Sequence-Specific Cleavage of Double Helical DNA by Triple Helix Formation

TLDR

Homopyrimidine oligodeoxyribonucleotides bearing a single EDTA⋅Fe moiety bind homopyrimidine‑homopurine tracts in double‑stranded DNA via triple‑helix formation and cleave the duplex at the binding site. The EDTA⋅Fe‑modified homopyrimidine probes induce sequence‑specific double‑strand breaks, with cleavage patterns indicating major‑groove binding parallel to the homopurine strand, sensitivity to single‑base mismatches, and potential utility for chromosome mapping.

Abstract

Homopyrimidine oligodeoxyribonucleotides with EDTA⋅Fe attached at a single position bind the corresponding homopyrimidine-homopurine tracts within large double-stranded DNA by triple helix formation and cleave at that site. Oligonucleotides with EDTA⋅Fe at the 5′ end cause a sequence specific double strand break. The location and asymmetry of the cleavage pattern reveal that the homopyrimidine-EDTA probes bind in the major groove parallel to the homopurine strand of Watson-Crick double helical DNA. The sequence-specific recognition of double helical DNA by homopyrimidine probes is sensitive to single base mismatches. Homopyrimidine probes equipped with DNA cleaving moieties could be useful tools for mapping chromosomes.