5'-Amino Modifier - CAS 114616-27-2

In this study, we designed 5'-amino-5'-deoxy-5'-hydroxymethylthymidine as a new oligonucleotide modification with an amino group directly attached to the 5'-carbon atom. We successfully synthesized two isomers of 5'-amino-5'-deoxy-5'-hydroxymethylthymidine via dihydroxylation of the 5'-vinyl group incorporated into 5'-deoxy-5'-C-methenylthymidine derivative. Moreover, it was found that the nuclease resistance, binding selectivity to single-stranded RNA, and triplex-forming ability of an oligonucleotide containing RT residues of the new compound were higher than those of the unmodified oligonucleotide.

Introduction of cationic modifications into an oligonucleotide can increase its nuclease resistance and duplex- or triplex-forming abilities. In a recent study, we found that the nuclease resistance and RNA binding selectivity of an oligonucleotide containing a 5'-(R)-amino-5'-deoxy-5'-(R)-hydroxymethylthymidine residue were greater than those of the unmodified oligonucleotide. In this article, we describe the synthesis of 5'-amino-5'-deoxy-5'-hydroxymethylthymidine via dihydroxylation of the 5'-alkene derivative using either of two commercial AD (asymmetric dehydroxylation) mixes or via epoxidation and ring opening. We also provide detailed protocols for the syntheses of oligonucleotides containing 5'-amino-5'-deoxy-5'-hydroxymethylthymidine residues. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 5'-amino-5'-deoxy-5'-hydroxymethylthymidine phosphoramidites 9a and 9b Basic Protocol 2: Synthesis of oligonucleotides 1 and 2 containing 5'-amino-5'-deoxy-5'-hydoxymethylthymidine residues (R T and S T).

This unit presents synthetic procedures for the preparation of 5'-amino-2',5'-dideoxy analogs of adenosine, cytidine, guanosine, and thymidine, as well as corresponding 5'-N-triphosphate nucleotides, using commercially available reagents. The modified nucleosides are prepared in high yields from naturally occurring 2'-deoxynucleosides using robust chemical reactions including tosylation, azide exchange, and the Staudinger reaction. Efficient conversion of these 5'-amino nucleosides to corresponding 5'-N-triphosphate nucleotides is achieved through a one-step reaction with trimetaphosphate in Tris-buffered aqueous solution. The 5'-amino modification renders these nucleoside and nucleotide analogs markedly increased reactivity, which is useful for a variety of biochemical, pharmaceutical, and genomic applications. Also included in this unit are protocols for polymerase incorporation of the 5'-amino nucleotides, either partially or completely replacing their naturally occurring counterparts, and subsequent sequence-specific cleavage at the modified nucleotides under mildly acidic conditions.