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Special Issue "Synthesis and Applications of Oligonucleotide Conjugate II"

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

Deadline for manuscript submissions: 31 October 2020.

Special Issue Editors

Prof. Dr. Harri Lönnberg
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Guest Editor
Department of Chemistry, University of Turku, 20014 Turku, Finland
Interests: Kinetic studies on chemical models of ribonucleases and ribozymes; Synthesis and application of oligonucleotide conjugates; Pro-drug strategies for phosphoester drugs; Novel approaches for medium scale synthesis of oligonucleotides
Special Issues and Collections in MDPI journals
Prof. Dr. Roger Strömberg
Website
Guest Editor
Karolinska Institutet, Department of Biosciences and Nutrition, Stockholm, Sweden
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

Conjugates of oligonucleotides with an unnatural organic structure or a constituent of some biopolymer are widely used cell biology research tools. Conventional conjugate groups consist of reporter groups for sensitive detection of oligonucleotides both in vitro and in vivo, chemically or photochemically reactive groups for site-selective cleavage or cross-linking to the target sequence, intercalators for stabilization of double helices, and chelating agents for high affinity binding of metal ions. More recently, covalent conjugates have received increased interest as a means to improve the delivery of therapeutic oligonucleotides to specific cell types. A breakthrough in this field was the approval of a siRNA drug, givosiran, for clinical use. This is a trivalent N-acetylgalactosamine conjugate bearing the conjugate group at the 3’ terminus of the antisense strand. In addition, lipid, carbohydrate, peptide, aptamer, and some small molecule conjugates have shown promise. In particular, targeting with aptamers or peptides seems to be an increasingly popular approach. In many cases, conjugation through a biodegradable linker is desirable. Preparation of oligonucleotide conjugates is challenging. Synthesis on a single solid support is possible but often requires modifications to the conventional protocol of oligonucleotide synthesis. Alternatively, bio-orthogonal post-synthetic conjugation in solution may be applied.

The present Special Issue is aimed at gathering new synthetic methodologies of oligonucleotide conjugates, as well as their novel applications.

Prof. Harri Lönnberg
Prof. Dr. Roger Strömberg
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 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 2000 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

  • oligonucleotides
  • aptamers
  • synthesis
  • conjugation
  • delivery
  • therapeutic oligonucleotides

Related Special Issue

Published Papers (1 paper)

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Research

Open AccessArticle
A Trisbenzimidazole Phosphoramidite Building Block Enables High-Yielding Syntheses of RNA-Cleaving Oligonucleotide Conjugates
Molecules 2020, 25(8), 1842; https://doi.org/10.3390/molecules25081842 - 16 Apr 2020
Abstract
The RNA cleaving catalyst tris(2-aminobenzimidazole) when attached to the 5’ terminus of oligonucleotides cuts complementary RNA strands in a highly site-specific manner. Conjugation was previously achieved by the acylation of an amino linker by an active ester of the catalyst. However, this procedure [...] Read more.
The RNA cleaving catalyst tris(2-aminobenzimidazole) when attached to the 5’ terminus of oligonucleotides cuts complementary RNA strands in a highly site-specific manner. Conjugation was previously achieved by the acylation of an amino linker by an active ester of the catalyst. However, this procedure was low yielding and not reliable. Here, a phosphoramidite building block is described that can be coupled to oligonucleotides by manual solid phase synthesis in total yields around 85%. Based on this chemistry, we have now studied the impact of LNA (locked nucleic acids) nucleotides on the rates and the site-specificities of RNA cleaving conjugates. The highest reaction rates and the most precise cuts can be expected when the catalyst is attached to a strong 5’ closing base pair and when the oligonucleotide contains several LNA units that are equally distributed in the strand. However, when placed in the 5’ position, LNA building blocks tend to diminish the specificity of RNA cleavage. Full article
(This article belongs to the Special Issue Synthesis and Applications of Oligonucleotide Conjugate II)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Contribution of antisense oligonucleotide and chemotherapy combination to cancer treatment
Authors: Asuman Bozkır
Affiliation: Ankara Üniversity,Faculty of Pharmacy, Department of Pharmaceutical Technology, 06560 Yenimahalle/ANKARA

Title: Highly multiplexed single-cell in situ RNA and DNA analysis by consecutive hybridization
Authors: Jia Guo
Affiliation: School of Molecular Sciences, Arizona State University
Abstract: Limitations on the number of RNA species and genomic loci that can be quantified in single cells in situ impede advances in our deep understanding of normal cell physiology and disease pathogenesis. Here we present a method for highly multiplexed single cell in situ RNA and DNA analysis by consecutive fluorescence in situ hybridization (C-FISH). In this method, individual transcripts or genomic loci are visualized as fluorescent spots with fixed locations in individual cells. In each cycle of C-FISH, fluorescently labeled oligonucleotides hybridize to the probe used in the previous cycle, and also introduce multiple binding sites for the probe of the following cycle. Through consecutive cycles of probe hybridization, fluorescence imaging and photobleaching, different RNA species or genomic loci can be identified as fluorescent spots with unique color sequences. Applying this approach, we demonstrate that with 2 fluorophores and 16 cycles of C-FISH, different transcripts or genomic loci are unambiguously identified in individual cells with close to “0” raw data error rate. These results suggest all the varied color sequences (216= 65,536) can be applied to identify distinct RNA species or genomic loci, which allows the transcriptome- or genome-wide single cell in situ analysis. This highly multiplexed single cell in situ RNA and DNA analysis technology will have wide applications in signaling network analysis, 3D genome architecture studies, molecular diagnosis and cellular targeted therapies

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