Straightforward Synthesis of Purine 4′-Alkoxy-2′-deoxynucleosides: First Report of Mixed Purine–Pyrimidine 4′-Alkoxyoligodeoxynucleotides as New RNA Mimics

Abstract

Purine and pyrimidine 4'-alkoxy-2'-deoxynucleosides were efficiently prepared from nucleoside 4'-5'-enol acetates in three steps by N-iodosuccinimide promoted alkoxylation, hydrolysis, and reduction followed by conversion to phosphoramidite monomers for the solid-phase synthesis of the oligonucleotides. Fully modified 4'-alkoxyoligodeoxynucleotides, which are characterized by a prevalent N-type (RNA-like) conformation, exhibited superior chemical and nuclease resistance as well as excellent hybridization properties with a strong tendency for RNA-selective hybridization, suggesting a potential application of 4'-alkoxy-oligodeoxynucleotides in antisense technologies.

Structural basis for the synergy of 4′- and 2′-modifications on siRNA nuclease resistance, thermal stability and RNAi activity

“…Earlier reports of 4′- C -modified nucleotides, including 4′- C -OMe-2′-deoxynucleotides ( 17 , 18 ) and 2′-F,4′- C -F pyrimidine nucleotides ( 19–21 ) and their incorporation into oligonucleotides support the notion of a preference for a Northern sugar pucker. The thermodynamic stability of RNA duplexes containing such nucleotides is similar to that of the native counterparts ( 21 ).…”

Synthesis and Antisense Properties of 2′β-F-Arabinouridine Modified Oligonucleotides with 4′-C-OMe Substituent

“…It is reported that the strong anomeric effect of the exocyclic oxygen atom attached to the C4′ carbon can drive the sugar part of 2′-deoxynucleotides toward the RNA-like C3′- endo (north) conformation. This conformational behavior is highly beneficial to the binding affinity to complementary RNA [ 15 , 16 ]. Moreover, Damha et al [ 17 ] demonstrated that introduction of 4′-F into 2′-F–araU switched the preferred sugar conformation from DNA-like to RNA-like by the similar anomeric effect of 4′-F.…”

“…Hence, it was predicted that the 4′- C -alkoxy-2′-F–arabinonucleotide derivatives would also pre-organize the sugar ring toward a north conformation, and enhance the hybridization properties for antisense oligonucleotides. Moreover, C4′ modifications on the ribose moiety, such as 4′-S [ 11 ], 4′- C -OMe [ 15 , 16 ], and 4′- C -aminomethyl [ 10 , 18 ], are reliable strategies to increase nuclease resistance. In particular, the C4′-modified 2′-F–uridine derivative, 2′-F,4′- C α-OMe–uridine, which was recently reported by Damha et al [ 19 ], was able to increase nuclease resistance due to the close proximity between 4′-OMe substituent and the vicinal 5′- and 3′-phosphate group.…”

Synthesis of 4′‐Methoxy 2′‐Deoxynucleoside Phosphoramidites for Incorporation into Oligonucleotides

“…In this unit, a robust synthetic protocol is described, providing phosphoramidites of RNA‐like 4′‐methoxy 2′‐deoxynucleosides, which are useful as monomers for the synthesis of oligonucleotides on solid phase according to conventional phosphoramidite chemistry. The protocol is based on previously published work (Petrová et al., ), and contains detailed procedures for the synthesis of phosphoramidite monomers of 4′‐methoxy 2′‐deoxyadenosine, 2′‐deoxyguanosine, 2′‐deoxycytidine, thymidine, and 2′‐deoxyuridine, respectively (Fig. and Table ).…”

“…In this unit, a robust synthetic protocol is described, providing phosphoramidites of RNA-like 4methoxy 2 -deoxynucleosides, which are useful as monomers for the synthesis of oligonucleotides on solid phase according to conventional phosphoramidite chemistry. The protocol is based on previously published work (Petrová et al, 2015), and contains detailed procedures for the synthesis of phosphoramidite monomers of 4 -methoxy 2deoxyadenosine, 2 -deoxyguanosine, 2 -deoxycytidine, thymidine, and 2 -deoxyuridine, respectively ( Fig. 1.38 The Basic Protocol describes the synthesis of 4 -methoxy 2 -deoxynucleoside phosphoramidites 7a-e for A, G, C, T, and U from the corresponding 4 ,5 -enol acetates 3a-e. 4 -Methoxy dNs 4a-e, obtained in one pot by successive N-iodosuccinimide-promoted methoxylation, hydrolysis, and reduction, are converted to 3 -O-phosphoramidites by a routine three-step procedure.…”