Synthesis and hybridization studies of α-configured arabino nucleic acids

Abstract

Synthesis of α-L-arabino- and α-D-arabino-configured pentofuranosyl nucleosides of four of the natural bases [thymine (ara-T), adenine (ara-A), cytosine (ara-C) and guanine (ara-G)] is reported together with hybridization properties of oligonucleotides containing α-L-ara-T and -A, α-D-ara-T and -A, and 2′-amino-α-L-ara-T monomers. 2′-O-Acetylated α-L-ara-T, -A, -C and -G, α-D-ara-T, -A, -C and -G, and N2′-acylated-α-L-ara-T phosphoramidite building blocks were synthesized and used together with standard DNA phosphoramidites for solid-phase synthesis of 18-mer oligonucleotides. Thermal denaturation experiments showed that incorporation of three or six of the arabino-configured monomers into DNA-oligonucleotides reduced the binding affinity towards antiparallel DNA/RNA complements. Fully modified α-L-ara-oligonucleotides did not hybridize with DNA/RNA complements, whereas hybridization of fully modified α-D-ara-oligonucleotides with complementary DNA/RNA in parallel strand orientation was confirmed.