Studies of sequence-specific recognition and interaction of bishairpin polyamide minor groove binders with target DNA duplexes

Abstract

The binding of bis-MGB to target DNA was studied by DNase footprint, native gel shift, circular dichroism, thermal dissociation, electrospray mass-spectrometry, and molecular modelling methods. A new method for the determination of the relative affinity of ligands against various dsDNA sequences was elaborated by using ESI-QTOF mass spectrometry. Information about affinity, sequence preferences, conformation and mode of interaction between bis-MGB and target DNA was obtained. Our experiments demonstrated that MGB have different affinity for similar cognate target sequences depending on the sequence context of the target region and other structural factors.