scholarly journals Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry

Biomedicines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 628
Author(s):  
Dagmara Baraniak ◽  
Jerzy Boryski
Keyword(s):  
Nucleic Acids ◽  
State Of The Art ◽  
Modified Oligonucleotides ◽  
Synthetic Genes ◽  
Chemically Modified ◽  
Amide Linkage ◽  
Dna And Rna ◽  
Modified Dna ◽  
Modified Nucleic Acids ◽  
Non Coding Rnas

This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.

scholarly journals Synthesis of chemically modified DNA

2016 ◽  
Vol 44 (3) ◽  
pp. 709-715 ◽  
Author(s):  
Arun Shivalingam ◽  
Tom Brown
Keyword(s):  
Synthetic Biology ◽  
Nucleic Acids ◽  
Full Potential ◽  
Chemical Modifications ◽  
Base Pairs ◽  
Chemically Modified ◽  
Naturally Occurring ◽  
Modified Dna ◽  
Modified Nucleic Acids

Naturally occurring DNA is encoded by the four nucleobases adenine, cytosine, guanine and thymine. Yet minor chemical modifications to these bases, such as methylation, can significantly alter DNA function, and more drastic changes, such as replacement with unnatural base pairs, could expand its function. In order to realize the full potential of DNA in therapeutic and synthetic biology applications, our ability to ‘write’ long modified DNA in a controlled manner must be improved. This review highlights methods currently used for the synthesis of moderately long chemically modified nucleic acids (up to 1000 bp), their limitations and areas for future expansion.

scholarly journals Transcription of 4′-thioDNA templates to natural RNA in vitro and in mammalian cells

2015 ◽  
Vol 51 (37) ◽  
pp. 7887-7890 ◽  
Author(s):  
Hideto Maruyama ◽  
Kazuhiro Furukawa ◽  
Hiroyuki Kamiya ◽  
Noriaki Minakawa ◽  
Akira Matsuda
Keyword(s):  
Nucleic Acids ◽  
Mammalian Cells ◽  
Genetic Material ◽  
Rna Polymerases ◽  
Chemically Modified ◽  
Biological Studies ◽  
Modified Nucleic Acids

Synthetic chemically modified nucleic acids, which are compatible with DNA/RNA polymerases, have great potential as a genetic material for synthetic biological studies.

Nuclease stability of boron-modified nucleic acids: application to label-free mismatch detection

2015 ◽  
Vol 13 (43) ◽  
pp. 10604-10608 ◽  
Author(s):  
Maëva Reverte ◽  
Jean-Jacques Vasseur ◽  
Michael Smietana
Keyword(s):  
Nucleic Acids ◽  
Boronic Acid ◽  
Enzymatic Degradation ◽  
Label Free ◽  
New Class ◽  
Mismatch Detection ◽  
Modified Dna ◽  
Modified Nucleic Acids

Boronic acid modified DNA emerged as a new class of resistant oligonucleotides against enzymatic degradation. This property has been used to develop an enzyme-assisted label free method for mismatch detection.

scholarly journals RNA Chemistry for RNA Biology

2019 ◽  
Vol 73 (5) ◽  
pp. 368-373 ◽  
Author(s):  
Pascal Röthlisberger ◽  
Christian Berk ◽  
Jonathan Hall
Keyword(s):  
Chemical Synthesis ◽  
Nucleic Acids ◽  
Chemical Biology ◽  
Rna Synthesis ◽  
Intrinsic Properties ◽  
Chemical Modifications ◽  
Chemically Modified ◽  
Wide Range ◽  
Rna Biology ◽  
Modified Nucleic Acids

Advances in the chemical synthesis of RNA have opened new possibilities to address current questions in RNA biology. Access to site-specifically modified oligoribonucleotides is often a pre-requisite for RNA chemical-biology projects. Driven by the enormous research efforts for development of oligonucleotide therapeutics, a wide range of chemical modifications have been developed to modulate the intrinsic properties of nucleic acids in order to fit their use as therapeutics or research tools. The RNA synthesis platform, supported by the NCCR RNA & Disease, aims to provide access to a large variety of chemically modified nucleic acids. In this review, we describe some of the recent projects that involved work of the platform and highlight how RNA chemistry supports new discoveries in RNA biology.

scholarly journals Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly

2021 ◽  
Author(s):  
Angela F. De Fazio ◽  
Doxi Misatziou ◽  
Ysobel R. Baker ◽  
Otto L. Muskens ◽  
Tom Brown ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Nanoparticle Assembly ◽  
Dna Intercalators ◽  
Chemically Modified ◽  
Modified Nucleic Acids

The chemical manipulation of DNA offers new tools to tune the properties of nanoparticle self assemblies.

scholarly journals Cyclic Automated Model Building (CAB) Applied to Nucleic Acids

Crystals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 280
Author(s):  
Maria Cristina Burla ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Model Building ◽  
State Of The Art ◽  
Molecular Replacement ◽  
Dna And Rna ◽  
Protein Model ◽  
Rna Fragments ◽  
Nucleic Acid Structures ◽  
Automated Model Building

Obtaining high-quality models for nucleic acid structures by automated model building programs (AMB) is still a challenge. The main reasons are the rather low resolution of the diffraction data and the large number of rotatable bonds in the main chains. The application of the most popular and documented AMB programs (e.g., PHENIX.AUTOBUILD, NAUTILUS and ARP/wARP) may provide a good assessment of the state of the art. Quite recently, a cyclic automated model building (CAB) package was described; it is a new AMB approach that makes the use of BUCCANEER for protein model building cyclic without modifying its basic algorithms. The applications showed that CAB improves the efficiency of BUCCANEER. The success suggested an extension of CAB to nucleic acids—in particular, to check if cyclically including NAUTILUS in CAB may improve its effectiveness. To accomplish this task, CAB algorithms designed for protein model building were modified to adapt them to the nucleic acid crystallochemistry. CAB was tested using 29 nucleic acids (DNA and RNA fragments). The phase estimates obtained via molecular replacement (MR) techniques were automatically submitted to phase refinement and then used as input for CAB. The experimental results from CAB were compared with those obtained by NAUTILUS, ARP/wARP and PHENIX.AUTOBUILD.

scholarly journals A triazole linkage that mimics the DNA phosphodiester group in living systems

2015 ◽  
Vol 48 (4) ◽  
pp. 429-436 ◽  
Author(s):  
Afaf H. El-Sagheer ◽  
Tom Brown
Keyword(s):  
Click Chemistry ◽  
Chemical Reaction ◽  
Chemical Process ◽  
Living Systems ◽  
Complementary Dna ◽  
Chemically Modified ◽  
Dna And Rna ◽  
Modified Dna ◽  
Dna Strands ◽  
Phosphodiester Group

AbstractWe describe the development of a chemical process based on the CuAAC reaction (click chemistry) to ligate DNA strands and produce an unnatural triazole backbone linkage. The chemical reaction is templated by a complementary DNA splint which accelerates the reaction and provides the required specificity. The resultant 1,4-triazole linkage is read through by DNA and RNA polymerases and is biocompatible in bacterial and human cells. This work has implications for the synthesis of chemically modified genes and other large modified DNA and RNA constructs.

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