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Advances in Catalytic DNA
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Advances in Catalytic DNA

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

Deadline for manuscript submissions: closed (31 July 2020) | Viewed by 18515

Special Issue Editors

Prof. Dr. Michael Smietana

E-Mail Website
Guest Editor
Institut des Biomolécules Max Mousseron (IBMM), Montpellier University, Place E. Bataillon, CC 1704, 34095 Montpellier, France
Interests: chemical biology and nucleic acid chemistry; DNA-based asymmetric catalysis; DNA-templated ligation; synthesis and application of modified oligonucleotide; drug design
Dr. Stellios Arseniyadis

E-Mail Website
Guest Editor
Queen Mary University of London, School of Biological and Chemical Sciences Mile End Road, London E1 4NS, UK
Interests: asymmetric organometallic catalysis; organocatalysis; biohybrid catalysis; natural product synthesis; synthetic methodologies
Prof. Dr. Sabine Müller

E-Mail Website
Guest Editor
Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
Interests: nucleic acid chemistry and biochemistry; RNA engineering; nucleic acid enzymes; aptamers; origin of life

Special Issue Information

Dear Colleagues,

It is now well accepted that DNA is no longer solely used for the storage and delivery of the genetic information in living systems. Indeed, DNA has also been shown to exhibit interesting enzyme-like catalytic activities. DNA-based enzymes (also called deoxyribozymes or DNAzymes) are single-stranded DNA molecules that are obtained by in vitro selection and that can catalyse specific chemical transformations.

In the meantime, double-stranded DNA also offers interesting catalytic features. Indeed, by anchoring a metallic co‑factor within the chiral double helix of DNA, it is now possible to program DNA to act as artificial metalloenzymes. The concept has been successfully applied to a variety of chemical transformations including Michael and oxo-Michael additions, Friedel–Crafts alkylations and both inter- and intramolecular cyclopropanations just to name a few.

Together, these catalytic DNAs offer a variety of potential biotechnological, biomedical and industrial applications. This Special Issue of Molecules, “Advances in Catalytic DNA”, aims at addressing the principles, the latest developments and the various applications of DNA-based catalysis. We cordially invite all researchers involved in this exciting field to contribute to the success of this Special Issue.

Prof. Michael Smietana
Dr. Stellios Arseniyadis
Prof. Sabine Müller
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 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

  • Catalytic DNA
  • Deoxyribozyme
  • DNA-based hybrid catalysis
  • DNAzyme
  • In vitro selection

Published Papers (4 papers)

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Research

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14 pages, 2370 KiB  
Article
New Deoxyribozymes for the Native Ligation of RNA
by Carolin P. M. Scheitl, Sandra Lange and Claudia Höbartner
Molecules 2020, 25(16), 3650; https://doi.org/10.3390/molecules25163650 - 11 Aug 2020
Cited by 6 | Viewed by 4640
Abstract
Deoxyribozymes (DNAzymes) are small, synthetic, single-stranded DNAs capable of catalyzing chemical reactions, including RNA ligation. Herein, we report a novel class of RNA ligase deoxyribozymes that utilize 5′-adenylated RNA (5′-AppRNA) as the donor substrate, mimicking the activated intermediates of protein-catalyzed RNA ligation. Four [...] Read more.
Deoxyribozymes (DNAzymes) are small, synthetic, single-stranded DNAs capable of catalyzing chemical reactions, including RNA ligation. Herein, we report a novel class of RNA ligase deoxyribozymes that utilize 5′-adenylated RNA (5′-AppRNA) as the donor substrate, mimicking the activated intermediates of protein-catalyzed RNA ligation. Four new DNAzymes were identified by in vitro selection from an N40 random DNA library and were shown to catalyze the intermolecular linear RNA-RNA ligation via the formation of a native 3′-5′-phosphodiester linkage. The catalytic activity is distinct from previously described RNA-ligating deoxyribozymes. Kinetic analyses revealed the optimal incubation conditions for high ligation yields and demonstrated a broad RNA substrate scope. Together with the smooth synthetic accessibility of 5′-adenylated RNAs, the new DNA enzymes are promising tools for the protein-free synthesis of long RNAs, for example containing precious modified nucleotides or fluorescent labels for biochemical and biophysical investigations. Full article
(This article belongs to the Special Issue Advances in Catalytic DNA)
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9 pages, 1466 KiB  
Article
Covalently Functionalized DNA Duplexes and Quadruplexes as Hybrid Catalysts in an Enantioselective Friedel–Crafts Reaction
by Surjendu Dey and Andres Jäschke
Molecules 2020, 25(14), 3121; https://doi.org/10.3390/molecules25143121 - 08 Jul 2020
Cited by 6 | Viewed by 2739
Abstract
The precise site-specific positioning of metal–ligand complexes on various DNA structures through covalent linkages has gained importance in the development of hybrid catalysts for aqueous-phase homogeneous catalysis. Covalently modified double-stranded and G-quadruplex DNA-based hybrid catalysts have been investigated separately. To understand the role [...] Read more.
The precise site-specific positioning of metal–ligand complexes on various DNA structures through covalent linkages has gained importance in the development of hybrid catalysts for aqueous-phase homogeneous catalysis. Covalently modified double-stranded and G-quadruplex DNA-based hybrid catalysts have been investigated separately. To understand the role of different DNA secondary structures in enantioselective Friedel–Crafts alkylation, a well-known G-quadruplex-forming sequence was covalently modified at different positions. The catalytic performance of this modified DNA strand was studied in the presence and absence of a complementary DNA sequence, resulting in the formation of two different secondary structures, namely duplex and G-quadruplex. Indeed, the secondary structures had a tremendous effect on both the yield and stereoselectivity of the catalyzed reaction. In addition, the position of the modification, the topology of the DNA, the nature of the ligand, and the length of the linker between ligand and DNA were found to modulate the catalytic performance of the hybrid catalysts. Using the optimal linker length, the quadruplexes formed the (−)-enantiomer with up to 65% ee, while the duplex yielded the (+)-enantiomer with up to 62% ee. This study unveils a new and simple way to control the stereochemical outcome of a Friedel–Crafts reaction. Full article
(This article belongs to the Special Issue Advances in Catalytic DNA)
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11 pages, 1289 KiB  
Article
Sensitive Detection of Nucleic Acids Using Subzyme Feedback Cascades
by Nicole Hasick, Andrea Lawrence, Radhika Ramadas and Alison Todd
Molecules 2020, 25(7), 1755; https://doi.org/10.3390/molecules25071755 - 10 Apr 2020
Cited by 5 | Viewed by 3183
Abstract
The development of Subzymes demonstrates how the catalytic activity of DNAzymes can be controlled for detecting nucleic acids; however, Subzymes alone lack the sensitivity required to detect low target concentrations. To improve sensitivity, we developed a feedback system using a pair of cross-catalytic [...] Read more.
The development of Subzymes demonstrates how the catalytic activity of DNAzymes can be controlled for detecting nucleic acids; however, Subzymes alone lack the sensitivity required to detect low target concentrations. To improve sensitivity, we developed a feedback system using a pair of cross-catalytic Subzymes. These were individually tethered to microparticles (MP) and separated by a porous membrane rendering them unable to interact. In the presence of a target, active PlexZymes® cleave a first Subzyme, which separates a first DNAzyme from its MP, allowing the DNAzyme to migrate through the membrane, where it can cleave a second Subzyme. This releases a second DNAzyme which can now migrate through the membrane and cleave more of the first Subzyme, thus initiating a cross-catalytic cascade. Activated DNAzymes can additionally cleave fluorescent substrates, generating a signal, and thereby, indicating the presence of the target. The method detected 1 fM of DNA homologous to the ompA gene of Chlamydia trachomatis within 30 min, demonstrating a 10,000-fold increase in sensitivity over PlexZyme detection alone. The Subzyme cascade is universal and can be triggered by any target by modifying the target sensing arms of the PlexZymes. Further, it is isothermal, protein-enzyme-free and shows great potential for rapid and affordable biomarker detection. Full article
(This article belongs to the Special Issue Advances in Catalytic DNA)
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Review

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24 pages, 842 KiB  
Review
Molecular Features and Metal Ions That Influence 10-23 DNAzyme Activity
by Hannah Rosenbach, Julian Victor, Manuel Etzkorn, Gerhard Steger, Detlev Riesner and Ingrid Span
Molecules 2020, 25(13), 3100; https://doi.org/10.3390/molecules25133100 - 07 Jul 2020
Cited by 20 | Viewed by 7309
Abstract
Deoxyribozymes (DNAzymes) with RNA hydrolysis activity have a tremendous potential as gene suppression agents for therapeutic applications. The most extensively studied representative is the 10-23 DNAzyme consisting of a catalytic loop and two substrate binding arms that can be designed to bind and [...] Read more.
Deoxyribozymes (DNAzymes) with RNA hydrolysis activity have a tremendous potential as gene suppression agents for therapeutic applications. The most extensively studied representative is the 10-23 DNAzyme consisting of a catalytic loop and two substrate binding arms that can be designed to bind and cleave the RNA sequence of interest. The RNA substrate is cleaved between central purine and pyrimidine nucleotides. The activity of this DNAzyme in vitro is considerably higher than in vivo, which was suggested to be related to its divalent cation dependency. Understanding the mechanism of DNAzyme catalysis is hindered by the absence of structural information. Numerous biological studies, however, provide comprehensive insights into the role of particular deoxynucleotides and functional groups in DNAzymes. Here we provide an overview of the thermodynamic properties, the impact of nucleobase modifications within the catalytic loop, and the role of different metal ions in catalysis. We point out features that will be helpful in developing novel strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. Consideration of these features will enable to develop improved strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. These insights provide the basis for improving activity in cells and pave the way for developing DNAzyme applications. Full article
(This article belongs to the Special Issue Advances in Catalytic DNA)
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