Scanning force microscopy of DNA translocation by the Type III restriction enzyme EcoP15I.

Type III restriction enzymes are multifunctional heterooligomeric enzymes that cleave DNA at a fixed position downstream of a non-symmetric recognition site. For effective DNA cleavage these restriction enzymes need the presence of two unmethylated, inversely oriented recognition sites in the DNA molecule. DNA cleavage was proposed to result from ATP-dependent DNA translocation, which is expected to induce DNA loop formation, and collision of two enzyme-DNA complexes. We used scanning force microscopy to visualise the protein interaction with linear DNA molecules containing two EcoP15I recognition sites in inverse orientation. In the presence of the cofactors ATP and Mg(2+), EcoP15I molecules were shown to bind specifically to the recognition sites and to form DNA loop structures. One of the origins of the protein-clipped DNA loops was shown to be located at an EcoP15I recognition site, the other origin had an unspecific position in between the two EcoP15I recognition sites. The data demonstrate for the first time DNA translocation by the Type III restriction enzyme EcoP15I using scanning force microscopy. Moreover, our study revealed differences in the DNA-translocation processes mediated by Type I and Type III restriction enzymes.

Molecular structure of single DNA complexes with positively charged dendronized polymers.

Positively charged dendronized polymers with protonated amine groups at the periphery and different dendron generations are cylindrically shaped nanoobjects whose radii and linear charge densities can be varied systematically. These polyelectrolytes have been complexed with DNA and subsequently adsorbed on precoated mica substrates. The analysis of scanning force microscopy data indicates that DNA wraps around the dendronized polymers. The calculated pitch is 2.30 +/- 0.27 and 2.16 +/- 0.27 nm for DNA wrapped around dendronized polymers of generation two and four, respectively. The complex with the second generation has been shown to be negatively charged, which is consistent with the theory of spontaneous overcharging of macro-ion complexes, when the electrostatic contribution to the free energy dominates over the elastic energy. The complexes may be of interest for the development of nonviral gene delivery systems.