Triple-Helix Formation by α Oligodeoxynucleotides and α Oligodeoxynucleotide-Intercalator Conjugates

Base-pair sequences in double-stranded DNA can be recognized by homopyrimidine oligonucleotides that bind to the major groove at homopurine·homopyrimidine sequences thereby forming a local triple helix. To make oligodeoxynucleotides resistant to nucleases, we replaced the natural (β) anomers of the nucleotide units by the synthetic (α) anomers. The 11-mer α oligodeoxynucleotide 5'-d(TCTCCTCCTTT)-3' binds to the major groove of DNA in an antiparallel orientation with respect to the homopurine strand, whereas a β oligonucleotide adopts a parallel orientation. When an intercalating agent was attached to the 3' end of the α oligodeoxynucleotide, a strong stabilization of the triple helix was observed. A 16-base-pair homopurine·homopyrimidine sequence of human immunodeficiency virus proviral DNA was chosen as a target for a 16-mer homopyrimidine α oligodeoxynucleotide. A restriction enzyme that cleaves DNA at the junction of the homopurine·homopyrimidine sequence was inhibited by triple-helix formation. The 16-mer α oligodeoxynucleotide substituted by an intercalating agent was ≈20 times more efficient than the unsubstituted oligomer. Nucleaseresistant α oligodeoxynucleotides offer additional possibilities to control gene expression at the DNA level.