Synthesis of Altritol Nucleoside Phosphoramidites for Oligonucleotide Synthesis

Abstract

This unit describes in detail the optimized preparations of altritol nucleoside phosphoramidite building blocks for oligonucleotide synthesis (aA, aG, aC, aU). D-Altritol nucleosides with adenine and uracil bases are obtained by nucleophilic opening of the epoxide ring of 1,5:2,3-dianhydro-4,6-O-benzylidene-D-allitol using the 1,8-diazabicyclo[5.4.0]undec-7-ene salts of the above-mentioned salts, while phase transfer catalysis (18-crown-6, K2CO3) is optimal for alkylation of 2-amino-6-chloropurine. The cytosine nucleoside is synthesized starting from the uracil congener. The 3'-hydroxyl function of hexitol sugar is protected with the benzoyl group.

Hybridization potential of oligonucleotides comprising 3′-O-methylated altritol nucleosides

“…Samples were infused at 3µL/min and spectra were obtained in positive (or: negative) ionization mode with a resolution of 15000 (FWHM) using leucine enkephalin as lock mass. Synthesis of HNA and ANA monomers was outlined before [10,30]. Assembly of ANA and HNA constructs likewise has been described previously [11,12].…”

“…2 and followed the pathway previously described for preparation of altrohexitol monomers [30]. Herein, ring opening of the 4,6-O-benzylidene-protected allitol epoxide (2) with uracil, adenine or 2-amino-6-chloropurine anions furnished the corresponding altrohexitol derivatives (3a, 3c and 3e) with 66-85% yield.…”

“…Baseprotection of 4b and 4c with a benzoyl group afforded 5b and 5c respectively, in 70% yield. The nucleobase of 4e was converted to guanine affording 4d, followed by protection with the dimethylformamidine (dmf) moiety yielding 76% of 5d following standard protocols [30,34].…”

“…The analog 3c [30] (2.4 g, 6.5 mmol) was coevaporated with dry DMF (3x12 mL). The foam was dissolved in dry DMF (35 mL) and cooled to -20°C.…”

Nucleic Acids with a Six‐Membered ‘Carbohydrate’ Mimic in the Backbone

“…Coupling yields for oligonucleotide synthesis were, however, generally lower than in the conventional RNA synthesis, and the full deprotection of the synthesized oligonucleotides was cumbersome, probably due to steric hindrance and the low solubility of the growing oligonucleotide in the solvents used for synthesis and deprotection. The 3'-O-Bz group proved to be the most suitable protecting system for oligonucleotide synthesis, deprotection, and purification [67] [69]. The problem of the Bz migration could be handled by carrying out the cleavage of the benzylidene group with TFA at 08 and precipitating the 3'-O-Bz protected nucleoside from the reaction mixture.…”