Synthesis and properties of oligonucleotides containing 2′-deoxynebularine and 2′-deoxyxanthosine

Abstract

The preparation of synthetic oligonucleotides containing 2′-deoxynebularine (dN) and 2′-deoxyxanthosine (dX) is described. The thermal stabilities of duplexes containing dX, dN, and 2′-deoxyinosine (dl) base-paired with the four natural bases have been measured. Xanthine base pairs have stabilities at pH 5.5 that are similar to those of dl-containing duplexes at neutral pH. When xanthine is paired with adenine or cytosine an unusual stabilization of the duplex structure is observed at acid pH. Incorporation of base mispairs opposite template xanthine sites were measured using Drosophila DNA polymerase α. The relative nucleoside incorporation rates are in the order: T≦C≦A≈G. These rates do not correlate with relative thermodynamic stabilities of base mispairs with xanthine obtained from Tm measurements: T