaterials in a programmed fashion and is a powerful tool in the nanotechnology and biology research fields. DNA also allows the construction of desired nanoscale structures via the design of DNA sequences. Structural nanotechnology, especially DNA origami, is widely used to design and create functionalized nanostructures and devices. In addition, DNA molecular machines have been created and are operated by specific DNA strands and external stimuli to perform linear, rotational, and reciprocating movements. Furthermore, complicated molecular systems have been created on DNA nanostructures by arranging multiple molecules and molecular machines precisely to mimic biological systems. Currently, DNA nanomachines, such as molecular motors, are operated on DNA nanostructures. Dynamic DNA nanostructures that have a mechanically controllable system have also been developed. In this review, we describe recent research on new DNA nanomachines and nanosystems that were built on designed DNA nanostructures. Full article
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Open AccessReview Applications of Ruthenium Complexes Covalently Linked to Nucleic Acid Derivatives
Molecules 2018, 23(7), 1515; https://doi.org/10.3390/molecules23071515
Received: 1 June 2018 / Revised: 19 June 2018 / Accepted: 20 June 2018 / Published: 22 June 2018
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Abstract
Oligonucleotides are biopolymers that can be easily modified at various locations. Thereby, the attachment of metal complexes to nucleic acid derivatives has emerged as a common pathway to improve the understanding of biological processes or to steer oligonucleotides towards novel applications such as
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Oligonucleotides are biopolymers that can be easily modified at various locations. Thereby, the attachment of metal complexes to nucleic acid derivatives has emerged as a common pathway to improve the understanding of biological processes or to steer oligonucleotides towards novel applications such as electron transfer or the construction of nanomaterials. Among the different metal complexes coupled to oligonucleotides, ruthenium complexes, have been extensively studied due to their remarkable properties. The resulting DNA-ruthenium bioconjugates have already demonstrated their potency in numerous applications. Consequently, this review focuses on the recent synthetic methods developed for the preparation of ruthenium complexes covalently linked to oligonucleotides. In addition, the usefulness of such conjugates will be highlighted and their applications from nanotechnologies to therapeutic purposes will be discussed. Full article
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