Syntheses and Oligonucleotide Incorporation of Nucleoside Analogues Containing Pendant Imidazolyl or Amino Functionalities – The Search for Sequence‐Specific Artificial Ribonucleases

Abstract

Keywords: Oligonucleotides / Nucleosides / Modified nucleosides / Artificial ribonucleaseOligonucleotide derivatives containing imidazolyl and amino functionalities have been proposed as artificial ribonucleases that might mimic the activities of RNase A but with greater sequence specificity. Such oligonucleotide reagents would have important applications as enhanced antisense reagents that obviate the need to recruit a cellular nuclease or nuclease complex. We present the syntheses of six nucleoside phosphoramidite analogues containing pendant protected imidazolyl or amino groups and their incorporation into oligonucleotides. We show that the six functionalised phos-

Facile functionalization at the C4 position of pyrimidine nucleosides via amide group activation with (benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP) and biological evaluations of the products

“…10,12 C4 triazoles 17–21 and tetrazoles 22–26 are common, stable reactive pyrimidine derivatives that have seen wide applications for nucleoside and nucleic acid modifications. A range of aryl sulfonates (Ar = p -toluenesulfonyl, 2-mesitylenesulfonyl, 2,4,6-triisopropylbenzenesulfonyl), 27–32 have also been explored as reactive reagents, not only for direct substitution reactions, but also for cross-coupling chemistry. 16,33 Among these, the 2,4,6-triisopropylbenzenesulfonyl derivatives have been shown to be reasonably stable but the 2-mesitylenesulfonyl analogues are not quite as stable.…”

“…27 By contrast, a p -toluenesulfonyl pyrimidine nucleoside was used directly after preparation. 32 Pyrimidine C4 tosylates have also been converted to N -methylpiperidinyl and N -methylpyrrolidinyl salts, as reactive nucleoside analogues. 34 …”

Identification of a pKa-regulating motif stabilizing imidazole-modified double-stranded DNA

“…The synthesis of the imidazole-modified nucleoside from thymidine is achieved in three steps as described by Holmes and Gait ( 27 ). In a first step, a palladium-catalyzed one-pot carboxamidation reaction is used to attach histamine (Sigma-Aldrich) to 5-iodo-2‘-deoxyuridine (Sigma-Aldrich) via an amide bond.…”

Synthesis of Functionalised Nucleosides for Incorporation into Nucleic Acid-Based Serine Protease Mimics

“…However, it has been shown that such a TFA treatment can lead to a certain amount of depurination of the oligonucleotide [34,38]. The research groups of Gait and Herdewijn both proved that removal of the Boc group from imidazole during standard deprotection procedures with saturated methanolic ammonia after oligonucleotide synthesis is possible [35,39], therefore in our second attempt, using urocanic acid (1), the imidazole moiety was Boc-protected using di-tert-butyldicarbonate as shown in Scheme 1. N Im -Boc-protected urocanic acid 2 was further coupled with the dimethoxytrityl protected 2'-amino-2'-deoxyuridine 4 in the presence of N- (3-dimethylaminopropyl)-N'-ethylcarbodiimide (EDC) and N-hydroxysuccinimide (NHS) to give 5 in 68% yield.…”

“…However, the DNP protection did not survive conditions used during purification of the final DMTr-protected nucleoside. Because it has further been proven that the DNP group gives yellow contaminated products after deprotection, we decided to change the protecting group into a tert-butoxycarbonyl (Boc) one [34], which is compatible with the reagents used during nucleoside-and oligonucleotide synthesis [35][36][37]. In principle, removal of the Boc group on a solid support can be accomplished with a 10% TFA solution after automated synthesis [37].…”