Synthesis of Oligonucleotides Containing 5-Carboxy-2‘-deoxyuridine at Defined Sites

Berthod, Thomas; Pétillot, Yves; Guy, A.; Cadet, Jean; Molko, D.

doi:10.1021/jo960614f

Cited by 15 publications

(7 citation statements)

References 14 publications

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“…5-Cyano-2’-deoxyuridine can be synthesized by treatment of 2’-deoxy-5-iodouridine with KCN, or by treatment of 5-trifluoromethyl-2’-deoxyuridine with concentrated NH 4 OH [ 62 ]. 5-Carboxy-2’-deoxyuridine can be obtained from the oxidation of thymidine by menadione-mediated photosensitization [ 63 ] or from the alkaline hydrolysis of 5-trifluoromethyl-2’-deoxyuridine [ 64 ]. In this work 5-substituted 2’-deoxyuridine derivatives were obtained via glycosylation of silylated 5-cyano- or 5-carboxy-uracil with acetylated 2-deoxyribose in the presence of tin (IV) chloride as Lewis acid catalyst.…”

Section: Resultsmentioning

confidence: 99%

Modified Nucleotides as Substrates of Terminal Deoxynucleotidyl Transferase

et al. 2017

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The synthesis of novel modified nucleotides and their incorporation into DNA sequences opens many possibilities to change the chemical properties of oligonucleotides (ONs), and, therefore, broaden the field of practical applications of modified DNA. The chemical synthesis of nucleotide derivatives, including ones bearing thio-, hydrazino-, cyano- and carboxy groups as well as 2-pyridone nucleobase-containing nucleotides was carried out. The prepared compounds were tested as substrates of terminal deoxynucleotidyl transferase (TdT). The nucleotides containing N4-aminocytosine, 4-thiouracil as well as 2-pyridone, 4-chloro- and 4-bromo-2-pyridone as a nucleobase were accepted by TdT, thus allowing enzymatic synthesis of 3’-terminally modified ONs. The successful UV-induced cross-linking of 4-thiouracil-containing ONs to TdT was carried out. Enzymatic post-synthetic 3’-modification of ONs with various photo- and chemically-reactive groups opens novel possibilities for future applications, especially in analysis of the mechanisms of polymerases and the development of photo-labels, sensors, and self-assembling structures.

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Section: Resultsmentioning

confidence: 99%

Modified Nucleotides as Substrates of Terminal Deoxynucleotidyl Transferase

et al. 2017

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“…While protected histidine is commercially available, we have synthesized histidine as a methyl ester ( 2 ) with thionyl chloride in methanol in good yield according to literature procedures [ 49 ]. Although basic hydrolysis of alkyl esters has been shown to imply long reaction times, side-product formation and low reaction yields [ 50 ], we found that methyl esters within DNA are hydrolysed under basic conditions even at room temperature using aqueous ammonia provided prolonged reaction times are respected [ 51 ]. Inspired by the results of Perrin and Joyce [ 26 , 52 ], who introduced a nucleoside containing an unprotected imidazole functionality into the DNA synthesis cycle without problems, we first tried to leave the imidazole unprotected in order to avoid extra protection and deprotection steps in the reaction sequence.…”

Section: Resultsmentioning

confidence: 99%

Versatile synthesis of amino acid functionalized nucleosides via a domino carboxamidation reaction

Gheerardijn

Begin

Madder

2014

Beilstein J. Org. Chem.

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SummaryFunctionalized oligonucleotides have recently gained increased attention for incorporation in modified nucleic acid structures both for the design of aptamers with enhanced binding properties as well as the construction of catalytic DNA and RNA. As a shortcut alternative to the incorporation of multiple modified residues, each bearing one extra functional group, we present here a straightforward method for direct linking of functionalized amino acids to the nucleoside base, thus equipping the nucleoside with two extra functionalities at once. As a proof of principle, we have introduced three amino acids with functional groups frequently used as key-intermediates in DNA- and RNAzymes via an efficient and straightforward domino carboxamidation reaction.

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“…Basic hydrolysis of these esters is frequently plagued by low yields, long reaction times, the need for large excesses of reagents, and the formation of by-products that are difficult to separate [45][46][47].…”

Section: Resultsmentioning

confidence: 99%