Sequence-Specific Recognition of Double-Stranded DNA by Synthetic Minor Groove Binder Conjugates. toward the Construction of Artificial Site-Specific Deoxyribonucleases

Abstract

Bis-conjugates of hairpin N-methylpyrrole/N-methylimidazole oligocarboxamide minor groove binders (MGB) possessing enhanced affinity and sequence-specificity for dsDNA were synthesized. Two hairpin MGBs were connected by their N-termini via an aminodiacetate linker. The binding of bis-MGB conjugates to the target DNA was studied by gel mobility retardation, footprinting, and circular dichroism; their affinity and binding mode in the DNA minor groove were determined. In order to functionalize the bis-MGB conjugates, DNA-cleaving agents such as phenanthroline or bipyridine were attached. Effective site-specific cleavage of target DNA in the presence of Cu ²⁺ ions was observed.

Keywords:

• Minor groove binder
• double-stranded DNA
• DNA recognition
• sequence specificity
• conjugate
• DNA cleavage