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Special Issue "Nucleoside Modifications"

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

Deadline for manuscript submissions: closed (31 March 2015)

Special Issue Editors

Guest Editor
Prof. Mahesh K. Lakshman (Website)

Department of Chemistry, The City College and The City University of New York, New York, NY 10031, USA
Interests: Nucleoside modification via metal-catalyzed and uncatalyzed processes, synthesis of novel nucleoside structures, chemical carcinogenesis, site-specific DNA modification, synthesis of polycyclic aromatic hydrocarbons and their metabolites, aryne chemistry, and generally applicable synthetic methodology
Guest Editor
Prof. Fumi Nagatsugi (Website)

Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi, Japan
Interests: Oligonucleotides, artificial molecules for binding to DNA and RNA, selective chemical reactions to DNA and RNA

Special Issue Information

Dear Colleagues,

Nucleosides are the fundamental components of genetic material, and are present in all living organisms, and in viruses. By virtue of their ubiquity, they are highly important biomolecules. Nucleosides consist of a heterocyclic aglycone and a sugar unit. For several decades, the natural nucleoside structures have inspired the development of chemical and biochemical modifications, leading to new nucleoside-like entities via aglycone, as well as saccharide, modifications. As a result, modified nucleosides and nucleoside analogues have wide spread utilities in biochemistry, biology, as pharmaceutical agents, and as biological probes. There is a constant need for access to novel nucleoside analogues for a plethora of applications, prompting the development of new methodologies.  This Special Issue aims to provide a forum for the dissemination of the latest information on new chemical methods for access to modified nucleosides, nucleoside analogues, and applications of these new molecules.

Professor Mahesh K. Lakshman
Professor Fumi Nagatsugi
Guest Editors

Submission

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a 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 monthly journal published by MDPI.

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Published Papers (14 papers)

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Research

Jump to: Review

Open AccessArticle Site-Selective Ribosylation of Fluorescent Nucleobase Analogs Using Purine-Nucleoside Phosphorylase as a Catalyst: Effects of Point Mutations
Molecules 2016, 21(1), 44; doi:10.3390/molecules21010044
Received: 13 November 2015 / Revised: 7 December 2015 / Accepted: 9 December 2015 / Published: 28 December 2015
Cited by 1 | PDF Full-text (870 KB) | HTML Full-text | XML Full-text
Abstract
Enzymatic ribosylation of fluorescent 8-azapurine derivatives, like 8-azaguanine and 2,6-diamino-8-azapurine, with purine-nucleoside phosphorylase (PNP) as a catalyst, leads to N9, N8, and N7-ribosides. The final proportion of the products may be modulated by point mutations in the enzyme active site. As an [...] Read more.
Enzymatic ribosylation of fluorescent 8-azapurine derivatives, like 8-azaguanine and 2,6-diamino-8-azapurine, with purine-nucleoside phosphorylase (PNP) as a catalyst, leads to N9, N8, and N7-ribosides. The final proportion of the products may be modulated by point mutations in the enzyme active site. As an example, ribosylation of the latter substrate by wild-type calf PNP gives N7- and N8-ribosides, while the N243D mutant directs the ribosyl substitution at N9- and N7-positions. The same mutant allows synthesis of the fluorescent N7-β-d-ribosyl-8-azaguanine. The mutated form of the E. coli PNP, D204N, can be utilized to obtain non-typical ribosides of 8-azaadenine and 2,6-diamino-8-azapurine as well. The N7- and N8-ribosides of the 8-azapurines can be analytically useful, as illustrated by N7-β-d-ribosyl-2,6-diamino-8-azapurine, which is a good fluorogenic substrate for mammalian forms of PNP, including human blood PNP, while the N8-riboside is selective to the E. coli enzyme. Full article
(This article belongs to the Special Issue Nucleoside Modifications)
Open AccessArticle Cladribine Analogues via O6-(Benzotriazolyl) Derivatives of Guanine Nucleosides
Molecules 2015, 20(10), 18437-18463; doi:10.3390/molecules201018437
Received: 17 August 2015 / Revised: 20 September 2015 / Accepted: 22 September 2015 / Published: 9 October 2015
Cited by 1 | PDF Full-text (1310 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Cladribine, 2-chloro-2′-deoxyadenosine, is a highly efficacious, clinically used nucleoside for the treatment of hairy cell leukemia. It is also being evaluated against other lymphoid malignancies and has been a molecule of interest for well over half a century. In continuation of our [...] Read more.
Cladribine, 2-chloro-2′-deoxyadenosine, is a highly efficacious, clinically used nucleoside for the treatment of hairy cell leukemia. It is also being evaluated against other lymphoid malignancies and has been a molecule of interest for well over half a century. In continuation of our interest in the amide bond-activation in purine nucleosides via the use of (benzotriazol-1yl-oxy)tris(dimethylamino)phosphonium hexafluorophosphate, we have evaluated the use of O6-(benzotriazol-1-yl)-2′-deoxyguanosine as a potential precursor to cladribine and its analogues. These compounds, after appropriate deprotection, were assessed for their biological activities, and the data are presented herein. Against hairy cell leukemia (HCL), T-cell lymphoma (TCL) and chronic lymphocytic leukemia (CLL), cladribine was the most active against all. The bromo analogue of cladribine showed comparable activity to the ribose analogue of cladribine against HCL, but was more active against TCL and CLL. The bromo ribose analogue of cladribine showed activity, but was the least active among the C6-NH2-containing compounds. Substitution with alkyl groups at the exocyclic amino group appears detrimental to activity, and only the C6 piperidinyl cladribine analogue demonstrated any activity. Against adenocarcinoma MDA-MB-231 cells, cladribine and its ribose analogue were most active. Full article
(This article belongs to the Special Issue Nucleoside Modifications)
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Open AccessArticle Non-Nucleosidic Analogues of Polyaminonucleosides and Their Influence on Thermodynamic Properties of Derived Oligonucleotides
Molecules 2015, 20(7), 12652-12669; doi:10.3390/molecules200712652
Received: 17 March 2015 / Revised: 8 July 2015 / Accepted: 9 July 2015 / Published: 13 July 2015
PDF Full-text (1018 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The rationale for the synthesis of cationic modified nucleosides is higher expected nuclease resistance and potentially better cellular uptake due to an overall reduced negative charge based on internal charge compensation. Due to the ideal distance between cationic groups, polyamines are perfect [...] Read more.
The rationale for the synthesis of cationic modified nucleosides is higher expected nuclease resistance and potentially better cellular uptake due to an overall reduced negative charge based on internal charge compensation. Due to the ideal distance between cationic groups, polyamines are perfect counterions for oligodeoxyribonucleotides. We have synthesized non-nucleosidic analogues built from units that carry different diol structures instead of sugar residues and functionalized with polyamines. The non-nucleosidic analogues were attached as internal or 5′-terminal modifications in oligodeoxyribonucleotide strands. The thermodynamic studies of these polyaminooligonucleotide analogues revealed stabilizing or destabilizing effects that depend on the linker or polyamine used. Full article
(This article belongs to the Special Issue Nucleoside Modifications)
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Open AccessArticle Carboxylated Acyclonucleosides: Synthesis and RNase A Inhibition
Molecules 2015, 20(4), 5924-5941; doi:10.3390/molecules20045924
Received: 17 December 2014 / Revised: 20 March 2015 / Accepted: 20 March 2015 / Published: 3 April 2015
PDF Full-text (1106 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Strategically designed carboxylated acyclonucleosides have been probed as a new class of RNase A inhibitors. Several experimental and theoretical studies have been performed to compile relevant qualitative and quantitative information regarding the nature and extent of inhibition. The inhibition constant (K [...] Read more.
Strategically designed carboxylated acyclonucleosides have been probed as a new class of RNase A inhibitors. Several experimental and theoretical studies have been performed to compile relevant qualitative and quantitative information regarding the nature and extent of inhibition. The inhibition constant (Ki) values were determined using a UV-based kinetics experiment. The changes in the secondary structure of the enzyme upon binding with the inhibitors were obtained from circular dichroism studies. The binding constants for enzyme-inhibitor interactions were determined with the help of fluorescence spectroscopy. Docking studies were performed to reveal the possible binding sites of the inhibitors within the enzyme. The cytosine analogues were found to possess better inhibitory properties in comparison to the corresponding uracil derivatives. An increment in the number of carboxylic acid groups (-COOH) in the inhibitor backbone was found to result in better inhibition. Full article
(This article belongs to the Special Issue Nucleoside Modifications)
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Open AccessArticle Synthesis and Biological Properties of 5-(1H-1,2,3-Triazol-4-yl)isoxazolidines: A New Class of C-Nucleosides
Molecules 2015, 20(4), 5260-5275; doi:10.3390/molecules20045260
Received: 4 February 2015 / Revised: 9 March 2015 / Accepted: 13 March 2015 / Published: 24 March 2015
Cited by 4 | PDF Full-text (702 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A novel series of C-nucleosides, featuring the presence of a 1,2,3-triazole ring linked to an isoxazolidine system, has been designed as mimetics of the pyrimidine nucleobases. An antiproliferative effect was observed for compounds 17a and 17b: the growth inhibitory effect [...] Read more.
A novel series of C-nucleosides, featuring the presence of a 1,2,3-triazole ring linked to an isoxazolidine system, has been designed as mimetics of the pyrimidine nucleobases. An antiproliferative effect was observed for compounds 17a and 17b: the growth inhibitory effect reaches the 50% in HepG2 and HT-29 cells and increases up to 56% in the SH-SY5Y cell line after 72 h of incubation at a 100 µM concentration. Full article
(This article belongs to the Special Issue Nucleoside Modifications)
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Open AccessArticle Synthesis of Peptide Nucleic Acids Containing a Crosslinking Agent and Evaluation of Their Reactivities
Molecules 2015, 20(3), 4708-4719; doi:10.3390/molecules20034708
Received: 26 January 2015 / Revised: 3 March 2015 / Accepted: 9 March 2015 / Published: 13 March 2015
Cited by 1 | PDF Full-text (1197 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Peptide nucleic acids (PNAs) are structural mimics of nucleic acids that form stable hybrids with DNA and RNA. In addition, PNAs can invade double-stranded DNA. Due to these characteristics, PNAs are widely used as biochemical tools, for example, in antisense/antigene therapy. Interstrand [...] Read more.
Peptide nucleic acids (PNAs) are structural mimics of nucleic acids that form stable hybrids with DNA and RNA. In addition, PNAs can invade double-stranded DNA. Due to these characteristics, PNAs are widely used as biochemical tools, for example, in antisense/antigene therapy. Interstrand crosslink formation in nucleic acids is one of the strategies for preparing a stable duplex by covalent bond formation. In this study, we have synthesized PNAs incorporating 4-amino-6-oxo-2-vinylpyrimidine (AOVP) as a crosslinking agent and evaluated their reactivities for targeting DNA and RNA. Full article
(This article belongs to the Special Issue Nucleoside Modifications)
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Open AccessArticle Construction of an Isonucleoside on a 2,6-Dioxobicyclo[3.2.0]-heptane Skeleton
Molecules 2015, 20(3), 4623-4634; doi:10.3390/molecules20034623
Received: 2 February 2015 / Revised: 3 March 2015 / Accepted: 4 March 2015 / Published: 12 March 2015
PDF Full-text (655 KB) | HTML Full-text | XML Full-text
Abstract
We have built a new isonucleoside derivative on a 2,6-dioxobicyclo[3.2.0]heptane skeleton as a potential anti-HIV agent. To synthesize the target compound, an acetal-protected dihydroxyacetone was first converted to a 2,3-epoxy-tetrahydrofuran derivative. Introduction of an azide group, followed by the formation of an [...] Read more.
We have built a new isonucleoside derivative on a 2,6-dioxobicyclo[3.2.0]heptane skeleton as a potential anti-HIV agent. To synthesize the target compound, an acetal-protected dihydroxyacetone was first converted to a 2,3-epoxy-tetrahydrofuran derivative. Introduction of an azide group, followed by the formation of an oxetane ring, gave a pseudosugar derivative with a 2,6-dioxobicyclo[3.2.0]heptane skeleton. The desired isonucleoside was obtained by constructing a purine base moiety on the scaffold, followed by amination. Full article
(This article belongs to the Special Issue Nucleoside Modifications)
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Open AccessArticle Tethering in RNA: An RNA-Binding Fragment Discovery Tool
Molecules 2015, 20(3), 4148-4161; doi:10.3390/molecules20034148
Received: 5 December 2014 / Revised: 20 January 2015 / Accepted: 17 February 2015 / Published: 4 March 2015
PDF Full-text (3613 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Tethering has been extensively used to study small molecule interactions with proteins through reversible disulfide bond forming reactions to cysteine residues. We describe the adaptation of Tethering to the study of small molecule binding to RNA using a thiol-containing adenosine analog (A [...] Read more.
Tethering has been extensively used to study small molecule interactions with proteins through reversible disulfide bond forming reactions to cysteine residues. We describe the adaptation of Tethering to the study of small molecule binding to RNA using a thiol-containing adenosine analog (ASH). Among 30 disulfide-containing small molecules screened for efficient Tethering to ASH-bearing RNAs derived from pre-miR21, a benzotriazole-containing compound showed prominent adduct formation and selectivity for one of the RNAs tested. The results of this screen demonstrate the viability of using thiol-modified nucleic acids to discover molecules with binding affinity and specificity for the purpose of therapeutic compound lead discovery. Full article
(This article belongs to the Special Issue Nucleoside Modifications)
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Open AccessArticle Hybridisation Potential of 1',3'-Di-O-methylaltropyranoside Nucleic Acids
Molecules 2015, 20(3), 4020-4041; doi:10.3390/molecules20034020
Received: 22 January 2015 / Revised: 16 February 2015 / Accepted: 24 February 2015 / Published: 3 March 2015
Cited by 1 | PDF Full-text (1221 KB) | HTML Full-text | XML Full-text
Abstract
In further study of our series of six-membered ring-containing nucleic acids, different 1',3'-di-O-methyl altropyranoside nucleoside analogs (DMANA) were synthesized comprising all four base moieties, adenine, cytosine, uracil and guanine. Following assembly into oligonucleotides (ONs), their affinity for natural oligonucleotides was [...] Read more.
In further study of our series of six-membered ring-containing nucleic acids, different 1',3'-di-O-methyl altropyranoside nucleoside analogs (DMANA) were synthesized comprising all four base moieties, adenine, cytosine, uracil and guanine. Following assembly into oligonucleotides (ONs), their affinity for natural oligonucleotides was evaluated by thermal denaturation of the respective duplexes. Data were compared with results obtained previously for both anhydrohexitol (HNAs) and 3'-O-methylated altrohexitol modified ONs (MANAs). We hereby demonstrate that ONs modified with DMANA monomers, unlike some of our previously described analogues with constrained 6-membered hexitol rings, did not improve thermodynamic stability of dsRNA complexes, most probably in view of an energetic penalty when forced in the required 1C4 pairing conformation. Overall, a single incorporation was more or less tolerated or even positive for the adenine congener, but incorporation of a second modification afforded a slight destabilization (except for A), while a fully modified sequence displayed a thermal stability of −0.3 °C per modification. The selectivity of pairing remained very high, and the new modification upon incorporation into a DNA strand, strongly destabilized the corresponding DNA duplexes. Unfortunately, this new modification does not bring any advantage to be further evaluated for antisense or siRNA applications. Full article
(This article belongs to the Special Issue Nucleoside Modifications)
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Open AccessArticle Development of New 1,3-Diazaphenoxazine Derivatives (ThioG-Grasp) to Covalently Capture 8-Thioguanosine
Molecules 2015, 20(1), 1078-1087; doi:10.3390/molecules20011078
Received: 9 December 2014 / Accepted: 7 January 2015 / Published: 9 January 2015
PDF Full-text (887 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The derivatives of 8-thioguanosine are thought to be included in the signal transduction system related to 8-nitroguanosine. In this study, we attempted to develop new 1,3-diazaphenoxazine (G-clamp) derivatives to covalently capture 8-thioguanosine (thioG-grasp). It was expected that the chlorine atom at the [...] Read more.
The derivatives of 8-thioguanosine are thought to be included in the signal transduction system related to 8-nitroguanosine. In this study, we attempted to develop new 1,3-diazaphenoxazine (G-clamp) derivatives to covalently capture 8-thioguanosine (thioG-grasp). It was expected that the chlorine atom at the end of the linker would be displaced by the nucleophilic attack by the sulfur atom of 8-thioguanosine via multiple hydrogen-bonded complexes. The thioG-grasp derivative with a propyl linker reacted efficiently with 8-thioguanosine to form the corresponding adduct. Full article
(This article belongs to the Special Issue Nucleoside Modifications)
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Open AccessCommunication Design and Synthesis of a Series of Truncated Neplanocin Fleximers
Molecules 2014, 19(12), 21200-21214; doi:10.3390/molecules191221200
Received: 23 October 2014 / Revised: 8 December 2014 / Accepted: 9 December 2014 / Published: 16 December 2014
PDF Full-text (794 KB) | HTML Full-text | XML Full-text
Abstract
In an effort to study the effects of flexibility on enzyme recognition and activity, we have developed several different series of flexible nucleoside analogues in which the purine base is split into its respective imidazole and pyrimidine components. The focus of this [...] Read more.
In an effort to study the effects of flexibility on enzyme recognition and activity, we have developed several different series of flexible nucleoside analogues in which the purine base is split into its respective imidazole and pyrimidine components. The focus of this particular study was to synthesize the truncated neplanocin A fleximers to investigate their potential anti-protozoan activities by inhibition of S-adenosylhomocysteine hydrolase (SAHase). The three fleximers tested displayed poor anti-trypanocidal activities, with EC50 values around 200 μM. Further studies of the corresponding ribose fleximers, most closely related to the natural nucleoside substrates, revealed low affinity for the known T. brucei nucleoside transporters P1 and P2, which may be the reason for the lack of trypanocidal activity observed. Full article
(This article belongs to the Special Issue Nucleoside Modifications)
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Open AccessArticle Formation of Mixed-Ligand Complexes of Pd2+ with Nucleoside 5'-Monophosphates and Some Metal-Ion-Binding Nucleoside Surrogates
Molecules 2014, 19(10), 16976-16986; doi:10.3390/molecules191016976
Received: 16 September 2014 / Revised: 8 October 2014 / Accepted: 17 October 2014 / Published: 22 October 2014
Cited by 5 | PDF Full-text (449 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Formation of mixed-ligand Pd2+ complexes between canonical nucleoside 5'-monophosphates and five metal-ion-binding nucleoside analogs has been studied by 1H-NMR spectroscopy to test the ability of these nucleoside surrogates to discriminate between unmodified nucleobases by Pd2+-mediated base pairing. The [...] Read more.
Formation of mixed-ligand Pd2+ complexes between canonical nucleoside 5'-monophosphates and five metal-ion-binding nucleoside analogs has been studied by 1H-NMR spectroscopy to test the ability of these nucleoside surrogates to discriminate between unmodified nucleobases by Pd2+-mediated base pairing. The nucleoside analogs studied included 2,6-bis(3,5-dimethylpyrazol-1-yl)-, 2,6-bis(1-methylhydrazinyl)- and 6-(3,5-dimethylpyrazol-1-yl)-substituted 9-(β-d-ribofuranosyl)purines 13, and 2,4-bis(3,5-dimethylpyrazol-1-yl)- and 2,4-bis(1-methylhydrazinyl)-substituted 5-(β-d-ribofuranosyl)-pyrimidines 45. Among these, the purine derivatives 1-3 bound Pd2+ much more tightly than the pyrimidine derivatives 4, 5 despite apparently similar structures of the potential coordination sites. Compounds 1 and 2 formed markedly stable mixed-ligand Pd2+ complexes with UMP and GMP, UMP binding favored by 1 and GMP by 2. With 3, formation of mixed-ligand complexes was retarded by binding of two molecules of 3 to Pd2+. Full article
(This article belongs to the Special Issue Nucleoside Modifications)
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Review

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Open AccessReview Palladium-Catalyzed Modification of Unprotected Nucleosides, Nucleotides, and Oligonucleotides
Molecules 2015, 20(5), 9419-9454; doi:10.3390/molecules20059419
Received: 24 March 2015 / Revised: 15 May 2015 / Accepted: 19 May 2015 / Published: 22 May 2015
Cited by 7 | PDF Full-text (1539 KB) | HTML Full-text | XML Full-text
Abstract
Synthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a [...] Read more.
Synthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a powerful method to attach groups to the base heterocycles through the formation of new carbon-carbon and carbon-heteroatom bonds. In this review, approaches to palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides are reviewed. Polar reaction media, such as water or polar aprotic solvents, allow reactions to be performed directly on the hydrophilic nucleosides and nucleotides without the need to use protecting groups. Homogeneous aqueous-phase coupling reactions catalyzed by palladium complexes of water-soluble ligands provide a general approach to the synthesis of modified nucleosides, nucleotides, and oligonucleotides. Full article
(This article belongs to the Special Issue Nucleoside Modifications)
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Open AccessReview Modification of Purine and Pyrimidine Nucleosides by Direct C-H Bond Activation
Molecules 2015, 20(3), 4874-4901; doi:10.3390/molecules20034874
Received: 15 February 2015 / Revised: 11 March 2015 / Accepted: 13 March 2015 / Published: 17 March 2015
Cited by 10 | PDF Full-text (1785 KB) | HTML Full-text | XML Full-text
Abstract
Transition metal-catalyzed modifications of the activated heterocyclic bases of nucleosides as well as DNA or RNA fragments employing traditional cross-coupling methods have been well-established in nucleic acid chemistry. This review covers advances in the area of cross-coupling reactions in which nucleosides are [...] Read more.
Transition metal-catalyzed modifications of the activated heterocyclic bases of nucleosides as well as DNA or RNA fragments employing traditional cross-coupling methods have been well-established in nucleic acid chemistry. This review covers advances in the area of cross-coupling reactions in which nucleosides are functionalized via direct activation of the C8-H bond in purine and the C5-H or C6-H bond in uracil bases. The review focuses on Pd/Cu-catalyzed couplings between unactivated nucleoside bases with aryl halides. It also discusses cross-dehydrogenative arylations and alkenylations as well as other reactions used for modification of nucleoside bases that avoid the use of organometallic precursors and involve direct C-H bond activation in at least one substrate. The scope and efficiency of these coupling reactions along with some mechanistic considerations are discussed. Full article
(This article belongs to the Special Issue Nucleoside Modifications)
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