Synthesis of a novel dioxane nucleoside having two bases, 2(R)-(5-fluorouracil-1-yl)-5(R)-hydroxymethyl-3(R)-(uracil-1-yl)-1,4-dioxane and its 2(S)-isomer, from uridine

Oligonucleotides with 1,4-dioxane-based nucleotide monomers

An epimeric mixture of H-phosphonates 5R and 5S has been synthesized in three steps from known secouridine 1. Separation of the epimers has been accomplished by RP-HPLC, allowing full characterization and incorporation of monomers X and Y into 9-mer oligonucleotides using H-phosphonates building blocks 5R and 5S, respectively. A single incorporation of either monomer X or monomer Y in the central position of a DNA 9-mer results in decreased thermal affinity toward both DNA and RNA complements (ΔT(m) = -3.5 °C/-3.5 °C for monomer X and ΔT(m) = -11.0 °C/-6.5 °C for monomer Y). CD measurements do not reveal major rearrangements of the duplexes formed, but molecular modeling suggests that local rearrangement of the sugar phosphate backbone and decreased base interactions with neighboring bases might be the origin of the decreased stability of duplexes.

Synthesis of a Novel Benzoyl Adenosine Analog Containing a 1, 4-Dioxane Sugar Analog and the Synthesis of a Corresponding Uracil Adenine Dinucleotide

Adenosine analogs in which the sugar unit was replaced by a 1,4-dioxane sugar equivalent, were prepared by coupling the 1,4-dioxane sugar analog as its anomeric acetates, with N6-benzoyl protected adenine. The 1,4-dioxane system was obtained in an enantioselective synthesis from (R,R)-dimethyl tartrate. Using standard phosphorimidite methodology, the adenine analog was further reacted with a 1,4-dioxane uridine analog to give the corresponding, protected dinucleotide, set-up for further condensation into larger oligonucleotides.

Synthesis of a novel, optically active uridine analog containing a 1,4-dioxane sugar moiety. Synthesis of the corresponding dinucleotide

A new optically active uridine nucleoside analogue in which a substituted 1,4-dioxane ring functioned as the sugar analogue was prepared from L-tartaric acid. The nucleoside analogue was further converted into the corresponding protected dinucleotide.