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Chemical Society Reviews Jun 2013Conjugation of oligonucleotides (ONs) to a variety of reporter groups has been the subject of intensive research during the last decade. Conjugation is indeed of great... (Review)
Review
Conjugation of oligonucleotides (ONs) to a variety of reporter groups has been the subject of intensive research during the last decade. Conjugation is indeed of great interest because it can be used not only to improve the existing ONs properties but also to impart new ones. In this context tremendous efforts have been made to conjugate carbohydrate moieties to ONs. Indeed carbohydrates play an important role in biological processes such as signal transduction and cell adhesion through the recognition with sugar-binding proteins (i.e. lectins) located on the surface of cells. For this reason, carbohydrate-oligonucleotide conjugates (COCs) have been first developed for improving the poor cellular uptake or tissue specific delivery of ONs through receptor-mediated endocytosis. Besides the targeted ONs delivery, carbohydrate-oligonucleotide conjugates (COCs) are also evaluated in the context of carbohydrate biochips in which surface coating with carbohydrates is achieved by using the DNA-directed immobilization strategy (DDI). Peptide nucleic acids (PNAs) have also been extensively investigated as a surrogate of DNA for diverse applications. Therefore attachment of carbohydrate moieties to this class of molecules has been studied. The aforementioned applications of COCs require mimicking of the natural processes, in which the weak individual protein-carbohydrate binding is overcome by using multivalent interactions. This tutorial review focuses on the recent advances in carbohydrate-oligonucleotide conjugates and describes the major synthetic approaches available. In addition, an overview of applications that have been developed using various scaffolds allowing multivalent interactions is provided. Finally recent results on the use of peptide nucleic acids as oligonucleotides surrogate are described.
Topics: Calixarenes; Carbohydrates; Cycloaddition Reaction; DNA; Lectins; Oligonucleotides; Peptide Nucleic Acids
PubMed: 23254681
DOI: 10.1039/c2cs35406c -
Biomedical Chromatography : BMC Jan 2018Phosphorothioate (PS) oligonucleotides are a rapidly rising class of drugs with significant therapeutic applications. However, owing to their complex structure and... (Review)
Review
Phosphorothioate (PS) oligonucleotides are a rapidly rising class of drugs with significant therapeutic applications. However, owing to their complex structure and multistep synthesis and purification processes, generation of low-level impurities and degradation products are common. Therefore, they require significant investment in quality control and impurity identification. This requires the development of advanced methods for analysis, characterization and quantitation. In addition, the presence of the PS linkage leads to the formation of chiral centers which can affect their biological properties and therapeutic efficiency. In this review, the different types of oligonucleotide impurities and degradation products, with an emphasis on their origin, mechanism of formation and methods to reduce, prevent or even eliminate their production, will be extensively discussed. This review will focus mainly on the application of chromatographic techniques to determine these impurities but will also discuss other approaches such as mass spectrometry, capillary electrophoresis and nuclear magnetic resonance spectroscopy. Finally, the chirality and formation of diastereomer mixtures of PS oligonucleotides will be covered as well as approaches used for their characterization and the application for the development of stereochemically-controlled PS oligonucleotides.
Topics: Chromatography, High Pressure Liquid; Electrophoresis; Humans; Magnetic Resonance Spectroscopy; Mass Spectrometry; Oligonucleotides; Quality Control; Stereoisomerism
PubMed: 28869310
DOI: 10.1002/bmc.4088 -
Nucleic Acid Therapeutics Aug 2012
Topics: Clinical Trials as Topic; Consensus Development Conferences as Topic; Drug Approval; Drug Discovery; Humans; Oligonucleotides; Practice Guidelines as Topic
PubMed: 22913593
DOI: 10.1089/nat.2012.0383 -
Nature Methods Aug 2018
Topics: DNA Nucleotidylexotransferase; DNA Primers; Genetic Techniques; Nucleic Acid Amplification Techniques; Oligonucleotides; Solid-Phase Synthesis Techniques; Transcription Termination, Genetic
PubMed: 30065377
DOI: 10.1038/s41592-018-0096-x -
Nature Communications Aug 2021Ligand-oligonucleotide transduction provides the critical pathway to integrate non-nucleic acid molecules into nucleic acid circuits and nanomachines for a variety of...
Ligand-oligonucleotide transduction provides the critical pathway to integrate non-nucleic acid molecules into nucleic acid circuits and nanomachines for a variety of strand-displacement related applications. Herein, a general platform is constructed to convert the signals of ligands into desired oligonucleotides through a precise kinetic control. In this design, the ligand-aptamer binding sequence with an engineered duplex stem is introduced between the toehold and displacement domains of the invading strand to regulate the strand-displacement reaction. Employing this platform, we achieve efficient transduction of both small molecules and proteins orthogonally, and more importantly, establish logical and cascading operations between different ligands for versatile transduction. Besides, this platform is capable of being directly coupled with the signal amplification systems to further enhance the transduction performance. This kinetically controlled platform presents unique features with designing simplicity and flexibility, expandable complexity and system compatibility, which may pave a broad road towards nucleic acid-based developments of sophisticated transduction networks.
Topics: Aptamers, Nucleotide; Kinetics; Ligands; Models, Genetic; Models, Molecular; Nucleic Acid Amplification Techniques; Nucleic Acid Conformation; Oligonucleotides; Signal Transduction; Spectrometry, Fluorescence
PubMed: 34341342
DOI: 10.1038/s41467-021-24962-4 -
Bioconjugate Chemistry Feb 2010The use of synthetic oligonucleotides and their mimics to inhibit gene expression by hybridizing with their target sequences has been hindered by their poor cellular... (Review)
Review
The use of synthetic oligonucleotides and their mimics to inhibit gene expression by hybridizing with their target sequences has been hindered by their poor cellular uptake and inability to reach the nucleus. Covalent postsynthesis or solid-phase conjugation of peptides to oligonucleotides offers a possible solution to these problems. As feasible chemistry is a prerequisite for biological studies, development of efficient and reproducible approaches for convenient preparation of peptide-oligonucleotide conjugates has become a subject of considerable importance. The present review gives an account of the main synthetic methods available to prepare covalent conjugation of peptides to oligonucleotides.
Topics: Oligonucleotides; Peptides
PubMed: 19856957
DOI: 10.1021/bc900158s -
Methods in Enzymology 2013After chemical synthesis, the oligonucleotide preparation contains the desired full-length oligonucleotide but also all of the DNA molecules that were aborted during...
After chemical synthesis, the oligonucleotide preparation contains the desired full-length oligonucleotide but also all of the DNA molecules that were aborted during each cycle in the synthesis, and the by-products generated during the chemical reactions. The purification of oligonucleotides is a critical step for demanding applications where the exact length or sequence of the oligonucleotide is important, or for oligonucleotides longer than 50 bases. There are several methods of increasing oligonucleotide purity, the choice of which will depend on modifications of the oligonucleotides and their intended use. Polyacrylamide gel purification (PAGE purification) is the method of choice when the highest percentage of full-length oligonucleotide is desired. This chapter describes a protocol for oligonucleotide purification using denaturing polyacrylamide gel electrophoresis, and includes oligonucleotide preparation, polyacrylamide gel electrophoresis, and purification from the gel slice by two different methods: by diffusion or by electroelution. This chapter also includes recommendations as well as protocol advice.
Topics: DNA; Electrophoresis, Polyacrylamide Gel; Nucleic Acid Denaturation; Oligonucleotides
PubMed: 24011037
DOI: 10.1016/B978-0-12-418687-3.00006-9 -
Nucleic Acid Therapeutics Apr 2016The Oligonucleotide Safety Working Group subcommittee on genotoxicity testing considers therapeutic oligonucleotides (ONs) unlikely to be genotoxic based on their... (Review)
Review
The Oligonucleotide Safety Working Group subcommittee on genotoxicity testing considers therapeutic oligonucleotides (ONs) unlikely to be genotoxic based on their properties and on the negative results for ONs tested to date. Nonetheless, the subcommittee believes that genotoxicity testing of new ONs is warranted because modified monomers could be liberated from a metabolized ON and incorporated into DNA and could hypothetically cause chain termination, miscoding, and/or faulty replication or repair. The standard test battery as described in Option 1 of International Conference on Harmonisation S2(R1) is generally adequate to assess such potential. However, for the in vitro assay for gene mutations, mammalian cells are considered more relevant than bacteria for most ONs due to their known responsiveness to nucleosides and their greater potential for ON uptake; on the other hand, bacterial assays may be more appropriate for ONs containing non-ON components. Testing is not recommended for ONs with only naturally occurring chemistries or for ONs with chemistries for which there is documented lack of genotoxicity in systems with demonstrated cellular uptake. Testing is recommended for ONs that contain non-natural chemical modifications and use of the complete drug product (including linkers, conjugates, and liposomes) is suggested to provide the most clinically relevant assessment. Documentation of uptake into cells comparable to those used for genotoxicity testing is proposed because intracellular exposure cannot be assumed for these large molecules. ONs could also hypothetically cause mutations through triple helix formation with genomic DNA and no tests are available for detection of such sequence-specific mutations across the entire genome. However, because the potential for triplex formation by therapeutic ONs is extremely low, this potential can be assessed adequately by sequence analysis.
Topics: Animals; Cells, Cultured; DNA Damage; Drug Evaluation, Preclinical; Humans; Mutagenicity Tests; Oligonucleotides
PubMed: 26978711
DOI: 10.1089/nat.2015.0534 -
Current Protocols in Nucleic Acid... Feb 2004A facile method for preparation of uridine 2'-carbamate derivatives based on reaction of 3',5'-disilyl-protected uridine with 1,1'-carbonyldiimidazole followed by... (Review)
Review
A facile method for preparation of uridine 2'-carbamate derivatives based on reaction of 3',5'-disilyl-protected uridine with 1,1'-carbonyldiimidazole followed by treatment with an aliphatic amine is presented. A phosphoramidite monomer suitable for automated oligonucleotide synthesis is obtained in a few steps. The compounds are useful for the introduction of various labels and modifications into an oligonucleotide chain. Although 2'-carbamate modification is somewhat destabilizing for DNA-DNA and DNA-RNA duplexes, it is suitable for the direction of ligands into the minor groove of duplexes or at non-base-paired sites (e.g., loops and bulges) of oligonucleotides. Pyrene-modified oligonucleotide 2'-carbamates show a considerable increase in fluorescence intensity upon hybridization to a complementary RNA (but not DNA).
Topics: Acylation; Base Sequence; Carbamates; Models, Biological; Oligonucleotides; Organophosphorus Compounds; Uridine
PubMed: 18428928
DOI: 10.1002/0471142700.nc0421s15 -
FASEB Journal : Official Publication of... Apr 1993Although many issues remain to be resolved, recent progress suggests that oligonucleotides may have therapeutic potential. The first therapeutic oligonucleotide, ISIS... (Review)
Review
Although many issues remain to be resolved, recent progress suggests that oligonucleotides may have therapeutic potential. The first therapeutic oligonucleotide, ISIS 2105, an oligonucleotide designed to treat genital warts, has completed Phase I clinical trials and is undergoing Phase II testing. Conceptually, oligonucleotides may interact with nucleic acid or nonnucleic acid receptors; however, rational design of oligonucleotide drugs to interact with nucleic acid receptors is significantly simpler because the factors that determine affinity and selectivity are better understood. Recent progress demonstrates that this information can be coupled to rapid advances in the medicinal chemistry of oligonucleotides to create new generations of oligonucleotide drugs with dramatically improved properties. The purposes of this review are to place oligonucleotide therapeutics in the context of modern molecular drug discovery and to summarize progress in understanding the pharmacodynamic properties of oligonucleotides designed to bind to nucleic acid receptors. The pharmacokinetic and toxicologic properties of oligonucleotides have been reviewed recently (1-4). The activities of oligonucleotides that bind to nonnucleic acid receptors will be considered in future reviews.
Topics: Animals; Humans; Oligonucleotides; RNA
PubMed: 7682523
DOI: 10.1096/fasebj.7.6.7682523