Triplex formation with α anomers of purine-rich and pyrimidine-rich oligodeoxynucleotides

Abstract

Nuclease-resistant α anomers of pyrimidine-rich CT- and purine-rich GA- and GT-containing oligonucleotides were investigated for their triplex-forming potential and compared with their corresponding nuclease-sensitive β anomers. Both 23mer CT-α and 23mer CT-β had quite similar triplex binding affinities. Synthetic 23mer GT-α oligonucleotides were capable of triplex formation with binding affinities slightly lower than corresponding 23mer GT-β oligonucleotides. The orientation of third strand GT-α binding was parallel to the purine strand of the duplex DNA target, whereas the orientation of third strand GT-β binding was found to be antiparallel. Triplex formation with both GT oligonucleotides showed the typical dependence on magnesium and temperature. In contrast, 23mer GA-α oligonucleotides did not support triplex formation in either orientation under a variety of experimental conditions, whereas the corresponding 23mer GA-β oligonucleotides demonstrated strong triplex formation in the antiparallel orientation. GA-α oligonucleotides covalently conjugated to acridine were similarly unable to demonstrate triplex formation. GA-α oligonucleotides, in contrast to GT-α oligonucleotides, were capable of self-association, detectable by gel retardation and UV spectroscopy, but competing self-association could not fully account for the lack of triplex formation. Thus for in vivo triplex gene regulation strategies using GT oligonucleotides the non-natural α anomer may be a feasible alternative to the natural β anomer, allowing for a comparable degree of triplex formation without rapid cellular degradation. However, α anomeric inversion does not appear to be a feasible alternative in applications involving GA oligonucleotides. © 1995, Oxford University Press.