Sequence-specific alkylation of double-helical DNA by oligonucleotide-directed triple-helix formation

Abstract

Affinity cleaving, a method that relies on the attachment of a nonspecific cleaving moiety, such as EDTA•Fe(ll), to a DNA binding molecule, facilitates the elucidation of the structural principles for DNA recognition. The determination of the sequence specificities, groove locations, and binding orientations of peptide analogues, protein-DNA binding motifs, and oligonucleotide-triple-helix motifs has provided reliable models for the sequence-specific recognition of double-helical DNA. It now becomes possible to combine these binding molecules with domains capable of base-specific and quantitative modification of DNA (Figure 1). We report the design and synthesis of an ligodeoxyribonucleotide equipped with an electrophile at the 5'-end that binds to double-helical DNA by triple-helix formation and alkylates predominantly at a single guanine base adjacent to the target DNA sequence in high yield.