scholarly journals Synthesis and properties of oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing adenine, guanine, or 5-methylcytosine nucleobases

2021 ◽  
Vol 17 ◽  
pp. 622-629
Author(s):  
Naohiro Horie ◽  
Takao Yamaguchi ◽  
Shinji Kumagai ◽  
Satoshi Obika
Keyword(s):  
Nucleic Acid ◽  
Binding Affinity ◽  
Antisense Oligonucleotides ◽  
Modified Oligonucleotides ◽  
Biophysical Properties ◽  
Chemical Modifications ◽  
Antisense Technology ◽  
Strong Affinity ◽  
The Stability

Chemical modifications have been extensively used for therapeutic oligonucleotides because they strongly enhance the stability against nucleases, binding affinity to the targets, and efficacy. We previously reported that oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing the thymine (T) nucleobase show excellent biophysical properties for applications in antisense technology. In this paper, we describe the synthesis of GuNA[Me] phosphoramidites bearing other typical nucleobases including adenine (A), guanine (G), and 5-methylcytosine (mC). The phosphoramidites were successfully incorporated into oligonucleotides following the method previously developed for the GuNA[Me]-T-modified oligonucleotides. The binding affinity of the oligonucleotides modified with GuNA[Me]-A, -G, or -mC toward the complementary single-stranded DNAs or RNAs was systematically evaluated. All of the GuNA[Me]-modified oligonucleotides were found to have a strong affinity for RNAs. These data indicate that GuNA[Me] could be a useful modification for therapeutic antisense oligonucleotides.

scholarly journals In vitro and in vivo properties of therapeutic oligonucleotides containing non-chiral 3′ and 5′ thiophosphate linkages

2019 ◽  
Vol 48 (1) ◽  
pp. 63-74 ◽  
Author(s):  
Jörg Duschmalé ◽  
Henrik Frydenlund Hansen ◽  
Martina Duschmalé ◽  
Erich Koller ◽  
Nanna Albaek ◽  
...  
Keyword(s):  
Antisense Oligonucleotides ◽  
Rnase H ◽  
Modified Oligonucleotides ◽  
In Vitro Experiments ◽  
Chemical Modifications ◽  
Pharmacokinetic Properties ◽  
Target Binding ◽  
The Individual

Abstract The introduction of non-bridging phosphorothioate (PS) linkages in oligonucleotides has been instrumental for the development of RNA therapeutics and antisense oligonucleotides. This modification offers significantly increased metabolic stability as well as improved pharmacokinetic properties. However, due to the chiral nature of the phosphorothioate, every PS group doubles the amount of possible stereoisomers. Thus PS oligonucleotides are generally obtained as an inseparable mixture of a multitude of diastereoisomeric compounds. Herein, we describe the introduction of non-chiral 3′ thiophosphate linkages into antisense oligonucleotides and report their in vitro as well as in vivo activity. The obtained results are carefully investigated for the individual parameters contributing to antisense activity of 3′ and 5′ thiophosphate modified oligonucleotides (target binding, RNase H recruitment, nuclease stability). We conclude that nuclease stability is the major challenge for this approach. These results highlight the importance of selecting meaningful in vitro experiments particularly when examining hitherto unexplored chemical modifications.

Advances in the synthesis and antisense technology applications of bridged nucleic acid monomers

2021 ◽  
Vol 25 ◽  
Author(s):  
Priyanka Mangla ◽  
Balaji Olety ◽  
Vivek K. Sharma
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Antisense Oligonucleotides ◽  
Cost Effective ◽  
Biophysical Properties ◽  
Technology Applications ◽  
Effective Synthesis ◽  
Target Rna ◽  
Ribose Sugar ◽  
Tremendous Impact

: Bridged nucleic acids (BNA) or locked nucleic acids (LNA) are a class of nucleic acids modification, which is obtained by connecting the 2'-O and 4'-C of ribose sugar using a methylene bridge. This ‘bridging or locking’ (hence the name) of ribose sugar has a tremendous impact both on the biological and biophysical properties of therapeutic nucleic acids. They have enhanced stability against nucleases and also have higher binding affinity for the target RNA. Owing to these advantages, BNA is one of the most preferred nucleic acid modifications of antisense oligonucleotides (ASOs). However, the synthesis of BNA monomers which are lengthy and low-yielding, requires extensive protection and deprotection of the sugar functionalities. In this article, we aim to review challenges associated with their synthesis, and discuss recent chemical, chemo-enzymatic, and transglycosylation strategies employed for efficient and cost-effective synthesis of BNA monomers and selected BNA analogues.

In vitro evaluation of hexitol nucleic acid antisense oligonucleotides

1999 ◽  
Author(s):  
Arthur Van Aerschot ◽  
Mark Vandermeeren ◽  
Johan Geysen ◽  
Walter Luyten ◽  
Marc Miller ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Antisense Oligonucleotides ◽  
In Vitro Evaluation

scholarly journals Nucleic-Acid-Binding Chromophores as Efficient Indicators of Aptamer-Target Interactions

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Kwabena Sarpong ◽  
Bhaskar Datta
Keyword(s):  
Nucleic Acid ◽  
High Sensitivity ◽  
Covalent Modification ◽  
Fluorescence Signal ◽  
Nucleic Acid Binding ◽  
Sensitivity And Selectivity ◽  
Target Molecules ◽  
Diagnostic Applications ◽  
The Stability ◽  
Simple Format

The binding affinity and specificity of nucleic acid aptamers have made them valuable candidates for use as sensors in diagnostic applications. In particular, chromophore-functionalized aptamers offer a relatively simple format for detection and quantification of target molecules. We describe the use of nucleic-acid-staining reagents as an effective tool for detecting and signaling aptamer-target interactions. Aptamers varying in size and structure and targeting a range of molecules have been used in conjunction with commercially available chromophores to indicate and quantify the presence of cognate targets with high sensitivity and selectivity. Our assay precludes the covalent modification of nucleic acids and relies on the differential fluorescence signal of chromophores when complexed with aptamers with or without their cognate target. We also evaluate factors that are critical for the stability of the complex between the aptamer and chromophore in presence or absence of target molecules. Our results indicate the possibility of controlling those factors to enhance the sensitivity of target detection by the aptamers used in such assays.

Synthesis and properties of GuNA purine/pyrimidine nucleosides and oligonucleotides

2020 ◽  
Vol 18 (46) ◽  
pp. 9461-9472
Author(s):  
Shinji Kumagai ◽  
Hiroaki Sawamoto ◽  
Tomo Takegawa-Araki ◽  
Yuuki Arai ◽  
Shuhei Yamakoshi ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Modified Oligonucleotides ◽  
Robust Method ◽  
Facile Synthesis ◽  
Pyrimidine Nucleosides ◽  
Thymine Adenine ◽  
Purine Pyrimidine

Facile synthesis of GuNA (guanidine-bridged nucleic acid) phosphoramidites bearing thymine, adenine, guanine, and 5-methylcytosine nucleobases and a robust method for the preparation of GuNA-modified oligonucleotides are described.

scholarly journals Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation

2021 ◽  
Author(s):  
Xiaoxuan Su ◽  
Wenxiao Ma ◽  
Boyang Cheng ◽  
Qian Wang ◽  
Zefeng Guo ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Antisense Oligonucleotides ◽  
Target Recognition ◽  
Vero Cells ◽  
Rnase L ◽  
Rna Targets ◽  
Infection Models ◽  
Antisense Sequence ◽  
Innate Antiviral Response ◽  
Chimeric Oligonucleotides

AbstractThere is an urgent need for effective antiviral drugs to alleviate the current COVID-19 pandemic. Here, we rationally designed and developed chimeric antisense oligonucleotides to degrade envelope and spike RNAs of SARS-CoV-2. Each oligonucleotide comprises a 3’ antisense sequence for target recognition and a 5’-phosphorylated 2’-5’ poly(A)4 for guided ribonuclease L (RNase L) activation. Since RNase L can potently cleave single strand RNA during innate antiviral response, the improved degradation efficiency of chimeric oligonucleotides was twice as much as classic antisense oligonucleotides in Vero cells, for both SARS-CoV-2 RNA targets. In pseudovirus infection models, one of chimeric oligonucleotides targeting spike RNA achieved potent and broad-spectrum inhibition of both SARS-CoV-2 and its recently reported N501Y and/or ΔH69/ΔV70 mutants. These results showed that the constructed chimeric oligonucleotides could efficiently degrade pathogenic RNA of SARS-CoV-2 facilitated by immune activation, showing promising potentials as antiviral nucleic acid drugs for COVID-19.

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