The interaction of DNA with bacteriophage phi 29 connector: a study by AFM and TEM.

The connector of bacteriophage phi 29 is involved in DNA packaging during viral morphogenesis and we have studied its in vitro binding to DNA using either linear or circular DNA. The protein-DNA complexes have been analyzed by transmission electron microscopy (TEM) and by atomic force microscopy (AFM) of samples directly deposited on mica. TEM showed the presence of a specific binding due to the interaction of the protein with the free ends of the DNA. The study of these samples by AFM showed two major types of morphologies: The interaction of the connector with circular DNA revealed that the strands of DNA that enter and exit the protein complex form an angle with a mean value of 132 degrees. Nevertheless, when the connector was incubated with linear DNA (and later circularized), there was an additional bend angle of about 168 degrees. Further morphological analysis of the latter samples by AFM revealed a structure of the protein-DNA complex consistent with the DNA traversing the connector, probably through the inner channel. On the other hand, images from the samples obtained by incubation of the connector with circular DNa were consistent with an interaction of the DNA with the outer side of the connector.