Change of the higher order structure of DNA induced by the complexation with intercalating synthetic polymer, as is visualized by fluorescence microscopy

Abstract

The electrophoretic movement and Brownian motion of T4DNA, lambda DNA and their complexes with polyacrylamide (PAAm) via intercalative unit from 5-[(4-acryloylamino)phenyl]-3-amino-7-(dimethylamino)-2-methylp henazinium chloride were observed using fluorescence microscopy. It was found that T4DNA/PAAm complex migrates slower than T4DNA alone in gel electrophoresis, although they exhibit similar conformational change during the migration. Quantitative analyses of the translational diffusion of the lambda DNA and its complex in solution demonstrate that the DNA molecules extend due to intercalative binding of PAAm, suggesting the pseudo-grafting structure of the complex.