Synthesis of Oligonucleotides Containing 2′-N-alkylaminocarbonyl-2′-amino-LNA (2′-urea-LNA) Moieties Using Post-Synthetic Modification Strategy

Abstract

The post-synthetic modification of an oligonucleotide is a powerful strategy for the synthesis of various analogs of the oligonucleotide, aiming to achieve the desired functions. In this study, we synthesized the thymidine phosphoramidite of 2′-N-pentafluorophenoxycarbonyl-2′-amino-LNA, which was introduced into oligonucleotides. Oligonucleotides containing a 2′-N-pentafluorophenoxycarbonyl-2′-amino-LNA unit could be isolated under ultra-mild deprotection conditions (50 mM K2CO3 in MeOH at room temperature for 4 h). Moreover, by treatment with various amines as a post-synthetic modification, the oligonucleotides were successfully converted into the corresponding 2′-N-alkylaminocarbonyl-2′-amino-LNA (2′-urea-LNA) derivatives. The duplex- and triplex-forming abilities of the synthesized oligonucleotides were evaluated by UV-melting experiments, which showed that 2′-urea-LNAs could stabilize the nucleic acid complexes, similar to the proto-type, 2′-amino-LNA. Thus, 2′-urea-LNAs could be promising units for the modification of oligonucleotides; the design of a substituent on urea may aid the formation of useful oligonucleotides. In addition, pentafluorophenoxycarbonyl, an amino moiety, acted as a precursor of the substituted urea, which may be applicable to the synthesis of oligonucleotide conjugates.

Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides

“…A class of 2’-urea-LNA analogues ( 58–62 ) has been prepared by reacting various amine-functionalized groups with a 2'- N -pentafluorophenoxycarbonyl-2'-amino-LNA monomer already incorporated into an ON. All modifications improved hybridization towards both DNA and RNA complements when compared to natural DNA nucleotides [ 96 ].…”

Parallel synthesis of oligonucleotides containing N-acyl amino-LNA and their therapeutic effects as anti-microRNAs

“…In addition, the 2′-nitrogen is suitable for advanced modifications by various chemical reactions during nucleic acid synthesis. [13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32] Previous studies have reported the development of oligonucleotides (ONs), containing 2′-N-substituted ALNA derivatives, such as 2′-N-alkyl, 13,15 2′-N-acyl, 14,[16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] 2′-N-alkoxycarbonyl, 31 and 2′-N-alkylaminocarbonyl. 32 Sensor molecules such as fluorescent dyes, spin labels, and radioisotopes can be incorporated into 2′-amino groups for use as ONs in biological analysis.…”

“…[13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32] Previous studies have reported the development of oligonucleotides (ONs), containing 2′-N-substituted ALNA derivatives, such as 2′-N-alkyl, 13,15 2′-N-acyl, 14,[16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] 2′-N-alkoxycarbonyl, 31 and 2′-N-alkylaminocarbonyl. 32 Sensor molecules such as fluorescent dyes, spin labels, and radioisotopes can be incorporated into 2′-amino groups for use as ONs in biological analysis. [14][15][16][17][18]22,23 ONs containing ALNAs functionalized fatty acid or sugar ligands into the 2′-nitrogen are expected to improve the pharmacokinetic profile.…”

“…[21][22][23]27,30 Hari et al reported the nucleophilic substitution of amines to an ALNA derivative bearing a 2′-N-pentafluorophenoxycarbonyl group. 32 These reactions were directed towards the substituent introduced on the 2′-nitrogen of ALNA, and direct PEM towards the 2′-nitrogen atom of ALNA [H] has not been reported so far.…”